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1656 variant records found |
[show instead phene records] |
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WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.
Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.
OMIA Variant ID | OMIA Phene-Species ID(s) | Species Name | Breed(s) | Variant Phenotype | Gene | Allele | Type of Variant | Source of Genetic Variant | Deleterious? | Reference Sequence | Chr. | g. or m. | c. or n. | p. | Verbal Description | EVA ID | Year Published | PubMed ID(s) | Acknowledgements |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2 | OMIA:000042-9031 | chicken | Wisconsin hypoalpha mutant (WHAM), United States of America (Chicken) | Analphalipoproteinaemia | ABCA1 | missense | Naturally occurring variant | yes | GRCg6a | Z | g.54877918C>T | c.265G>A | p.(E89K) | 2002 | 12364545 | Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool | |||
1126 | OMIA:002238-9913 | taurine cattle | Shorthorn (Cattle) | Ichthyosis, ABCA12-related | ABCA12 | missense | Naturally occurring variant | yes | ARS-UCD1.2 | 2 | g.103016791A>G | c.6776T>C | p.(L2259P) | NM_001191294.2:c.6776T>C; NP_001178223.2:p.(Leu2259Pro) | rs5334475100 | 2019 | 31568573 | ||
1220 | OMIA:002238-9913 | taurine cattle | Polled Hereford (Cattle) | Ichthyosis, ABCA12-related | ABCA12 | insertion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 2 | g.103043495_103043496insG | c.5689_5690insC | p.(S1784Ifs*33) | BTA 2:103043495–103043496insG; ENSBTAT00000004518.6:c.5689‐5690insC; ENSBTAP00000004518.6:p.(Ser1784Ilefs*33) (Eager et al., 2020) | rs3423092881 | 2020 | 32567073 | ||
195 | OMIA:002238-9913 | taurine cattle | Chianina (Cattle) | Ichthyosis, ABCA12-related | ABCA12 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 2 | NC_037329.1:g.103030489T>C | NM_001191294.2:c.5804A>G | NP_001178223.2:p.(H1935R) | previously listed in OMIA as ARS-UCD1.2:g.103025585T>C, g. coordinates have been corrected after review of original paper and incorrectly assigned EVA rs ID has been removed [29/08/2024] | 2008 | 18344998 | |||
1379 | OMIA:002238-9823 | pig | Bama Xiang Zhu, China (Pig) | Ichthyosis | ABCA12 | splicing | Chemical mutagenesis (ENU) | unknown | Sscrofa11.1 | 15 | NC_010457.5:g.117250799T>C | Intronic mutation IVS49-727 A>G results in splicing alteration resulting in a 132-nt insertion and a premature stop codon (Wang et al., 2019) | 2019 | 30925591 | |||||
1050 | OMIA:002179-9615 | dog | Labrador Retriever (Dog) | Stargardt disease 1 | ABCA4 | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 6 | g.55146556dup | c.4176dup | p.(F1393Lfs*3) | Mäkeläinen et al. (2019): "ENSCAFT00000005367 exon28 4170dupC* V1390fs" Importantly, the same authors also explain in Table S3 that "*The insertion is found in a cytosine mononucleotide-repeat region [55,146,550–55,146,556] and it is arbitrary at what position the actual insertion occurs. In the text we have denoted the insertion as c.4176insC, p.F1393Lfs*1395)." Variant information changed to reflect HGVS nomenclature | 2019 | 30889179 | |||
607 | OMIA:001402-9615 | dog | Border Collie (Dog) | Adverse reaction to certain drugs | ABCB1 | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 14 | CanFam3.1 | published as c.73insAAT - the allele is reflected by the reference sequence CanFam3.1 and NM_001003215.2 as reference: g.13737172_13737174; c.73_75, p.N25; causality of this variant should be reviewed | 2010 | 21113104 | |||||
469 | OMIA:001402-9615 | dog | Australian Shepherd (Dog) Border Collie (Dog) Collie (Dog) German Shepherd Dog (Dog) Long-Haired Whippet (Dog) Miniature Australian Shepherd Dog (Dog) Old English Sheepdog (Dog) Shetland Sheepdog (Dog) Silken Windhound (Dog) Waller (Dog) White Swiss Shepherd Dog (Dog) | Adverse reaction to certain drugs | ABCB1 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 14 | NC_006596.3:g.13726596_13726599del | NM_001003215.2:c.228_231del | NM_001003215.2:p.(D77Afs*16) | 2001 | 11692082 | Variant information initially gleaned from or confirmed by Donner et al. (2016) PLoS One 11:e0161005 and later updated to reflect HGVS nomenclature. | |||
442 | OMIA:001402-9615 | dog | Border Collie (Dog) | Adverse reaction to certain drugs | ABCB1 | regulatory | Naturally occurring variant | no | CanFam3.1 | 14 | NC_006596.3:g.13742402A>C | published as Canfam2 chr14:16692274T>G, c.-6-180T>G, possible regulatory variant associated with resistance to phenobarbital treatment in epileptic Border Collies; an association between the variant and the phenotype was not supported in a different study: PMID: 31685133 | rs852787132 | 2011 | 21488961 | Genomic coordinates in CanFam3.1 and EVA ID provided by Zoe Shmidt and Robert Kuhn. | |||
1322 | OMIA:001402-9685 | domestic cat | Balinese (Cat) Domestic Longhair Domestic medium-haired Domestic Shorthair Maine Coon (Cat) Maine Coon Polydactyl (Cat) Ragdoll (Cat) Russian Blue (Cat) Siamese (Cat) Turkish Angora (Cat) | Adverse reaction to certain drugs | ABCB1 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | A2 | g.93144355_93144356del | c.1930_1931del | NM_001171064.2; published as ABCB1:1930_1931delTC; resuling in a frameshift generating a series of stop codons immediately downstream from the deletion. The protein product is predicted to be severely truncated (~50%) and non functional (Mealey and Burke, 2015). | 2015 | 25660379 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. Additional breeds reported based on PMID:34125616 and PMID:35709088 | |||
1574 | OMIA:002710-9615 | dog | Manchester Terrier (Dog) | Cardiomyopathy, dilated, ABCC9-related | ABCC9 | SCDY/DCM | missense | Naturally occurring variant | unknown | Dog10K_Boxer_Tasha | 27 | NC_006609.4:g.21042635C>T | XM_022410972.2:c.3557G>A | XP_022266680.2:p.(R1186Q) | XM_022410972.2; XP_022266680.2 | 2023 | 37239348 | ||
1499 | OMIA:002589-8839 | Mallard | Blue eggshell | ABCG2 | regulatory | Naturally occurring variant | no | BGI_duck1.0 | NW_004676534.1 | g.[3573054A>G;3573085A>G] | The BGI_duck1.0 reference genome represents the blue eggshell genotype. | 2020 | 33186356 | ||||||
1477 | OMIA:002561-9913 | taurine cattle | Deutsche Holstein Schwarzbunt, Germany (Cattle) | Infertility | ABHD16B | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.3 | 13 | NC_037340.1:g.53957903G>A | NM_001038541.2:c.652C>T | NP_001033630.1:p.(Q218*) | ENSBTAT00000045249.4; ENSBTAP00000055253.1 | rs468948776 | 2020 | 31963602 | ||
1388 | OMIA:002368-9615 | dog | Golden Retriever (Dog) | Ichthyosis, ABHD5-related | ABHD5 | ICH2 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 23 | g.2587000_2587013del | c.1006_1019del | p.(D336Sfs*6) | XM_542689.5; XP_542689.2 | 2022 | 34791225 | ||
1504 | OMIA:002594-9823 | pig | N-acetyl-galactosamine intestinal concentration | ABO | deletion, gross (>20) | Naturally occurring variant | unknown | 1 | 2.3kb deletion encompassing exon 8 | 2022 | 35477154 | ||||||||
1177 | OMIA:001089-9542 | Japanese macaque | Antigen B | ABO | haplotype | Naturally occurring variant | no | Allele B reflects the peptide haplotype p.266Met + p.268Ala | 2000 | 10984838 | |||||||||
21 | OMIA:001089-9544 | Rhesus monkey | Antigen A | ABO | haplotype | Naturally occurring variant | no | p.266L + p.268G | Allele A is reflected in the peptide haplotype p.266Leu + p.268Gly | 1998 | 9583803 | ||||||||
20 | OMIA:001089-9541 | crab-eating macaque | A antigen | ABO | haplotype | Naturally occurring variant | no | p.266L + p.268G | Allele A is reflected in the peptide haplotype p.266Leu + p.268Gly | 1998 | 9583803 | ||||||||
1174 | OMIA:001089-9544 | Rhesus monkey | Antigen B | ABO | haplotype | Naturally occurring variant | no | p.266M + p.268A | Allele B is a reflection of the peptide haplotype p.266Met + p.268Ala | 1998 | 9583803 | ||||||||
1175 | OMIA:001089-9541 | crab-eating macaque | B antigen | ABO | haplotype | Naturally occurring variant | unknown | p.266M + p.268A | Allele B is a reflection of the peptide haplotype p.266Met + p.268Ala | 1998 | 9583803 | ||||||||
22 | OMIA:001089-9579 | agile gibbon | Alleles A and B | ABO | missense | Naturally occurring variant | no | c.2178C>A and c.2185G>C | Haplotype c.2178C + c.2185G is allele A; haplotype c.2178A + c.2185C is allele B | 2009 | 19298858 | ||||||||
23 | OMIA:001089-9580 | common gibbon | Blood group system ABO | ABO | missense | Naturally occurring variant | no | c.2178C>A and c.2185G>C | 2009 | 19298858 | |||||||||
532 | OMIA:001089-9598 | chimpanzee | O (lack of antigen) | ABO | O^del | deletion, small (<=20) | Naturally occurring variant | no | c.514_522delGTGCTGGAG | p.(V172-E174del) | 1999 | 10380696 | |||||||
24 | OMIA:001089-9598 | chimpanzee | O (lack of antigen) | ABO | O^x | missense | Naturally occurring variant | no | c.791A>C | p.(Y264C) | 1999 | 10380696 | |||||||
1497 | OMIA:002585-9615 | dog | Cavalier King Charles Spaniel (Dog) | medium-chain acyl-CoA dehydrogenase | ACADM | delins, gross (>20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 6 | g.71401388_71401389delinsCATAATTCTTAGACAATATTGAGAATTAAC | c.444_445delinsGTTAATTCTCAATATTGTCTAAGAATTATG | p.(T150Ifs*6) | XM_038541645.1; XP_038397573.1 | 2022 | 36292732 | |||
972 | OMIA:002140-9615 | dog | German Hunting Terrier (Dog) | Exercise induced metabolic myopathy | ACADVL | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 5 | NC_006587.3:g.32193689C>A | XM_546581.5:c.1728C>A | XP_546581.3:p.(Y576*) | XM_546581.5; XP_546581.3 | 2018 | 29491033 | |||
429 | OMIA:001271-9913 | taurine cattle | Dexter (Cattle) | Bulldog calf | ACAN | BD2 | regulatory | Naturally occurring variant | yes | ARS-UCD1.2 | 21 | g.20377856C>T | c.-198C>T | rs3423095877 | 2007 | 17952705 | Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
590 | OMIA:001271-9913 | taurine cattle | Dexter (Cattle) Highland (Cattle) | Bulldog calf | ACAN | BD1 | insertion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 21 | g.20422104_20422105insGGCA | c.2266_2267insGGCA | Variant initially identified in Dexter cattle and later reported in additional breeds: PMID:26885599 | 2007 | 17952705 | Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
1060 | OMIA:001271-9915 | indicine cattle (zebu) | Miniature Zebu, United Kingdom of Great Britain and Northern Ireland (Cattle) | Bulldog calf | ACAN | insertion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 21 | g.20428539_20428540insC | c.5688_5689insC | p.(V1897fs*9) | cDNA position based on transcript NM_173981.2 | 2018 | 30305023 | |||
1001 | OMIA:001271-9796 | horse | Miniature Horse (Horse) | Dwarfism, ACAN-related | ACAN | D4 | deletion, gross (>20) | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.95257479_95257499del | XM_005602799.2:c.7633_7653del | XP_005602856.2:p.(F2545_C2551del) | Genomic positions were previosuly incorreclty listed in OMIA as g.95257458_95257500del (until 10/01/2022) and g.95257480_95257500del (until 13/06/2024). Coordinates presented in the table reflect the published rs1095048839. IT is thanking Rebecca Bellone for spotting an error in the genomic coordinates which are now corrected (26/11/2024). |
rs1095048839 | 2018 | 30058072 | |
788 | OMIA:001271-9796 | horse | Miniature Horse (Horse) Shetland Pony (Horse) | Dwarfism, ACAN-related | ACAN | D3* | missense | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.95282140C>G | XM_023650286.1:c.1513G>C | XP_023506054.1:p.(A505P) | ENSECAT00000040213.1:c.1513G>C ENSECAP00000032890.1:p.Ala505Pro This variant was named D3* by Eberth et al. (2018) | rs1095048823 | 2017 | 27942904 | Variant coordinates obtained from Eberth et al. (2018) and EVA_ID link |
1000 | OMIA:001271-9796 | horse | Miniature Horse (Horse) Quarter Horse (Horse) Warmblood (Horse) | Dwarfism, ACAN-related | ACAN | D2 | missense | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.95284530C>T | XP_023506054.1:c.1270C>T | XP_023506054.1:p.(V424M) | rs3091781465 | 2018 | 30058072 | Breed information updated based on PMID: 38600096 | |
999 | OMIA:001271-9796 | horse | Miniature Horse (Horse) | Dwarfism, ACAN-related | ACAN | D1 | deletion, small (<=20) | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.95291271del | XM_023650281.1:c.245del | XP_023506054.1:p.(K82Rfs*54) | 220110: changed g.95291270del to g.95291271del based on HGVS 3'rule. ENSECAT00000040213.1:c.245del ENSECAP00000032890.1:p.Lys82ArgfsTer54 | rs1095048841 | 2018 | 30058072 | |
323 | OMIA:000702-9031 | chicken | Nanomelia | ACAN | nonsense (stop-gain) | Naturally occurring variant | yes | GRCg6a | 10 | g.13502829C>A | c.4537G>T | p.(E1513*) | 1994 | 7827752 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||
1045 | OMIA:002177-9615 | dog | Akita (Dog) American Akita (Dog) | Amelogenesis imperfecta, ACP4-related | ACPT | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 1 | g.106051997dupC | c.1189dupG | p.(A397Gfs) | XM_541473.2; XP_541473.2; ACPT is a synonym of ACP4 | 2019 | 30877375 | |||
1419 | OMIA:002226-9913 | taurine cattle | Brown Swiss (Cattle) | Haplotype with homozygous deficiency BH34 | ACSL5 | BH34 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 26 | NC_037353.1:g.32940521C>G | NM_001075650.1:c.528C>G | NP_001069118.1:p.(N176K) | NM_001075650.1 | rs5357452907 | 2021 | 34915862 | |
1259 | OMIA:002226-9615 | dog | Australian Kelpie (Dog) | Intestinal lipid malabsorption | ACSL5 | deletion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 28 | g.23380074_23483377del | NC_006610.3CFA28:g.23380074_23483377del (O/Brien et al., 2020) | 2020 | 33106515 | |||||
1073 | OMIA:000388-9685 | domestic cat | Domestic Shorthair | Fibrodysplasia ossificans progressiva | ACVR1 | missense | Naturally occurring variant | yes | Felis_catus_9.0 | C1 | g.150014354C>T | c.617G>A | p.(R206H) | XM_023259334.1; XP_023115102.1 | 2019 | 31007133 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | ||
633 | OMIA:001520-9615 | dog | Glen of Imaal Terrier (Dog) | Cone-rod dystrophy 3 | ADAM9 | deletion, gross (>20) | Naturally occurring variant | yes | 16 | "a deletion of exons 15 and 16 which alters the reading frame leading to a premature stop codon" in the ADAM9 gene | 2010 | 20691256 | |||||||
43 | OMIA:001870-9615 | dog | Beagle (Dog) | Glaucoma, primary open angle | ADAMTS10 | missense | Naturally occurring variant | yes | CanFam3.1 | 20 | NC_006602.3:g.53096339C>T | XM_022406266.1:c.1981G>A | XP_022261974.1:p.(G661R) | XM_849227.3; XP_854320.1 | 2011 | 21379321 | |||
101 | OMIA:001870-9615 | dog | Norwegian Elkhound (Dog) | Glaucoma, primary open angle | ADAMTS10 | missense | Naturally occurring variant | yes | CanFam3.1 | 20 | NC_006602.3:g.53101896C>T | XM_022406266.1:c.1159G>A | XP_022261974.1:p.(A387T) | XM_849227.3; XP_854320.1 | 2014 | 25372548 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
685 | OMIA:001976-9615 | dog | Basset Hound (Dog) | Glaucoma, primary open angle, ADAMTS17-related | ADAMTS17 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 3 | g.40614853_40614872del | c.194_213del | p.(L68Gfs*) | XM_022416850.1; XP_022272558.1 | 2015 | 26474315 | |||
1086 | OMIA:001976-9615 | dog | Petit Basset Griffon Vendeen (Dog) | Glaucoma, primary open angle, ADAMTS17-related | ADAMTS17 | inversion | Naturally occurring variant | yes | CanFam3.1 | 3 | g.40812274_45768123inv | c.1721+2668_*4831255inv | XM_545825.4; Forman et al. (2015): "a 4.96 Mb inversion . . . with breakpoints in intron 12 of ADAMTS17 (chr3:40,812,274) and a downstream intergenic region (chr3:45,768,123) [Canfam3.1]… Analysis of RNAseq data revealed novel exon expression for ADAMTS17 due to cryptic splicing occurring 3’ of the exons located immediately upstream of the inversion event." | 2015 | 26683476 | ||||
942 | OMIA:000588-9615 OMIA:001976-9615 | dog | Chinese Shar-Pei (Dog) | Primary open-angle glaucoma (POAG), primary lens luxation (PLL), or both | ADAMTS17 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 3 | g.40935387_40935392del | c.3069_3074del | p.(V1024_V1025del) | XM_014112382.2; XP_013967857.1; published as c.3070_3075delCGTGGT; p.(V1025_V1026del) | 2018 | 29287154 | |||
365 | OMIA:000588-9615 | dog | American Toy Terrier (Dog) Chinese Crested (Dog) German Hunting Terrier (Dog) Jack Russell Terrier (Dog) Lancashire Heeler (Dog) Miniature Bull Terrier (Dog) Parson Russell Terrier (Dog) Patterdale Terrier (Dog) Rat Terrier (Dog) Sealyham Terrier (Dog) Tenterfield Terrier (Dog) Tibetan Terrier (Dog) Toy Fox Terrier (Dog) Volpino Italiano (Dog) Welsh Terrier (Dog) Wire Fox Terrier (Dog) Yorkshire Terrier (Dog) | Lens luxation | ADAMTS17 | splicing | Naturally occurring variant | yes | CanFam3.1 | 3 | NC_006585.3:g.40782144G>A | XM_022416850.1:c.1473+1G>A | XM_022416850.1; additional breeds reported by PMID:22050825 and PMID:37582787 | rs1152388408 | 2010 | 20375329 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
96 | OMIA:001976-9615 | dog | Basset Fauve de Bretagne (Dog) | Glaucoma, primary open angle, ADAMTS17-related | ADAMTS17 | missense | Naturally occurring variant | yes | CanFam3.1 | 3 | NC_006585.3:g.40808345G>A | XM_022416851.1:c.1552G>A | XP_022272559.1:p.(G518S) | XM_022416851.1; XP_022272559.1 | 2015 | 26474315 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
486 | OMIA:000328-9913 | taurine cattle | Belgian Blue (Cattle) | Ehlers-Danlos syndrome, type VII (Dermatosparaxis) | ADAMTS2 | delins, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 7 | g.2017035_2017051delinsAGC | c.464_480delinsAGC | 1999 | 10417273 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||||
1513 | OMIA:000328-9615 | dog | Alapaha Blue Blood Bulldog (Dog) American Pit Bull Terrier (Dog) | Ehlers-Danlos syndrome, type VII (Dermatosparaxis) | ADAMTS2 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 11 | g.2280117delC | c.10delC | p.(P4Rfs*175) | 2022 | 36421833 | ||||
1117 | OMIA:000328-9615 | dog | Doberman Pinscher (Dog) | Ehlers-Danlos syndrome, type VII (Dermatosparaxis) | ADAMTS2 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 11 | NC_006593.3:g.2408978C>T | XM_843844.4:c.769C>T | XP_848937.1:p.(R257*) | 2019 | 31294848 | ||||
1514 | OMIA:000328-9615 | dog | Catahoula Leopard Dog (Dog) | Ehlers-Danlos syndrome, type VII (Dermatosparaxis) | ADAMTS2 | missense | Genome-editing (CRISPR-Cas9) | yes | CanFam3.1 | 11 | NC_006593.3:g.2491238G>A | XM_843844.4:c.2897G>A | XP_848937.1:p.(R966H) | 2022 | 36421833 | ||||
1589 | OMIA:000328-9685 | domestic cat | Domestic Shorthair | Ehlers-Danlos syndrome | ADAMTS2 | delins, small (<=20) | Naturally occurring variant | yes | F.catus_Fca126_mat1.0 | A1 | g.90995621dup | c.698dup | p.(Ser235fs*3) | XM_023254116.2; XP_023109884.2 | 2023 | 37462293 | |||
318 | OMIA:000328-9940 | sheep | Dorper (Sheep) | Ehlers-Danlos syndrome, type VII (Dermatosparaxis) | ADAMTS2 | nonsense (stop-gain) | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 5 | g.1938399G>T | c.424G>T | p.(E142*) | XM_012156230:c.424G>T, XP_012011620:p.Glu142* (Joller et al., 2017) | 2012 | 22497338 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | ||
857 | OMIA:000328-9940 | sheep | Dorper (Sheep) | Ehlers-Danlos syndrome, type VII (Dermatosparaxis) | ADAMTS2 | nonsense (stop-gain) | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 5 | g.2088231G>A | c.805G>A | p.(V269M) | XM_012156230:c.805G>A, XP_012011620:p.Val269Met (Joller et al., 2017) | 2015 | 25354687 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | ||
537 | OMIA:001140-9615 | dog | Nova Scotia Duck Tolling Retriever (Dog) | Cleft lip with or without cleft palate | ADAMTS20 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 27 | g.10553479_10553480del | c.1358_1359del | p.(K453Ifs*4) | XM_022410988.1; XP_022266696.1; published as c.1360_1361delAA and p.(K453Ifs*3); coordinates in the table have been updated to a recent reference genome and / or transcript and HGVS nomenclature | 2015 | 25798845 | Genomic position in CanFam3.1 provided by Mateo Etcheveste and Robert Kuhn. | ||
1163 | OMIA:001562-9913 | taurine cattle | Cikasto govedo, Slovenia (Cattle) | Pulmonary hypoplasia and anasarca syndrome | ADAMTS3 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 6 | NC_037333.1:g.87462016G>A | NM_001192797.1:c.1222C>T | NP_001179726.1:p.(H408T) | NM_001192797.1: c.1222C>T; NP_001179726.1: p.(His408Tyr) (Häfliger et al., 2020) | rs5334475098 | 2020 | 32069517 | ||
1750 | OMIA:001562-9940 | sheep | Persian (Sheep) | Pulmonary hypoplasia with anasarca | ADAMTS3 | splicing | Naturally occurring variant | yes | Oarv3.1 | 6 | NC_019463.1:g.87124344del | XM_012180125.1:c.2055+3del | XP_012035515.1:p.(V680_V685del) | the variant results in the activation of a cryptic splice site within exon 14 | 2024 | 39409761 | |||
60 | OMIA:001509-9615 | dog | Beagle (Dog) | Musladin-Lueke syndrome | ADAMTSL2 | missense | Naturally occurring variant | yes | CanFam3.1 | 9 | NC_006591.3:g.49931561C>T | XM_014116955.2:c.661C>T | XP_013972430.1:p.(R221C) | 2010 | 20862248 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
935 | OMIA:001511-9913 | taurine cattle | Angus (Cattle) | Contractual arachnodactyly (Fawn calf syndrome) | ADAMTSL3 | deletion, gross (>20) | Naturally occurring variant | yes | 21 | "a large (~58 kilobase pair) deletion affecting the ADAMTSL3 gene" | 2014 | Reference not in PubMed; see OMIA 001511-9913 for reference details | |||||||
1435 | OMIA:002535-9913 | taurine cattle | Original Schweizer Braunvieh, Switzerland (Cattle) | Congenital cataract | ADAMTSL4 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 3 | NC_037330.1:g.20146737C>T | NM_001101061.1:c.2327G>A | NP_001094531.1:p.(R776H) | NM_001101061.1; NP_001094531.1 | rs5353205567 | 2022 | 35233794 | ||
466 | OMIA:001577-9615 | dog | Curly Coated Retriever (Dog) | Glycogen storage disease IIIa | AGL | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 6 | g.50050457del | c.4223del | p.(K1408Sfs*6) | NM_001048096.1; NP_001041561.1; published as c.4223delA; genomic position adjusted to HGVS 3' rule | 2007 | 17338148 | Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn | ||
934 | OMIA:002135-9913 | taurine cattle | Angus (Cattle) | Arthrogryposis multiplex congenita, AGRN-related | AGRN | deletion, gross (>20) | Naturally occurring variant | yes | 16 | A 23,363 bp deletion "encompasses the entirety of the ISG15 ubiquitin-like modifier (ISG15) gene . . . one or both of the 5' regulatory region of the hairy and enhancer split 4 (HES4) and of the agrin (AGRN) gene and of the first two exons of the AGRN gene" (Beever and Marron, 2011) | 2011 | Reference not in PubMed; see OMIA 002135-9913 for reference details | |||||||
233 | OMIA:000662-9940 | sheep | Romney Marsh (Sheep) | Motor neuron disease, lower | AGTPBP1 | missense | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 2 | NC_040253.1:g.35795594G>C | XM_015093043.2:c.2909G>C | XP_014948529.2:p.(R970P) | protein and cDNA positions are based on XP_014948529.2 and XM_015093043.2, respectively | 2012 | 22588130 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | ||
75 | OMIA:001672-9615 | dog | Coton de Tulear (Dog) | Primary hyperoxaluria type I (Oxalosis I) | AGXT | missense | Naturally occurring variant | yes | CanFam3.1 | 25 | g.50968854G>A | c.304G>A | p.(G102S) | XP_003639939.1:p.Gly102Ser | rs397510072 | 2012 | 22486513 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
1252 | OMIA:001672-9940 | sheep | Zwartbles (Sheep) | Type 1 Primary Hyperoxaluria | AGXT | missense | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 1 | NC_040252.1:g.801189C>T | XM_027966918.1:c.584G>A | XP_027822719.1:p.(C195Y) | NC_040252.1: g.801189C>T; XM_027966918.1: c.584G>A; XP_027822719.1: p.Cys195Tyr (Letko et al., 2020) | 2020 | 33003365 | |||
1214 | OMIA:001222-9685 | domestic cat | Persian (Cat) | Leber congenital amaurosis | AIPL1 | nonsense (stop-gain) | Naturally occurring variant | yes | Felis_catus_9.0 | E1 | g.940445C>T | c.577C>T | p.(R193*) | XM_023243858.1:c.577C>T | 2016 | 27030474 | The genomic location on Felis_catus_9.0 and transcript information is based on Rodney et al. 2021 (PMID: 33785770) | ||
1629 | OMIA:002788-9913 | taurine cattle | Holstein Friesian (Cattle) | Subfertility, AK9-related | AK9 | splicing | Naturally occurring variant | yes | ARS-UCD1.2 | 9 | g.40620329A>G | rs457222030 | 2021 | 34028060 | |||||
1094 | OMIA:002205-9615 | dog | Collie Rough (Dog) | Recurrent inflammatory pulmonary disease | AKNA | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 11 | g.68576241_68576244del | c.2717_2720delACAG | p.(D906Afs*173) | XM_014117950.2: c.2717_2720delACAG; XP_013973425.1:p.(Asp906Alafs*173) | 2019 | 31357536 | |||
1240 | OMIA:002250-9615 | dog | Saluki (Dog) | Succinic Semialdehyde Dehydrogenase Deficiency | ALDH5A1 | missense | Naturally occurring variant | yes | CanFam3.1 | 35 | NC_006617.3:g.22572768G>A | XM_014110599.2:c.866G>A | XP_013966074.2:p.(G288D) | XM_014110599.2: c.866G>A; XP_013966074.2: p.(Gly288Asp) (Vernau et al., 2020) | 2020 | 32887425 | |||
1292 | OMIA:002316-9685 | domestic cat | American Shorthair (Cat) Exotic Shorthair (Cat) Munchkin (Cat) Scottish Fold (Cat) Sphynx (Cat) | Cardiomyopathy, hypertrophic | ALMS1 | missense | Naturally occurring variant | unknown | Felis_catus_9.0 | A3 | g.92439157G>C | c.7384G>C | p.(G2462R) | cDNA and protein positions have been predicted using Ensemble VEP based on transcript ENSFCAT00000077013.1; variant initially reported in Sphynx cats and in a later study (Akiyama et al., 2023) identified in other breeds. Turba et al., 2023 report additional variants in the vicinity that can result in allele dropout in DNA tests and indicate "the need to verify the correspondence between the g.92439157 C variant frequency and the prevalence of HCM" due to high allele frequency of the variant in Sphynx cats in their study. Seo et al. (2024) also identified this variant frequently in Sphynx cats but reported that the variant "was not associated with the HCM diagnosis in the studied population." | rs5334475133 | 2021 | 33639992 | ||
1021 | OMIA:002162-9615 | dog | Karelian Bear Dog (Dog) | Hypophosphatasia | ALPL | missense | Naturally occurring variant | yes | CanFam3.1 | 2 | NC_006584.3:g.77561953A>C | XM_005617214.3:c.1301T>G | XP_005617271.1:p.(V434G) | XM_005617214.3; XP_005617271.1 | 2019 | 30700765 | |||
1486 | OMIA:002162-9940 | sheep | Hypophosphatasia | ALPL | missense | Genome-editing (CRISPR-Cas9) | yes | Oar_rambouillet_v1.0 | 2 | NC_040253.1:g.260716094G>C | XM_027965561.1:c.1077C>G | XP_027821362.1:p.(I359M) | XM_027965561.1; XP_027821362.1 | 2018 | 30446691 | ||||
550 | OMIA:002717-9685 | domestic cat | Burmese (Cat) | Brachycephaly | ALX1 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | B4 | g.110088245_110088256del | c.497_508del | p.(A166_T169del) | XM_003989090.4; XP_003989139.1; published as c.496delCTCTCAGGACTG | 2016 | 26610632 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | ||
764 | OMIA:001009-9913 | taurine cattle | Shorthorn (Cattle) | Tibial hemimelia | ALX4 | deletion, gross (>20) | Naturally occurring variant | yes | 15 | Deletion of 45,694 bp including exon 1 of ALX4 | 2012 | Reference not in PubMed; see OMIA 001009-9913 for reference details | |||||||
763 | OMIA:001009-9913 | taurine cattle | Galloway (Cattle) | Tibial hemimelia | ALX4 | ALX4dup-GAU / ALX4dup-LfL | duplication | Naturally occurring variant | yes | ARS-UCD1.2 | 15 | NC_037342.1:g.74384919_74384938dup | NM_001030304.1:c.713_732dup | NP_001025475.1:p.(Q245fs) | Initially reported as g.75154399_75154418dup in UMD3.1 and g.74384916_74384935dup in ARS-UCD1.2.. Updated to current coordinates after publication of a correction by the authors (PMID: 39298916) [23/09/2024]. The variant is now identical to a variant reported by Buitkamp et al. (2023, PMID:36585373), which was previously listed as omia.variant:1516. Both variants are now merged into one entry and omia.variant:1516 is redundant. | 2015 | 26076463 | The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. The same ARS-UCD1.2 location in the reverse order was included in the paper by Buitkamp et al. (2022). The allele name ALX4dup-GAU was also given by Buitkamp et al. (2022). | |
280 | OMIA:002775-9615 | dog | Miniature Schnauzer (Dog) | Persistent Mullerian duct syndrome | AMHR2 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 27 | NC_006609.3:g.1794738G>A | XM_543632.6:c.262C>T | XP_543632.4:p.(R88*) | XM_543632.6; XP_543632.4; published as c.241C>T; coordinates in the table have been updated to a recent reference genome and / or transcript | 2009 | 18723470 | |||
639 | OMIA:000565-9615 | dog | Giant Schnauzer (Dog) | Intestinal cobalamin malabsorption, AMN-related | AMN | deletion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 8 | g.70807271_70807303del | c.1113_1145del | p.(G372_A382del) | NM_001002960.1; NP_001002960.1 | 2005 | 15845892 | Genomic position in CanFam3.1 provided by Robert Kuhn and Mateo Etcheveste. | ||
426 | OMIA:000565-9615 | dog | Australian Shepherd (Dog) | Intestinal cobalamin malabsorption, AMN-related | AMN | start-lost | Naturally occurring variant | yes | ROS_Cfam_1.0 | 8 | NC_051812.1:g.71077084G>A | NM_001002960.1:c.3G>A | NP_001002960.1:p.(M1?) | NM_001002960.1; NP_001002960.1 | 2005 | 15845892 | |||
1677 | OMIA:002838-9615 | dog | Cirneco dell'Etna (Dog) | Cirneco oculo-neurological syndrome | AMPD2 | CONS | deletion, small (<=20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 6 | g.42698170del | c.2131del | p.(D711Mfs12*) | XM_038541065.1; XP_038396993.1; NC_049227.1 | 2024 | 38397227 | ||
353 | OMIA:002539-9615 | dog | Dalmatian (Dog) | Respiratory distress syndrome | ANLN | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 14 | NC_006596.3:g.47812143C>T | XM_005628719.3:c.31C>T | XP_005628776.1:p.(R11*) | 2017 | 28222102 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
422 | OMIA:001353-9615 | dog | German Shepherd Dog (Dog) | Platelet receptor for factor X, deficiency of | ANO6 | splicing | Naturally occurring variant | yes | CanFam3.1 | 27 | NC_006609.3:g.8912219C>T | XM_005636953.1:c.1934+1G>A | XM_005636953.1 | 2015 | 26414452 | Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool | |||
927 | OMIA:002083-9913 | taurine cattle | Japanese Black, Japan (Cattle) | Abortion (embryonic lethality), ANXA10-related | ANXA10 | repeat variation | Naturally occurring variant | yes | 8 | "a "34-kb deleted-type" CNV "associated with embryonic mortality at 30-60 days after artificial insemination. The CNV harbors exon 2 to 6 of ANNEXIN A10 (ANXA10). . . . Western blot analysis showed that the CNV results in a null allele of ANXA10." | 2016 | 27881083 | |||||||
580 | OMIA:000248-9615 | dog | Collie (Dog) | Neutropenia, cyclic | AP3B1 | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 3 | g.28663129_28663130insA | c.2407_2408insA | p.(T803Nfs*5) | NM_001002974.2; NP_001002974.1; a single base pair (A) insertion in exon 20 of the AP3 beta gene (AP3B1) | rs1152388405 | 2003 | 12897784 | ||
286 | OMIA:000001-9913 | taurine cattle | Blanco Orejinegro, Colombia (Cattle) Holstein Friesian (Cattle) | Abortion due to a nonsense mutation in APAF1 on haplotype HH1 | APAF1 | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.3 | 5 | g.62810245C>T | XM_015471110.2:c.1735C>T | XP_015326596.1:p.(Q579*) | Variant initially reported in Holstein Friesian cattle and later reported in additional breeds: PMID:34779908. Previously listed in OMIA as: p.(Q581*), c.1741C>T, updated to recent transcript information [03/09/2024] | rs448942533 | 2016 | 27289157 | Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |
1206 | OMIA:001916-9615 | dog | Jack Russell Terrier (Dog) | Familial Adenomatous Polyposis | APC | delins, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 3 | g.312131_312132delinsAA | c.[462_463delinsTT] | p.(K155X) | XM_014111995.2; XP_013967470.1 | 2020 | 32445578 | Reference assembly and genomic location kindly provided by Kyoko Yoshizaki, 17 Dec 2020 | ||
731 | OMIA:001965-9913 | taurine cattle | Holstein (black and white) (Cattle) | Holstein cholesterol deficiency | APOB | insertion, gross (>20) | Naturally occurring variant | yes | 11 | "1.3kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing [p.Gly135ValfsX10)]" | 2016 | 26763170 | |||||||
436 | OMIA:000991-9796 | horse | Quarter Horse (Horse) | Androgen insensitivity syndrome (AIS) | AR | regulatory | Naturally occurring variant | yes | EquCab3.0 | X | NC_009175.3:g.52728703A>G | NM_001163891.1:c.1A>G | mutation in start codon for NP_001157363.1; | 2012 | 22095250 | The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022 | |||
1143 | OMIA:000991-9796 | horse | Tennessee Walking Horse (Horse) | Androgen insensitivity syndrome (AIS) | AR | deletion, small (<=20) | Naturally occurring variant | yes | EquCab3.0 | X | NC_009175.3:g.52728885del | NM_001163891.1:c.183del | NP_001157363.1:p.(R63Gfs) | published as c.183delT and p.(Ser61fs); c. and p. information in the table has been updated to HGVS nomenclature | 2020 | 31936796 | The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022 | ||
783 | OMIA:000991-9796 | horse | Warmblood (Horse) | Androgen insensitivity syndrome | AR | deletion, gross (>20) | Naturally occurring variant | yes | EquCab3.0 | X | NC_009175.3:g.52808634_52808658del | NM_001163891.1:c.1630_1654del | the deletion is predicted to create a frameshift: "resulting in altered amino acid composition from p.543Lys and a premature stop codon 44 amino acid residues downstream in exon 3 | 2017 | 28192783 | ||||
786 | OMIA:000991-9796 | horse | Thoroughbred (Horse) | Androgen insensitivity syndrome | AR | missense | Naturally occurring variant | yes | EquCab3.0 | X | NC_009175.3:g.52872393G>C | NM_001163891.1:c.2042G>C | NP_001157363.1:p.(W681S) | 2016 | 27073903 | The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022; p. coordinates obtained from Villagomez et al. (2019) | |||
1144 | OMIA:000991-9796 | horse | Thoroughbred (Horse) | Androgen insensitivity syndrome (AIS) | AR | missense | Naturally occurring variant | yes | EquCab3.0 | X | NC_009175.3:g.52878093C>T | NM_001163891.1:c.2132C>T | NP_001157363.1:p.(A711V) | 2020 | 31936796 | ||||
1752 | OMIA:001201-9685 | domestic cat | Orange coat colour | ARHGAP36 | deletion, gross (>20) | Naturally occurring variant | no | Felis_catus_9.0 | X | NC_018741.3:g.110432079_110437152del | Published by Toh et al. (2024) as g.109186183_109191258del based on the AnAms1.0 reference genome (Matsumoto et al., 2024). This deletion is located within the first intron of ARHGAP36 (Toh et al., 2024). Coordinates in this table are based on a reference genome avialable in the NCBI genome data viewer. | 2024 | 39605675 | ||||||
960 | OMIA:001917-9615 | dog | Leonberger (Dog) Saint Bernard (Dog) | Polyneuropathy, ARHGEF10-related | ARHGEF10 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 16 | g.54349199_54349208del | c.1955_1958+6del | XM_005630036.3; XP_005630093.1; published as c.1955_1958+6delCACGGTGAGC - eliminating the 3'-splice junction of exon 17 and creating an alternate splice site leading to a truncated protein | 2014 | 25275565 | Genomic coordinates in CanFam3.1 provided by Robert Kuhn | |||
780 | OMIA:001334-9913 | taurine cattle | Swedish Red (Cattle) | Sperm, short tail | ARMC3 | deletion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 13 | g.24024660del | c.1442del | p.(A451fs*26) | rs797454424 | 2016 | 26923438 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||
56 | OMIA:000666-9615 | dog | Miniature Schnauzer (Dog) | Mucopolysaccharidosis VI | ARSB | deletion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 3 | g.27870127_27870182del | c.-24_32del | NM_001048133.1 | 2020 | 32985704 | g. coordinate kindly provided by Karthik Raj 29 Oct 2020 | |||
640 | OMIA:000666-9615 | dog | Poodle, Miniature (Dog) | Mucopolysaccharidosis VI | ARSB | deletion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 3 | g.27870253_27870274del | c.103_124del | p.(A35Gfs*108) | NM_001048133.1; NP_001041598.1 | 2012 | 22329490 | Variant information initially provided by Karthik Raj and Urs Giger | ||
859 | OMIA:000666-9615 | dog | Great Dane (Dog) | Mucopolysaccharidosis VI | ARSB | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 3 | NC_006585.3:g.27870445C>T | NM_001048133.1:c.295C>T | NP_001041598.1:p.(Q99*) | NM_001048133.1; NP_001041598.1 | 2018 | 29157190 | Variant information initially provided by Karthik Raj and Urs Giger, and confirmed by Ensembl's VEP | ||
1258 | OMIA:000666-9615 | dog | Miniature Pinscher (Dog) | Mucopolysaccharidosis VI | ARSB | missense | Naturally occurring variant | yes | CanFam3.1 | 3 | NC_006585.3:g.27950471G>A | NM_001048133.1:c.910G>A | NP_001041598.1:p.(G304R) | NM_001048133.1; NP_001041598.1 | 2020 | 32985704 | g. coordinate kindly provided by Karthik Raj 29 Oct 2020 | ||
1320 | OMIA:000666-9685 | domestic cat | Siamese (Cat) | Mucopolysaccharidosis VI, mild, in L476P/D520N cats | ARSB | missense | Naturally occurring variant | yes | Felis_catus_9.0 | A1 | g.145138738C>T | c.1558G>A | p.(D520N) | NM_001142259.1; NP_001135731.1; D520N/D520N and L476P/D520N cats have normal growth and appearance. L476P/D520N cats have a very mild MPS VI phenotype (increased incidence of degenerative joint disease). | 1998 | 9421472 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | ||
132 | OMIA:000666-9685 | domestic cat | Domestic Shorthair Siamese (Cat) | Mucopolysaccharidosis VI | ARSB | missense | Naturally occurring variant | yes | Felis_catus_9.0 | A1 | g.145138869A>G | c.1427T>C | p.(L476P) | NM_001142259.1; NP_001135731.1 | rs5334475159 | 1996 | 8910299 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
67 | OMIA:001503-9615 | dog | American Staffordshire Terrier (Dog) | Neuronal ceroid lipofuscinosis, 4A | ARSG | missense | Naturally occurring variant | yes | CanFam3.1 | 9 | NC_006591.3:g.15071276G>A | XM_005624176.3:c.296G>A | XP_005624233.1:p.(R99H) | 2010 | 20679209 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
712 | OMIA:000201-9913 | taurine cattle | Normande (Cattle) | Brindle | ASIP | Abr | insertion, gross (>20) | Naturally occurring variant | no | 13 | "insertion of a full-length Bos taurus LINE element" | 2006 | 16827753 | ||||||
1321 | OMIA:002200-9915 | indicine cattle (zebu) | Brahman (Cattle) Nellore, India (Sheep) | Darkness of hair coat | ASIP | delins, gross (>20) | Naturally occurring variant | unknown | 13 | 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons (Trigo et al.2021) | 2021 | 33910501 | |||||||
1199 | OMIA:000201-9925 | goat | Peacock Goat (Goat) Valais Grüenochte | Peacock | ASIP | A^pc | repeat variation | Naturally occurring variant | no | 13 | "The ASIP allele in Peacock goats, which we propose to term “peacock” (A^pc), has a quadruplication of the same ~45 kb region having five copies in the A^b allele. It is additionally flanked by triplicated segments of 27,996 bp and 41,807 bp on the left and right side of the quadruplicated sequence (Fig 3, S4 Fig, S5 Table). The central part of the A^pc allele has exactly the same breakpoints as the A^b allele suggesting a common origin of A^b and A^pc." (Henkel et al., 2019) "63'158'171-63'203'851: 4 copies (corresponds to the CNV in the Ab allele)" (Table S5; Henkel et al., 2019) 200922: Marius picked this g. entry up as requiring attention: "g.63130175_63245658 (3 copies)". Because this will take time to sort out, I have removed it from the g. field for the time being. | 2019 | 31841508 | ||||||
1200 | OMIA:000201-9925 | goat | Bezoar (Goat) Valais Blackneck (Goat) Valais Copperneck | Wild type or Bezaur | ASIP | A^bz | reference sequence allele | Naturally occurring variant | no | 13 | "The goat genome reference sequence is derived from a San Clemente goat, which has a similar coat color pattern as bezoars. The genome reference therefore supposedly represents the wildtype allele at the ASIP locus, termed “bezoar” (Abz) [8]. Bezoars and all other Swiss goat breeds did not show any CNVs at the ASIP locus." (Henkel et al., 2019) | 2019 | 31841508 | ||||||
1075 | OMIA:001602-93934 | Japanese quail | Feather colour, fawn-2/beige | ASIP | Y^f2 | duplication | Naturally occurring variant | no | 20 | Robic et al. (2019) concluded "that fawn-2 and beige are the same allele, and that it is caused by a 70,895-bp tandem duplication . . . [with breakpoints] (NC-029535 [1,371,395(or 98)–1,442,295 (or 98)]) . . . located downstream of the ITCH exon 1 and upstream of the ASIP exon e4 (5′ UTR). . . . The 70,895 bp of the duplicated region include the entire AHCY gene on one strand, and parts of the ASIP and ITCH genes on the other strand." | 2019 | 30987584 | |||||||
665 | OMIA:000201-10042 | North American deer mouse | New Hampshire (Chicken) | Melanic (non-agouti) | ASIP | deletion, gross (>20) | Naturally occurring variant | no | "a 125-kb deletion, which includes the upstream regulatory region and exons 1 and 2 of Agouti, results in a loss of Agouti expression" | 2009 | 19649329 | ||||||||
251 | OMIA:000201-61386 | Kodkod | Melanism (black coat) | ASIP | missense | Naturally occurring variant | no | p.(C126Y) | 2015 | 25695801 | |||||||||
252 | OMIA:000201-61406 | Colocolo | Melanism (black coat) | ASIP | missense | Naturally occurring variant | no | p.(R120C) | 2015 | 25695801 | |||||||||
1119 | OMIA:000201-10141 | domestic guinea pig | Recessive black | Asip | deletion, small (<=20) | Naturally occurring variant | no | c.181_184delTTCA | MH026115: c.181_184delTTCA; the deletion leads to a truncated protein of 77 amino acids due to the premature stop codon. | 2019 | 30746725 | ||||||||
330 | OMIA:000201-10042 | North American deer mouse | Alaska, United States of America (North American deer mouse) | Melanic (non-agouti) | ASIP | nonsense (stop-gain) | Naturally occurring variant | no | c.193?>? | p.(Q65*) | 2009 | 19649329 | |||||||
333 | OMIA:000201-9691 | leopard | Coat colour, black (black panther) | ASIP | nonsense (stop-gain) | Naturally occurring variant | no | c.333C>A | p.(C111*) | 2012 | 23251368 | ||||||||
1219 | OMIA:000201-9858 | Western roe deer | Melanistic (black) | ASIP | missense | Naturally occurring variant | no | c.33G>T | p.(L11F) | 2020 | 32545389 | ||||||||
1587 | OMIA:000201-9691 | leopard | Coat colour, black (black panther) | ASIP | missense | Naturally occurring variant | no | c.353C>A | p.(C113F) | 2023 | 37440497 | ||||||||
1666 | OMIA:000201-10007 | tassel-eared squirrel | Coat colour, black | ASIP | missense | Naturally occurring variant | no | c.370T>C | p.(C124R) | 2024 | 38396615 | ||||||||
504 | OMIA:001602-93934 | Japanese quail | Feather colour, recessive black | ASIP | rb | deletion, small (<=20) | Naturally occurring variant | no | 20 | c.373_380del | "A deletion of 8 bases was found in the ASIP gene" | 2008 | 18287406 | ||||||
253 | OMIA:000201-61455 | Asiatic golden cat | Black | ASIP | missense | Naturally occurring variant | no | c.384C>G | p.(C128W) | 2012 | 23251368 | ||||||||
1010 | OMIA:000201-9838 | Arabian camel | Black and dark-brown coat colour | ASIP | haplotype | Naturally occurring variant | no | c.[23delT;c.25G>A] | KU179868; c.[23delT;c.25G>A]. As described by Almathen et al. (2018), this haplotype comprises "a 1-bp deletion (23delT/T) and a SNP (25G/A) in exon 2 of ASIP". | 2018 | 29893870 | ||||||||
654 | OMIA:001602-93934 | Japanese quail | Feather colour, lethal yellow | ASIP | Y | deletion, gross (>20) | Naturally occurring variant | yes | 20 | g.1463709_1604872del | Nadeau et al. (2008): "a >90-kb [141162bp] deletion upstream of ASIP" | 2008 | 18287407 | The g. coordinates were provided by Robic et al. (2019) | |||||
1196 | OMIA:000201-9925 | goat | Appenzell (Goat) Girgentana, Italy (Goat) Saanen (Goat) | White or tan | ASIP | A^Wt | repeat variation | Naturally occurring variant | no | ARS1.2 | 13 | "CNV [copy number variation] affecting a region of less that 100 kb including the ASIP and AHCY genes" (Fontanesi et al., 2009)."spans 154,677 bp ofthe reference genome sequence and comprises the entire coding sequence ofthe ASIP, AHCYand ITCH genes. The individual copies are arranged in tandem in a head to tail orientation." (Henkel et al., 2019) 200922: moved the g. entry to here (g.63,226,824-63,381,501 (3 copies)) until it can be standardised | 2009 | 20016133 | |||||
1197 | OMIA:000201-9925 | goat | Grisons Striped (Goat) Toggenburg (Goat) | Swiss markings | ASIP | A^sm | repeat variation | Naturally occurring variant | no | ARS1.2 | 13 | "8 tandem copies of a 13,433 bp sequence from the 5’-flanking region of ASIP" (Henkel et al., 2019) 200922: moved g. entry to here (g.63,129,198-63,142,631 (8 copies)) until it can be fixed | 2019 | 31841508 | |||||
1198 | OMIA:000201-9925 | goat | Chamois Coloured (Goat) St Gallen Booted Goat (Goat) | Badgerface | ASIP | A^b | repeat variation | Naturally occurring variant | no | ARS1.2 | 13 | "a five-fold amplification of45,680 bp located ~61 kb downstream ofthe Asm amplification" (Henkel et al., 2019) 200922: move the g. entry to here (g.63,158,171-63,203,851 (5 copies)), until it can be fixed | 2019 | 31841508 | |||||
149 | OMIA:000201-9793 | ass (donkey) | Âne de Provence, France (Ass) Âne normand, France (Ass) Dezhou, China (Ass) Miniature, United States of America (Ass) | No light points | ASIP | NLP | missense | Naturally occurring variant | no | ASM1607732v2 | 15 | NC_052191.1:g.25406489T>C | XM_044748287.1:c.349T>C | XP_044604222.1:p.(C117R) | The Dezhou reference genome ASM1607732v2 represents the 'no light points' variant: NC_052191.1:g.25406489C |
2015 | 25887951 | ||
1382 | OMIA:000201-9615 | dog | Dominant yellow | ASIP | DY | reference sequence allele | Naturally occurring variant | no | CanFam3.1 | 24 | CanFam3.1 | The reference sequence CanFam3.1 represents the dominant yellow phenotype. | 2021 | 34385618 | |||||
1386 | OMIA:000201-9615 | dog | Black saddle | ASIP | BS | delins, gross (>20) | Naturally occurring variant | no | CanFam3.1 | 24 | g.23378062_23379640delins[MT319116.1:424_663] | Likely causal regulatory promoter variant | 2021 | 34385618 | |||||
1385 | OMIA:000201-9615 | dog | Black back 3 | ASIP | BB3 | haplotype | Naturally occurring variant | no | CanFam3.1 | 24 | g.[23353288_23353472del;23354716_23354751A[4];23377890_23378086del;23378320_23378343del;g.23378858_2 | Haplotype containing a likely causal regulatory promoter variant | 2021 | 34385618 | |||||
1380 | OMIA:000201-9615 | dog | Agouti | ASIP | AG | haplotype | Naturally occurring variant | no | CanFam3.1 | 24 | g.[23353288_23353472del;23354716_23354751A[4];23377890_23378086del;23378320_23378343del] | Haplotype containing a likely causal regulatory promoter variant | 2021 | 34385618 | |||||
1383 | OMIA:000201-9615 | dog | Black back 1 | ASIP | BB1 | haplotype | Naturally occurring variant | no | CanFam3.1 | 24 | g.[23353288_23353472del;23354716_23354751A[4];23378062_23378231delins[MT319115.1:424_674] | Haplotype containing a likely causal regulatory promoter variant | 2021 | 34385618 | |||||
1384 | OMIA:000201-9615 | dog | Black back 2 | ASIP | BB2 | haplotype | Naturally occurring variant | no | CanFam3.1 | 24 | g.[23353288_23353472del;23354716_23354751A[4];23378062_23379640delins[MT319116.1:424_663]] | Haplotype containing a likely causal regulatory promoter variant | 2021 | 34385618 | |||||
1381 | OMIA:000201-9615 | dog | Shaded yellow | ASIP | SY | haplotype | Naturally occurring variant | no | CanFam3.1 | 24 | g.[23353288_23353472del;23354716_23354751A[4]] | Haplotype containing a likely causal regulatory promoter variant | 2021 | 34385618 | |||||
30 | OMIA:000201-9615 | dog | German Shepherd Dog (Dog) | Recessive black | ASIP | missense | Naturally occurring variant | no | CanFam3.1 | 24 | NC_006606.3:g.23393552C>T | NM_001007263.1:c.286C>T | NP_001007264.1:p.(R96C) | rs851336386 | 2004 | 15520882 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
509 | OMIA:000201-9796 | horse | American Trotter (Horse) Arab (Horse) Belgian Draft (Horse) Clydesdale (Horse) Freiberger (Horse) Icelandic Horse (Horse) Morgan (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Thoroughbred (Horse) Warmblood (Horse) Welsh Pony (Horse) | Coat colour, recessive black | ASIP | a | deletion, small (<=20) | Naturally occurring variant | no | EquCab3.0 | 22 | NC_009165.3:g.26067463_26067473del | NM_001164017.1:c.187_197del | published as g.2174_2184del and c.191_201del - coordinates in the table updated to a recent reference genome. | rs3091770233 | 2001 | 11353392 | Coordinates in EquCab3.0 kindly provided by Haley Rutstein, working under the guidance of Professor Ernie Bailey. Breed information based on PMID: 38600096 | |
1452 | OMIA:002549-9685 | domestic cat | Bengal (Cat) | Coat colour and pattern, charcoal | ASIP | A^Pben | missense | Naturally occurring variant | no | Felis_catus_9.0 | A3 | c.251A>G | p.(Q84R) | variant contributes to A^Pbe haplotype associated with charcoal colour/pattern (in exon 4, not present in Felis_catus_9.0) | 2014 | 25143047 | |||
1453 | OMIA:002549-9685 | domestic cat | Bengal (Cat) | Coat colour and pattern, charcoal | ASIP | A^Pben | missense | Naturally occurring variant | no | Felis_catus_9.0 | A3 | c.302A>G | p.(D101G) | variant contributes to A^Pbe haplotype associated with charcoal colour/pattern (in exon 4, not present in Felis_catus_9.0) | 2014 | 25143047 | |||
1450 | OMIA:002549-9685 | domestic cat | Bengal (Cat) | Coat colour and pattern, charcoal | ASIP | A^Pben | missense | Naturally occurring variant | no | Felis_catus_9.0 | A3 | g.25086548A>G | c.142T>C | p.(S48P) | NM_001009190.1; NP_001009190.1; variant contributes to A^Pbe haplotype associated with charcoal colour/pattern | 2014 | 25143047 | ||
493 | OMIA:000201-9685 | domestic cat | Coat colour, non-agouti (black) | ASIP | a | deletion, small (<=20) | Naturally occurring variant | no | Felis_catus_9.0 | A3 | g.25086566_25086567del | c.123_124del | p.(M42Efs*59) | NM_001009190.1; NP_001009190.1; "a 2 bp deletion in the ASIP gene [at nucleotide positions 123-124]" | rs5334475125 | 2003 | 12620197 | The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770 | |
1451 | OMIA:002549-9685 | domestic cat | Bengal (Cat) | Coat colour and pattern, charcoal | ASIP | A^Pben | missense | Naturally occurring variant | no | Felis_catus_9.0 | A3 | g.25086649C>G | c.41G>C | p.(C14S) | NM_001009190.1; NP_001009190.1; variant contributes to A^Pbe haplotype associated with charcoal colour/pattern | 2014 | 25143047 | ||
1734 | OMIA:000201-30532 | fallow deer | Coat colour, black | ASIP | splicing | Naturally occurring variant | unknown | GCF_033118175.1 | 23 | NC_083703.1:g.63827550G>A | XM_061127099.1:c.225+1G>A | 2024 | 39202415 | ||||||
1735 | OMIA:000201-30532 | fallow deer | Coat colour, black | ASIP | duplication | Naturally occurring variant | no | GCF_033118175.1 | 23 | NC_083703.1:g.63830157_63830161dup | 2024 | 39202415 | |||||||
1708 | OMIA:000201-9337 | common brushtail possum | Coat colour, non-agouti (black) | ASIP | missense | Naturally occurring variant | unknown | mTriVul1.pri | 3 | NC_050575.1:g.100483705C>T | XM_036748710.1:c.343C>T | XP_036604605.1:p.(R115C) | 2024 | 39086822 | |||||
714 | OMIA:000201-9940 | sheep | Merino (Sheep) | White fleece | ASIP | Wt | insertion, gross (>20) | Naturally occurring variant | no | Oar_rambouillet_v1.0 | 13 | a 190kb tandem duplication encompassing the ASIP gene, the neighbouring AHCY gene and the promoter for a third gene ITCH | 2008 | 18493018 | |||||
1111 | OMIA:000201-9940 | sheep | Recessive black | ASIP | a | deletion, small (<=20) | Naturally occurring variant | no | Oar_rambouillet_v1.0 | 13 | g.66475132_66475136del | published as g.100_105del / D5 and predicted to result in a frame shift followed by a premature stop codon 63 amino acids downstream of the start site | 2002 | 12354151 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | ||||
1112 | OMIA:000201-9940 | sheep | Recessive black | ASIP | a | missense | Naturally occurring variant | no | Oar_rambouillet_v1.0 | 13 | NC_040264.1:g.66474980T>A | NM_001134303.1:c.376T>A | NP_001127775.1:p.(C126S) | Published as g.5172T>A (Norris et al. 2008). cDNA and protein positions based on NM_001134303.1 and NP_001127775.1 | 2008 | 18493018 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | ||
1134 | OMIA:000201-9986 | rabbit | Black and tan | ASIP | a^t | deletion, gross (>20) | Naturally occurring variant | no | OryCun2.0 | 4 | g.5455408_5466123del | Letko et al. (2020): NC_013672.1:g.5,455,408_5,466,123del | 2020 | 31729778 | |||||
567 | OMIA:000201-9986 | rabbit | New Zealand White (Rabbit) | Black (non-agouti) | ASIP | a | insertion, small (<=20) | Naturally occurring variant | no | UM_NZW_1.0 | 4 | NC_067377.1:g.13094745_13094746insT | NM_001122939.1:c.5_6insA | NP_001116411.1:p.(N2Kfs21*) | Reported by Letko et al. (2020): NM_001122939.1:c.5_6insA, the OryCun2.0 reference genome represents the nonagouti allele. | 2010 | 20004240 | ||
667 | OMIA:000201-9627 | red fox | Dark Standard Silver | ASIP | deletion, gross (>20) | Naturally occurring variant | no | VulVul2.2 | NW_020356514.1 | A 16.5-kb deletion resulting in "a 166-nt deletion in the Standard Silver fox cDNA, spanning the second exon ... .This deletion removes the start codon and entire signal peptide" | 1997 | 9054949 | |||||||
1309 | OMIA:002325-9685 | domestic cat | Encephalopathy, spongy | ASPA | missense | Naturally occurring variant | yes | Felis_catus_9.0 | E1 | g.13585610C>G | c.859G>C | p.(A287P) | XM_006939957.4; XP_006940019.1 | 2021 | 33779415 | ||||
111 | OMIA:002099-9615 | dog | German Shepherd Dog (Dog) | Ichthyosis, ASPRV1-related | ASPRV1 | missense | Naturally occurring variant | yes | CanFam3.1 | 10 | NC_006592.3:g.68587027A>G | XM_014117456.1:c.1052T>C | XP_013972931.1:p.(L351P) | XM_014117456.1; XP_013972931.1 | 2017 | 28249031 | Genomic position in CanFam3.1 provided by Robert Kuhn and Mateo Etcheveste. | ||
1673 | OMIA:002099-9615 | dog | Pembroke Welsh Corgi (Dog) | Ichthyosis, non-epidermolytic | ASPRV1 | deletion, small (<=20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 10 | NC_049231.1:g.69888722_69888723del | XM_038551592.1:c.594_595del | XP_038407520.1:p.(L199Rfs*342) | 2024 | 38549226 | ||||
289 | OMIA:000194-9913 | taurine cattle | Blanco Orejinegro, Colombia (Cattle) Brown Swiss (Cattle) Holstein Friesian (Cattle) | Citrullinaemia | ASS1 | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.3 | 11 | NC_037338.1:g.100781668C>T | NM_173892.4:c.256C>T | NP_776317.1:p.(R86*) | Variant initially identified in Holstein Friesian and later reported in additional breeds: PMID:30014197, PMID:34779908. | rs5334475062 | 1989 | 2813370 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |
65 | OMIA:001471-9615 | dog | Poodle, Standard (Dog) | Neonatal encephalopathy with seizures | ATF2 | missense | Naturally occurring variant | yes | CanFam3.1 | 36 | NC_006618.3:g.19078954A>C | XM_005640334.3:c.152T>G | XP_005640391.1:p.(M51R) | 2008 | 18074159 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
94 | OMIA:001954-9615 | dog | Lagotto Romagnolo (Dog) | Neurodegenerative vacuolar storage disease | ATG4D | missense | Naturally occurring variant | yes | CanFam3.1 | 20 | NC_006602.3:g.50618958C>T | XM_542069.6:c.1288G>A | XP_542069.1:p.(A430T) | 2015 | 25875846 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
1067 | OMIA:001552-9615 | dog | Australian Cattle Dog (Dog) | Neuronal ceroid lipofuscinosis, 12 | ATP13A2 | missense | Naturally occurring variant | yes | CanFam3.1 | 2 | NC_006584.3:g.81208162C>T | XM_005617949.3:c.1118C>T | XP_005618006.1:p.(T373I) | XM_005617949.3; XP_005618006.1 | 2019 | 30956123 | |||
400 | OMIA:001552-9615 | dog | Tibetan Terrier (Dog) | Neuronal ceroid lipofuscinosis, 12 | ATP13A2 | splicing | Naturally occurring variant | yes | CanFam3.1 | 2 | NC_006584.3:g.81210367del | XM_005617949.3:c.1623del | XM_005617949.3; XP_005618006.1; variant was published as c.1623delG p.P541fs*597 by Farias et al. (2011); Wöhlke et al. (2011) provided an alternate transcript position c.1620delG and proposed that the variant causes exon 16 skipping in NCL-affected Tibetan terriers. The sequence information provided by Wöhlke et al. (2011) corresponds to XM_005617949.3:c.1623del | 2011 | 21362476 22022275 | ||||
734 | OMIA:002110-9615 | dog | Belgian Shepherd Dog (Dog) | Ataxia, cerebellar, ATP1B2-related | ATP1B2 | insertion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 5 | g.32551064_32551065ins[LT796559.1:g.50_276] | c.130_131ins[LT796559.1:g.50_276] | XM_546597.5; "a 227 bp SINE insertion into exon 2 of the ATP1B2 gene" | 2017 | 28620085 | ||||
188 | OMIA:001450-9913 OMIA:001464-9913 | taurine cattle | Belgian Blue (Cattle) Maas-Rijn-Ijssel (Cattle) | Congenital muscular dystonia 1 | ATP2A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 25 | NC_037352.1:g.25933247G>A | NM_001075767.1:c.1675C>T | NP_001069235.1:p.(R559C) | Variant is reported to cause congenital muscular dystonia 1 in Belgian Blue cattle (OMIA 001450-9913) and congenital pseudomyotonia in a Dutch improved red and white cross-bred calf (OMIA:001464_9913). | rs5334475104 | 2008 | 18344998 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). | |
219 | OMIA:001464-9913 | taurine cattle | Romagnola (Cattle) | Pseudomyotonia, congenital | ATP2A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 25 | NC_037352.1:g.25939141C>A | NM_001075767.1:c.857G>T | NP_001069235.1:p.(G286V) | This variant was identified as part of a haplotype with the G211V variant in Romagnola cattle. Akyürek et al. (2022; PMID: 36293223) suggest that the G286V variant is likely to be benign and that the G211V is likely to be causal. | rs3423529256 | 2012 | 23046865 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |
218 | OMIA:001464-9913 | taurine cattle | Romagnola (Cattle) | Pseudomyotonia, congenital | ATP2A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 25 | NC_037352.1:g.25939366C>A | NM_001075767.1:c.632G>T | NP_001069235.1:p.(G211V) | rs5334474971 | 2012 | 23046865 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
205 | OMIA:001464-9913 | taurine cattle | Chianina (Cattle) Marchigiana (Cattle) Romagnola (Cattle) | Pseudomyotonia, congenital | ATP2A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 25 | NC_037352.1:g.25940510C>T | NM_001075767.1:c.491G>A | NP_001069235.1:p.(R164H) | Variant initially identified in Chianina cattle and later reported in additional breeds: PMID: 35717834 | rs3423529241 | 2008 | 18786632 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |
1192 | OMIA:002265-9615 | dog | Irish Terrier (Dog) | Darier disease | ATP2A2 | insertion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 26 | g.8200944_8200945insN[(205)] | c.2098-3_2098-2insN[(205)] | p.(T700Vfs*6) | NM_001003214.1; NP_001003214.1; Linek et al. (2020): "a heterozygous SINE insertion [~205bp] into the ATP2A2 gene, at the end of intron 14, close to the boundary of exon 15", giving rise to NP_001003214.1:p.(Thr700Valfs*6) | 2020 | 32354065 | |||
1533 | OMIA:002265-9615 | dog | Shih Tzu (Dog) | Darier disease | ATP2A2 | missense | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 26 | NC_049247.1:g.8434781A>C | NM_001003214.1:c.2425A>C | NP_001003214.1:p.(N809H) | NM_001003214.1; NP_001003214.1 | 2023 | 36883421 | |||
107 | OMIA:002608-9615 | dog | Labrador Retriever (Dog) | Modifier of copper toxicosis | ATP7A | missense | Naturally occurring variant | yes | CanFam3.1 | X | NC_006621.3:g.60279238C>T | XM_005641519.2:c.980C>T | XP_005641576.1:p.(T327I) | rs852523339 | 2016 | 26747866 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The phenotype was renamed from 'Menkes disease' to 'Modifier of copper toxicosis' based on feedback from Tom Nagels [10/01/2023]. | ||
1347 | OMIA:001071-9685 | domestic cat | Wilson disease | ATP7B | missense | Naturally occurring variant | yes | A1 | p.(P550L) | 2020 | 31687873 | ||||||||
106 | OMIA:001071-9615 | dog | Labrador Retriever (Dog) | Wilson disease | ATP7B | missense | Naturally occurring variant | yes | CanFam3.1 | 22 | NC_006604.3:g.225112G>A | XM_005633828.3:c.4151G>A | XP_005633885.1:p.(R1384Q) | XM_005633831.3; XP_005633888.1; variant published as c.4358G>A / p.(R1453Q) and the variant coordinates in this table have been changed to reflect recent transcript IDs; conflicting evidence in regard to causality of this variant are reported in the literature - see https://omia.org/OMIA001071/9615/ for details | rs851958524 | 2016 | 26747866 | 30 Dec 2020: correct genomic location provided by Angelica K Kallenberg | |
1590 | OMIA:001071-9685 | domestic cat | Domestic Longhair | Wilson disease | ATP7B | missense | Naturally occurring variant | yes | Felis_catus_9.0 | A1 | g.19609511T>A | c.3670T>A | p.(W1224R) | XM_023251165.1; XP_023106933.1; variant heterozygous in a single affected cat | 2023 | 37427085 | |||
1136 | OMIA:001071-9685 | domestic cat | Wilson disease | ATP7B | missense | Naturally occurring variant | yes | Felis_catus_9.0 | A1 | g.19611002C>G | c.3890C>G | p.(T1297R) | XM_023251176.1; XM_023251176.1 | 2019 | 30561139 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | |||
1076 | OMIA:001645-10036 | golden hamster | Black tremor | Atrn | insertion, gross (>20) | Naturally occurring variant | yes | Kuramoto et al. (2002): "an approximately 10-kb DNA fragment, which had 557-bp direct repeats in both ends and was flanked by the identical 6-bp target duplication sequences, [that] was inserted into exon 24" | 2002 | 11773967 | |||||||||
348 | OMIA:000487-9796 | horse | Belgian Draft (Horse) Friesian (Horse) Warmblood (Horse) | Hydrocephalus | B3GALNT2 | nonsense (stop-gain) | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.76887901C>T | XM_001491545.6:c.1423C>T | XP_001491595.2:p.(Q475*) | XM_001491545; XP_001491595; Ducro et al. (2015): "The nomenclature for the mutation is c.1423C>T [GenBank:XM_001491545] corresponding to p.Gln475* [GenBank:XP_001491595]". As at 25 April 2019, Ensembl's Variant Effect Predictor (VEP) gives the EquCab3 c. and p. coordinates as having not changed from the EquCab2 coordinates reported by Ducro et al. (2015). The Ensembl ref is ENSECAT00000049072 | rs3429464524 | 2015 | 26452345 | c. and p. variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. EquCab3 g. coordinate provided by Meredith O’Connell, working under the supervision of Professor Ernie Bailey, 24 April 2019. Breed information updated based on PMID: 38600096 | |
439 | OMIA:001885-9940 | sheep | Lacaune (Sheep) | Fecundity, Lacaune, FecL | B4GALNT2 | regulatory | Naturally occurring variant | no | Oar_v3.1 | 11 | g.36938224T>A | c.766+2831A>T | ENSOART00000006875.1:c.766+2831A>T ENSOART00000006877.1:c.781+2831A>T | rs588626728 | 2013 | 24086150 | |||
440 | OMIA:001885-9940 | sheep | Lacaune (Sheep) | Fecundity, Lacaune, FecL | B4GALNT2 | regulatory | Naturally occurring variant | no | Oar_v3.1 | 11 | g.37034573A>G | 2013 | 24086150 | ||||||
421 | OMIA:002068-9796 | horse | Friesian (Horse) | Dwarfism, Friesian | B4GALT7 | splicing | Naturally occurring variant | yes | EquCab3.0 | 14 | NC_009157.3:g.3772591C>T | XM_023617086.1:c.50G>A | XP_023472854.1:p.(R17K) | rs3447120064 | 2016 | 27793082 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. FN thanks Elizabeth Huffman, who updated the g. coordinates to EquCab3, working under the supervision of Professor Ernie Bailey; 23 April 2020. | ||
1676 | OMIA:002837-9646 | giant panda | Coat colour, brown white | BACE2 | deletion, gross (>20) | Naturally occurring variant | no | 1 | c.176_200del | Published as c.176_200delTCGCCCTGGAGCCCGCCGGCGGCGC; g.4545815_4545839del | 2024 | 38437540 | |||||||
1391 | OMIA:002484-9615 | dog | Shetland Sheepdog (Dog) | Bardet-Biedl syndrome 2 | BBS2 | missense | Naturally occurring variant | yes | CanFam3.1 | 2 | g.59693737G>C | c.1222G>C | p.(A408P) | ENSCAFT00000014523.5; ENSCAFP00000013435.4 | 2021 | 34828377 | |||
356 | OMIA:002045-9615 | dog | Puli (Dog) | Bardet-Biedl syndrome 4 | BBS4 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 30 | g.36063748A>T | c.58A>T | p.(K20*) | 2017 | 28533336 | ||||
1131 | OMIA:002216-9544 | Rhesus monkey | Bardet-Biedl syndrome 7 | BBS7 | deletion, small (<=20) | Naturally occurring variant | yes | Mmul_8.0.1 | c.160delG | p.(A54fs) | 2019 | 31589838 | |||||||
1049 | OMIA:002178-9823 | pig | Landrace (Pig) Large White (Pig) Yorkshire (Pig) | Abortion, BBS9 and BMPER-related | BBS9 | deletion, gross (>20) | Naturally occurring variant | yes | Sscrofa11.1 | 18 | NC_010460.4:g.39817373_40029300del | Derks et al. (2018): "a large deletion in complete LD with the SSC18 haplotype of approximately 212kb (position 39,817,373 to 40,029,300), spanning a part of the BBS9 gene ... [and reducing] expression of the downstream BMPER gene". Initially reported in Large White and later reported in other breeds (PMID:39327728). | 2018 | 30231021 | |||||
635 | OMIA:001592-9615 | dog | Cavalier King Charles Spaniel (Dog) | Episodic falling | BCAN | deletion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 7 | g.41325010_41340731delinsAAGGCC | c.-13991_466+85delinsGGCCTT | XM_005622698.1; a 15.7kb deletion in the BCAN gene removing the first 3 exons | 2012 | 21821125 | ||||
298 | OMIA:000627-9913 | taurine cattle | Polled Hereford (Cattle) | Maple syrup urine disease | BCKDHA | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.2 | 18 | g.50551011C>T | c.148C>T | p.(Q50*) | cDNA position based on ENSBTAT00000021342.6 | rs5334475064 | 1990 | 2303405 | ||
200 | OMIA:000627-9913 | taurine cattle | Shorthorn (Cattle) | Maple syrup urine disease | BCKDHA | missense | Naturally occurring variant | yes | ARS-UCD1.2 | 18 | g.50560242C>T | c.1380C>T | p.(P372L) | rs3423447991 | 1999 | 10425233 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
1333 | OMIA:001079-9940 | sheep | spælsau (Sheep) | yellow fat | BCO2 | insertion, gross (>20) | Naturally occurring variant | yes | 15 | "insertion of a 7.9 kb endogenous Jaagsiekte Sheep Retrovirus (enJSRV) sequence in the first intron of the BCO2 gene" (Kent et al. 2021) | 2021 | 34193038 | |||||||
549 | OMIA:001079-9986 | rabbit | Flemish Giant (Rabbit) New Zealand White (Rabbit) | Yellow fat | BCO2 | deletion, small (<=20) | Naturally occurring variant | yes | 1 | delAAT | 2015 | 26002694 | |||||||
1375 | OMIA:002466-48883 OMIA:002466-48882 OMIA:002466-87173 OMIA:002466-48884 OMIA:002466-48885 OMIA:002466-48886 OMIA:002466-1553461 | medium ground-finch | Beak colour, yellow | BCO2 | synonymous | Naturally occurring variant | no | 24 | g.6166878G>A | p.(V?V) | synonymous change 32 bp into exon 4 | 2021 | 34687609 | ||||||
305 | OMIA:001079-9913 | taurine cattle | Holstein Friesian (Cattle) | Yellow fat | BCO2 | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.3 | 15 | NC_037342.1:g.22552375G>A | NM_001101987.2:c.306G>A | NP_001095457.2:p.(W102*) | UMD3.1 position is g.22877552G>A; cDNA position is based on XM_024975217.1 | rs109226280 | 2009 | 19398771 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. | |
1559 | OMIA:002466-9135 | common canary | Beak and leg colour, red | BCO2 | missense | Naturally occurring variant | no | NW_022042652.1 | g.75258192G>A | p.R413H | 2020 | 31930402 | XP_009096268.1, genomic position as reported by Bovo et al. (2023) PMID:37194440 | ||||||
320 | OMIA:001079-9940 | sheep | spælsau (Sheep) | Yellow fat | BCO2 | nonsense (stop-gain) | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 15 | NC_040266.1:g.25024133C>T | XM_012095240.3:c.196C>T | XP_011950630.2:p.(Q66*) | Oar_v3.1 position is g.21947481C>T | rs1090867485 | 2010 | 20122251 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
737 | OMIA:001554-9615 | dog | Finnish Lapphund (Dog) Lapponian Herder (Dog) | Multifocal retinopathy 3 | BEST1 | cmr3 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 18 | g.54470590del | c.1388del | p.(P463Hfs) | NM_001097545.1; NP_001091014.1; published as c.1388delC; variant initially identified in Lapponian Herder and later reported in additional breeds: PMID:27525650 | rs397509969 | 2010 | 21197113 | Variant information and allele abbreviation gleaned from or confirmed by Donner et al. (2016) PLoS One 11:e0161005 and genomic position in CanFam3.1 and EVA ID provided by Mateo Etcheveste and Robert Kuhn. |
59 | OMIA:001553-9615 | dog | Coton de Tulear (Dog) | Multifocal retinopathy 2 | BEST1 | cmr2 | missense | Naturally occurring variant | yes | CanFam3.1 | 18 | NC_006600.3:g.54476143C>T | NM_001097545.1:c.482G>A | NP_001091014.1:p.(G161D) | NM_001097545.1; NP_001091014.1 | 2007 | 17460247 | Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn. | |
275 | OMIA:001444-9615 | dog | Boerboel (Dog) Bull Mastiff (Dog) English Mastiff (Dog) Great Pyrenees (Dog) | Multifocal retinopathy 1 | BEST1 | cmr1 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 18 | NC_006600.3:g.54478586G>A | NM_001097545.1:c.73C>T | NP_001091014.1:p.(R25*) | NM_001097545.1; NP_001091014.1 | 2007 | 17460247 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
398 | OMIA:001660-9615 | dog | Great Dane (Dog) | Inherited myopathy of Great Danes | BIN1 | splicing | Naturally occurring variant | yes | CanFam3.1 | 19 | NC_006601.3:g.23522400A>G | XM_014121413.2:c.786-2A>G | XP_013976888.1:p.(R262_K263insASASRPFPQ) | XM_014121413.2; XP_013976888.1; published as IVS10-2A>G, updated in this table to HGVS nomenclature | 2013 | 23754947 | |||
1770 | OMIA:002917-9615 | dog | Mixed Breed (Dog) | Biliverdinuria | BLVRA | deletion, gross (>20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 18 | NC_049239.1:g.6532022_6551313del | XP_038418561.1:p.[K117_K296del] | 2024 | 39766828 | |||||
1771 | OMIA:002917-9615 | dog | Mixed Breed (Dog) | Biliverdinuria | BLVRA | deletion, gross (>20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 18 | NC_049239.1:g.6543863_6545908 | XP_038418561.1:p.[A154fs] | 2024 | 39766828 | |||||
755 | OMIA:002306-9940 | sheep | Tunisian Barbary (Sheep) | Fecundity, Barbarine | BMP15 | FecX(Bar) | complex rearrangement | Naturally occurring variant | no | Oar_rambouillet_v1.0 | X | g.[56600937insG;56600945_56600947del;56600948C>A] | c.[301G>T;302_304delCTA;310insC] | p.(A101Cfs*113) | "a composite polymorphism associating a single nucleotide substitution (c.301G > T), a 3 bp deletion (c.302_304delCTA) and a C insertion (c.310insC) in the ovine BMP15 cDNA leading to a frame shift at protein position 101" - cDNA positions based on NM_001114767 | 2017 | 28506298 | ||
244 | OMIA:002306-9940 | sheep | Belclare (Sheep) Cambridge (Sheep) | Fecundity, Belclare | BMP15 | FecX(B) | missense | Naturally occurring variant | no | Oar_rambouillet_v1.0 | X | NC_040278.1:g.56594843C>A | NM_001114767.1:c.1100G>T | NP_001108239.1:p.(S367I) | 2004 | 14627550 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | ||
238 | OMIA:002306-9940 | sheep | Olkuska (Sheep) | Fecundity, Olkuska | BMP15 | FecX(O) | missense | Naturally occurring variant | no | Oar_rambouillet_v1.0 | X | NC_040278.1:g.56594934T>G | NM_001114767.1:c.1009A>C | NP_001108239.1:p.(N337H) | Protein and cDNA positions based on NP_001108239.1 and NM_001114767.1, respectively. | 2013 | 23637641 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | |
236 | OMIA:002306-9940 | sheep | Lacaune (Sheep) | Fecundity, Lacaune | BMP15 | FecX(L) | missense | Naturally occurring variant | no | Oar_rambouillet_v1.0 | X | NC_040278.1:g.56594981C>T | NM_001114767.1:c.962G>A | NP_001108239.1:p.(C321Y) | cDNA position based on NP_001108239.1 | 2007 | 17038554 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | |
237 | OMIA:002306-9940 | sheep | Grivette (Sheep) | Fecundity, Grivette | BMP15 | FecX(Gr) | missense | Naturally occurring variant | no | Oar_rambouillet_v1.0 | X | NC_040278.1:g.56594993G>A | NM_001114767.1:c.950C>T | NP_001108239.1:p.(T317I) | protein and cDNA positions based on NP_001108239.1 and NM_001114767.1, respectively | 2013 | 23637641 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | |
235 | OMIA:002306-9940 | sheep | Romney Marsh (Sheep) | Fecundity, Inverdale | BMP15 | FecX(I) | missense | Naturally occurring variant | no | Oar_rambouillet_v1.0 | X | NC_040278.1:g.56595047A>T | NM_001114767.1:c.896T>A | NP_001108239.1:p.(V299D) | protein and cDNA positions based on NP_001108239.1 and NM_001114767.1, respectively | rs398521635 | 2000 | 10888873 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. |
335 | OMIA:002306-9940 | sheep | Romney Marsh (Sheep) | Fecundity, Hanna | BMP15 | FecX(H) | nonsense (stop-gain) | Naturally occurring variant | no | Oar_rambouillet_v1.0 | X | NC_040278.1:g.56595072G>A | NM_001114767.1:c.871C>T | NP_001108239.1:p.(Q291*) | previously listed as c.1184C>T; protein and cDNA position based on NP_001108239.1 and NM_001114767.1, respectively | rs413916687 | 2000 | 10888873 | |
334 | OMIA:002306-9940 | sheep | Cambridge (Sheep) | Fecundity, Galway | BMP15 | FecX(G) | nonsense (stop-gain) | Naturally occurring variant | no | Oar_rambouillet_v1.0 | X | NC_040278.1:g.56595225G>A | NM_001114767.1:c.718C>T | NP_001108239.1:p.(Q239*) | rs425019156 | 2004 | 14627550 | ||
521 | OMIA:002306-9940 | sheep | Rasa Aragonesa, Spain (Sheep) | Fecundity, Rasa Aragonesa | BMP15 | FecX(R) | deletion, small (<=20) | Naturally occurring variant | no | Oar_rambouillet_v1.0 | X | NC_040278.1:g.56595467_56595483del | NM_001114767.1:c.460_476del | NP_001108239.1:p.(W154Nfs*55) | published as c.525_541delTGGGTCCAGAAAAGCCC based on AF236079, protein and cDNA position in table based on NP_001108239.1 and NM_001114767.1, respectively | 2008 | 18355397 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | |
1345 | OMIA:002306-9940 | sheep | Blanc Du Massif Central (Sheep) Noir du Velay, France (Sheep) | Fecundity | BMP15 | FecX(N) | regulatory | Naturally occurring variant | unknown | Oar_v3.1 | X | g.50977717T>A | 2020 | 32636872 | |||||
1341 | OMIA:002306-9940 | sheep | Rasa Aragonesa, Spain (Sheep) | Fecundity | BMP15 | FecX(RA) | missense | Naturally occurring variant | unknown | Oar_v3.1 | X | NC_019484.1:g.50970948C>T | NM_001114767.1:c.1172C>T | NP_001108239.1:p.(T400I) | protein position based on ENSOART00000010201 | 2020 | 31927415 | ||
1281 | OMIA:002306-9823 | pig | German Landrace (Pig) | Infertility and increased litter size | BMP15 | nonsense (stop-gain) | Naturally occurring variant | yes | Sscrofa11.1 | X | NC_010461.5:g.44618787C>T | NM_001005155.2:c.634C>T | NP_001005155.2:p.(R212*) | 2021 | 33413103 | ||||
241 | OMIA:000383-9940 | sheep | Booroola (Sheep) Small Tailed Han, China (Sheep) | Fecundity, Booroola | BMPR1B | FecB(B) | missense | Naturally occurring variant | no | Oar_rambouillet_v1.0 | 6 | g.34010859T>C | c.914A>G | p.(Q305R) | Position on Oar_v3.1: g.29382188T>C | rs418841713 | 2001 | 11259271 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool, the genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. |
1254 | OMIA:000576-9823 | pig | Yorkshire (Pig) | Knobbed acrosome defect | BOLL | deletion, gross (>20) | Naturally occurring variant | yes | Sscrofa11.1 | 15 | NC_010457.5:g.101549770_101604750del | 2020 | 32975846 | ||||||
1766 | OMIA:002913-9913 | taurine cattle | Holstein Friesian (Cattle) | Cardiac malformation, BRI3BP-related | BRI3BP | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 17 | NC_037344.1:g.50813902C>T | NM_001099087.1:c.478G>A | NP_001092557.1:p.(V160I) | likely de novo variant | 2025 | 39593234 | |||
851 | OMIA:002132-9615 | dog | German Shorthaired Pointer (Dog) | Abortion (embryonic lethality), BTBD17-related | BTBD17 | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 9 | g.6048201_6048202insG | c.85+206_85+207insG | ROS_Cfam_1.0:g.6720627_6720628insG ENSCAFT00845033049.1:c.85+206_85+207insG; the homozygous variant genotype is associated with embryonic lethality in German Shorthaired Pointer, but may not be causal as the variant was observed at a high frequency in both heterozygous and homozygous form across normal dogs from multiple breeds (PMID:37582787) | rs852549625 | 2017 | 29053721 | |||
981 | OMIA:001991-9913 | taurine cattle | Nordic Red (Cattle) | Stillbirth | BTBD9 | deletion, gross (>20) | Naturally occurring variant | yes | 23 | "∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8)" | 2016 | 27091210 | |||||||
325 | OMIA:001622-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup C | BTN1A1 | nonsense (stop-gain) | Naturally occurring variant | no | GRCg6a | 28 | g.903289G>T | c.165C>A | p.(C55*) | rs735807319 | 2005 | 16051833 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
455 | OMIA:000155-9615 | dog | Brittany Spaniel (Dog) | C3 deficiency | C3 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 20 | g.53573746del | c.2136del | p.(F712Lfs*11) | XM_038428862.1; XP_038284790.1 "a deletion of a cytosine at position 2136 (codon 712), leading to a frameshift that generates a stop codon 11 amino acids downstream" | 1998 | 9510185 | |||
1737 | OMIA:002886-9823 | pig | Large White (Pig) | Timothy syndrome 1 | CACNA1C | missense | Genome-editing (CRISPR-Cas9) | unknown | Sscrofa11.1 | 5 | NC_010447.5:g.69316114G>A | XM_021092981.1:c.1216G>A | XP_020948640.1:p.(G406R) | 2023 | 38665938 | ||||
1660 | OMIA:002819-9913 | taurine cattle | Holstein Friesian (Cattle) | Muscle weakness | CACNA1S | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 16 | NC_037343.1:g.79613592C>T | XM_024976574.1:c.3853G>A | XP_024832342.1:p.G1285S | ENSBTAT00000065901.3; ENSBTAP00000054797.3 | rs3423414874 | 2024 | 38246543 | ||
1087 | OMIA:002201-9913 | taurine cattle | Normande (Cattle) | Abortion due to haplotype NH7 | CAD | missense | Naturally occurring variant | yes | ARS-UCD1.2 | 11 | g.72409143T>C | p.(Y452C) | published as CAD g.72399397T>C; p.Tyr452Cys | rs5334475092 | 2019 | 31056337 | The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. | ||
1490 | OMIA:002573-151761 | yellow-crowned parrot | Lewy body-like disease | CADPS2 | missense | Naturally occurring variant | yes | c.1675G>C | p.(V559L) | 2022 | 36086934 | ||||||||
105 | OMIA:001820-9615 | dog | Parson Russell Terrier (Dog) | Ataxia, spinocerebellar | CAPN1 | missense | Naturally occurring variant | yes | CanFam3.1 | 18 | NC_006600.3:g.52009339C>T | XM_540866.5:c.344G>A | XP_540866.2:p.(C115Y) | XM_540866.5; XP_540866.2 | 2013 | 23741357 | Genomic coordinates in CanFam3.1 provided by Robert Kuhn | ||
1692 | OMIA:002854-9615 | dog | Miniature Schnauzer (Dog) | Immunodeficiency, susceptibility to Mycobacterium avium complex | CARD9 | deletion, small (<=20) | yes | CanFam3.1 | 9 | NC_006591.3:g.49115079_49115081del | XM_844178.5:c.493_495del | XP_849271.2: p.(K165del) | 2024 | 38710903 | |||||
1674 | OMIA:002835-9615 | dog | Cavalier King Charles Spaniel (Dog) | Immunodeficiency, CARMIL2-related | CARMIL2 | missense | Naturally occurring variant | yes | CanFam3.1 | 5 | NC_006587.3:g.81801920G>A | XM_022419456.1:c.871C>T | XP_022275164.1:p.(R291*) | NC_006587.3; XM_022419456.1; XP_022275164.1 | rs3330142729 | 2024 | 38535207 | ||
49 | OMIA:001138-9615 | dog | American Foxhound (Dog) Beagle (Dog) English Foxhound (Dog) Harrier (Dog) Poodle, Miniature (Dog) Treeing Walker Coonhound (Dog) | Hypocatalasia | CAT | missense | Naturally occurring variant | yes | CanFam3.1 | 18 | NC_006600.3:g.33397548C>T | NM_001002984.1:c.979G>A | NP_001002984.1:p.(A327T) | Variant initially identified in Beagle and later reported in additional breeds: PMID:29708978, PMID27525650 | 2000 | 11137458 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
516 | OMIA:001416-9612 | gray wolf | Coat colour, dominant black | CBD103 | K^B | deletion, small (<=20) | Naturally occurring variant | no | 3bp deletion of the CBD103 gene | 2009 | 19197024 | ||||||||
520 | OMIA:001416-9614 | coyote | Coat colour, dominant black | CBD103 | deletion, small (<=20) | Naturally occurring variant | no | 3bp deletion of the CBD103 gene | 2009 | 19197024 | |||||||||
458 | OMIA:001416-9615 | dog | Coat colour, dominant black | CBD103 | ΔG23 = K^B | deletion, small (<=20) | Naturally occurring variant | no | CanFam3.1 | 16 | g.58965449_58965451del | c.231_233del | p.(G78del) | "a 3-base pair (bp) deletion in the second exon of CBD103, the ortholog of human DEFB103, that predicts an in-frame glycine deletion (ΔG23)" | rs851502010 | 2007 | 17947548 | Genomic location provided by Professor Claire Wade August 2018. Allele designations taken from Ollivier et al. (2013) | |
1032 | OMIA:002167-9913 | taurine cattle | Nordic Red (Cattle) | Asthenospermia | CCDC189 | splicing | Naturally occurring variant | yes | ARS-UCD1.2 | 25 | g.26880841C>T | Touru et al. (2019): "a variant disrupting a canonical 5’ splice donor site (GCA_000003055.3:Chr25:g.27138357C>T) in CCDC189 (transcript - ID:ENSBTAT00000045037) encoding the coiled-coil domain containing protein 189." | rs5334474909 | 2019 | 30975085 | ||||
266 | OMIA:001540-9615 | dog | Old English Sheepdog (Dog) | Ciliary dyskinesia, primary | CCDC39 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 34 | NC_006616.3:g.13952270G>A | XM_545213.6:c.286C>T | XP_545213.3:p.(R96*) | 2011 | 21131972 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
1403 | OMIA:002342-9940 | sheep | Blanc Du Massif Central (Sheep) Lacaune (Sheep) | Ciliary dyskinesia, primary (respiratory failure) | CCDC65 | LDHH6 | nonsense (stop-gain) | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 3 | NC_040254.1:g.147207999C>A | XM_004006389.4:c.521G>T | XP_004006438.1:p.(E111*) | XM_004006389.4; XP_004006438.1; published as NC_040254.1:g.147,207,999C>A | rs1085624756 | 2021 | 35052387 | |
1274 | OMIA:001521-9615 | dog | Portuguese Water Dog (Dog) | Progressive retinal atrophy, early onset | CCDC66 | EOPRA | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 20 | g.33717704_33717705insT | c.2262_c.2263insA | p.(V747Sfs*8) | 2020 | 33273526 | |||
574 | OMIA:001521-9615 | dog | Schapendoes (Dog) | Generalized PRA | CCDC66 | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 20 | g.33745452_33745453insT | c.521_522insA | p.(N174Kfs*2) | NM_001168012.1; NP_001161484.1; genomic coordinates in accordance with HGVS 3'-rule | 2010 | 19777273 | Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn. | ||
538 | OMIA:001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | deletion, small (<=20) | Naturally occurring variant | no | 28 | c.502_511delCGCTCACCCC | 2015 | 25873518 | ||||||||
539 | OMIA:001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | deletion, small (<=20) | Naturally occurring variant | no | 28 | c.502_516delCGCTCACCCCGCCCC | 2015 | 25873518 | ||||||||
395 | OMIA:001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | splicing | Naturally occurring variant | no | 28 | c.506-515del10 | 2012 | 22171251 | ||||||||
396 | OMIA:001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | splicing | Naturally occurring variant | no | 28 | c.507-511del5 | 2012 | 22171251 | ||||||||
603 | OMIA:001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | tva^r2 | insertion, small (<=20) | Naturally occurring variant | no | GRCg6a | 28 | g.985659_985660insCTCG | c.48_49insCTCG | p.(P18Afs) | NM_001044645.1; NP_001038110.1 | 2004 | 15564460 | Genomic position in GRCg6a provided by Joshua Khamis. | ||
12 | OMIA:001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | tva^r | missense | Naturally occurring variant | no | GRCg6a | 28 | g.985980C>G | c.185C>G | p.(C62W) | NM_001044645.1; NP_001038110.1; published as c.120C>G and p.(C40W); coordinates in the table have been updated to a recent reference genome and / or transcript | 2004 | 15564460 | Genomic position in GRCg6a provided by Joshua Khamis. | ||
1340 | OMIA:002386-9544 | Rhesus monkey | OKT4 epitope deficiency | CD4 | missense | Naturally occurring variant | unknown | 11 | c.C793T | p.(A265W) | 2021 | 33893743 | |||||||
1528 | OMIA:002626-9913 | taurine cattle | Japanese Black, Japan (Cattle) | Haplotype with homozygous deficiency JBH17, CDC45-related | CDC45 | splicing | Naturally occurring variant | yes | UMD_3.1.1 | 17 | g.74743512G>T | located in a splicing donor site at a distance of 5 bp, affecting pre-mRNA splicing | 2021 | 33758295 | |||||
1496 | OMIA:002584-9615 | dog | Beauceron (Dog) | Deafness, CDH23-related | CDH23 | missense | Naturally occurring variant | yes | CanFam3.1 | 4 | g:22340631C>T | c.700C>T | p.(P234S) | ON462053; XM_022417544.1; XP_022273252.1 | 2023 | 36308003 | The UU_Cfam_GSD_1.0 genomic variant coordinate is: g.Chr4:23074925C>T | ||
3 | OMIA:000102-9031 | chicken | Sex-linked extreme dilution | CDKN2A | B0 | complex rearrangement | Naturally occurring variant | no | Z | The B0 allele is characterised by two non-coding variants:Â "The first, SNP1, is within the CDKN2A (ARF) promoter region, 265 bp upstream of the transcription start site (according to GenBank AY138245), and the second, SNP2, is located at nucleotide position 385 bp in CDKN2A intron 1" | 2010 | 20374521 | |||||||
5 | OMIA:000102-9031 | chicken | Sex-linked dilution | CDKN2A | B2 | missense | Naturally occurring variant | no | GRCg6a | Z | g.78856557G>A | c.28C>T | p.(R10C) | rs1059941965 | 2010 | 20374521 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
4 | OMIA:000102-9031 | chicken | Sex-linked barring | CDKN2A | B1 | missense | Naturally occurring variant | no | GRCg6a | Z | g.78856559A>T | c.26T>A | p.(V9D) | rs3388417177 | 2010 | 20374521 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
863 | OMIA:001890-198806 | ruff | Male body size/courtship behaviour | CENPN | inversion | Naturally occurring variant | unknown | "a 4.5Mb inversion on the ruff orthologue of chicken chromosomr GGA11 which, due to the well-known lethality of recombinants within an inversion, has created a supergene determining male breeding behaviour, body size and plumage colour" | 2016 | 26569123 | |||||||||
991 | OMIA:001830-9913 | taurine cattle | Holstein (black and white) (Cattle) | Abortion due to haplotype HH7 | CENPU | deletion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 27 | g.15123637_15123640del | Hozé et al. (2019): "Considering that CENPU is transcribed in the antisense orientation, this mutation is predicted to result in deletion of the nucleotides located at position +3 to + 6 bp after the splicing donor site of exon 11. Using cross-species nucleotide alignment, we observed that the nucleotide at position +3 is entirely conserved among vertebrates . . . , which suggests that it plays an important role in regulation of CENPU splicing. If modified after exon 11, the abnormal splicing of CENPU could cause mRNA decay or the production of a protein modified after residue 319 out of 409 AA. Based on these factors, we assumed that mutation g.14168130_14168133delTACT on chromosome 27 alters the splicing of CENPU and is embryonic lethal." | 2020 | 31733857 | |||||
964 | OMIA:001502-9913 | taurine cattle | Montbéliarde (Cattle) | Caprine-like Generalized Hypoplasia Syndrome | CEP250 | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.2 | 13 | g.64710424C>T | c.493C>T | p.(Q165*) | rs5334474991 | 2015 | 25902731 | Coordinates obtained from and/or confirmed by EBI's VEP | ||
384 | OMIA:001244-9685 | domestic cat | Abyssinian (Cat) American Curl (Cat) American Shorthair (Cat) American Wirehair (Cat) Balinese (Cat) Bengal (Cat) Colorpoint Shorthair (Cat) Cornish Rex (Cat) Devon Rex (Cat) Donskoy (Cat) European Shorthair (Cat) Havana (Cat) Highlander (Cat) Maine Coon (Cat) Manx (Cat) Munchkin (Cat) Ocicat (Cat) Oriental Longhair (Cat) Oriental Shorthair (Cat) Peterbald (Cat) Pixiebob Longhair (Cat) Ragdoll (Cat) Scottish Fold (Cat) Siamese (Cat) Singapura (Cat) Somali (Cat) Sphynx (Cat) Tennessee Rex (Cat) Tonkinese (Cat) | Retinal degeneration II | CEP290 | splicing | Naturally occurring variant | yes | Felis_catus_9.0 | B4 | g.112522818A>C | c.7584+9T>G | XM_023256243.1; published as IVS50 + 9T>G. The cat sequenced to generate the Felis_catus_9.0 reference genome is homozygous for the likely causal variant. The genomic and cDNA coordinates had therefore been previously listed in this table as g.112522818TC>A and c.7584+9G>T. The information has been updated based on feedback from 潘旭 to reflect that the likely causal variant is c.7584+9G and that the normal allele is c.7584+9T[6/4/2023]. | 2007 | 17507457 | The genomic location on Felis_catus_9.0 and transcript information is based on Rodney et al. 2021 (PMID: 33785770). Variant was initially identified in the Abyssinian and Somali breeds but identified to be present in several other breeds (Menotti-Raymond et al., 2020; Pubmed:19747862; PMID:35709088) | |||
177 | OMIA:000636-9823 | pig | Membranoproliferative glomerulonephritis type II | CFH | missense | Naturally occurring variant | yes | Sscrofa11.1 | 10 | NW_018085100.1:g.2553907T>G | NM_214281.2:c.3551T>G | NP_999446.1:p.(I1184R) | CFH is located on Chr10 in Sscrofa10.2 g.2553907T>G, but recorded as 'unplaced/NW_018085100.1' in Sscrofa11.1., published as c.3610T>G; p.(I1166R) | 2002 | 12466119 | The genomic location on Sscrofa11.1 was determined by Stephanie Shields (27/05/2020) | |||
1479 | OMIA:001794-9940 | sheep | Romney (Sheep) | Cystic fibrosis | CFTR | nonsense (stop-gain) | Genome-editing (CRISPR-Cas9) | yes | Oar_rambouillet_v1.0 | 4 | NC_040255.1:g.57192317C>A | NM_001009781.1:c.1621G>T | NP_001009781.1:p.(G541*) | NM_001009781.1; NP_001009781.1; published as p.(G542X), coordinates in this table are updated to recent reference sequence | 2021 | 34632318 | |||
1478 | OMIA:001794-9940 | sheep | Romney (Sheep) | Cystic fibrosis | CFTR | deletion, small (<=20) | Genome-editing (CRISPR-Cas9) | yes | Oar_rambouillet_v1.0 | 4 | NC_040255.1:g.57218683_57218685del | NM_001009781.1:c.1518_1520del | NP_001009781.1:p.(F507del) | NM_001009781.1; NP_001009781.1; published as p.(F508del), coordinates are updated in this table to recent reference sequence | 2021 | 34632318 | |||
61 | OMIA:002072-9615 | dog | Old Danish Pointing Dog (Dog) | Myasthenic syndrome, congenital | CHAT | missense | Naturally occurring variant | yes | CanFam3.1 | 28 | NC_006610.3:g.1484906G>A | XM_005637485.3:c.85G>A | XP_005637542.1:p.(V29M) | XM_005637485.3; XP_005637542.1 | 2007 | 17586598 | 20181218 Thanks to Maarten de Groot for advising FN of the genomic location of this variant. | ||
838 | OMIA:002125-9913 | taurine cattle | Montbéliarde (Cattle) | Neurocristopathy | CHD7 | deletion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 14 | g.26402250_26402254del | p.(K594Afs*29) | 2017 | 28904385 | |||||
1691 | OMIA:002767-7957 | goldfish | Twin-tail | chordinA | nonsense (stop-gain) | Naturally occurring variant | unknown | p.(E127*) | 2014 | 24569511 | |||||||||
554 | OMIA:002022-9913 | taurine cattle | Red Dane (Cattle) | Arthrogryposis multiplex congenita, CHRNB1-related | CHRNB1 | deletion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.3 | 19 | NC_037346.1:g.27122027del | NM_174516.2:c.55del | NP_776941.1:p.(A19Pfs47*) | Published as Chr19:27757270CG > C; CHRNB1 c.55delG; (p.Ala19Profs47*) | rs5334474854 | 2016 | 27364156 | The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. | |
490 | OMIA:000685-9915 | indicine cattle (zebu) | Brahman (Cattle) | Myasthenic syndrome, congenital, CHRNE-related | CHRNE | 470del20 | deletion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 19 | g.26485848_26485867del | c.470_489del | Kraner et al. (2002): "a loss of 20 bp within the coding sequence of exon 5 (Fig. 2), between nucleotide 469 and 490 (nucleotide numbering referring to the cDNA sequence published under accession number X02597". These authors (and subsequent authors) call this variant "470del20". The current (2020) HGVS nomenclature is c.470_489del 200922: g. information move here (g.27119615) until standardised | rs5334475050 | 2002 | 12481987 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. | |
614 | OMIA:000685-9615 | dog | Jack Russell Terrier (Dog) | Myasthenic syndrome, congenital, due to CHRNE | CHRNE | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 5 | NC_006587.3:g.31705136dup | XM_014113502.2:c.729dup | XP_013968977.2:p.(G244Rfs*274) | published as c.633_634insC, previously reported in OMIA as c.636_637insC; coordinates in the table updated to NCBI trancript IDs and in accordance to HGVS rules (3'-rule and reported as duplication) [27/08/2024] | 2015 | 26429099 | |||
804 | OMIA:000685-9615 | dog | Heideterrier (Dog) Smooth Fox Terrier (Dog) | Myasthenic syndrome, congenital, due to CHRNE | CHRNE | duplication | Naturally occurring variant | yes | CanFam3.1 | 5 | NC_006587.3:g.31707450dup | XM_014113502.2:c.1508dup | XP_013968977.2:p.(S503Rfs*14) | published as Chr5:31,707,450_31,707,451insG, XM_014113502.1:c.1436_1437insG, XP_013968977.1:p.Ser479ArgfsTer14; in Heideterrier; information in the table updated to new transcript and in accordance with HGVS recommendations [27/08/2024]; for additional breed inforamtion see Pubmed:38853290 |
2017 | 28508416 | |||
1729 | OMIA:000685-9615 | dog | English Springer Spaniel (Dog) | Myasthenic syndrome, congenital, CHRNE-related | CHRNE | missense | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 5 | NC_049226.1:chr5:31915101C>A | XM_038536566.1:c.1509C>A | XP_038392494.1:p.(S503R) | reported in two affected dogs | 2024 | 38853290 | |||
1664 | OMIA:000698-9940 | sheep | Merino (Sheep) | Myotonia | CLCN1 | missense | Naturally occurring variant | yes | ARS-UI_Ramb_v3.0 | 4 | NC_056057.1:g.107930611C>T | XM_004008136.5:c.844C>T | XP_004008185.4:p.(P282S) | rs3487175777 | 2024 | 39765607 | |||
224 | OMIA:000698-9925 | goat | Myotonia | CLCN1 | missense | Naturally occurring variant | yes | ARS1.2 | 4 | NC_030811.1:g.13857007C>G | XM_013963554.2:c.2656G>C | XP_013819008.1:p.(A886P) | Previously listed in OMIA based on ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000031898.1:c.2590G>C; p.(P864A); c. and p. updated based on NCBI transcript IDs [26/08/2024] | rs5334475115 | 1996 | 8855341 | |||
609 | OMIA:000698-9615 | dog | Australian Cattle Dog (Dog) Border Collie (Dog) | Myotonia | CLCN1 | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 16 | NC_006598.3:g.6344748_6344749insT | NM_001003124.2:c.2647_2648insA | NP_001003124.1:p.(R883Qfs*18) | published as c.2665insA; p.(R889fs); coordinates in the table have been updated to a recent reference genome and / or transcript | 2007 | 17552451 | |||
1041 | OMIA:000698-9615 | dog | Labrador Retriever (Dog) | Myotonia | CLCN1 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 16 | NC_006598.3:g.6348929T>A | NM_001003124.2:c.2275A>T | NP_001003124.1:p.(R759X) | published as "Chr16:6348929 T A CLCN1 ENSCAFG00000003619.3 stopgain" |
2018 | 29934119 | |||
62 | OMIA:000698-9615 | dog | Miniature Schnauzer (Dog) | Myotonia | CLCN1 | missense | Naturally occurring variant | yes | CanFam3.1 | 16 | NC_006598.3:g.6366383G>A | NM_001003124.2:c.803C>T | NP_001003124.1:p.(T268M) | 1999 | 10452529 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
1364 | OMIA:000698-9615 | dog | American Bulldog (Dog) | Myotonia | CLCN1 | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 16 | NC_006598.3:g.6369245_6369246insAGAG | NM_001003124.2:c.436_437insCTCT | NP_001003124.1:p.(Y146Sfs*49) | 2020 | 33246886 | ||||
1570 | OMIA:000698-9615 | dog | Mixed Breed (Dog) | Myotonia | CLCN1 | deletion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 16 | NC_006598.3:g.[6367458_6367478del;6367482del;6367485A>C] | NM_001003124.2:c.[703T>G;706del;710_730del] | NP_001003124.1:p.[(F235V;V236fs)] | published as c.[705T>G; 708del; 712_732del], coordinates in the table have been updated to the CanFam3.1 reference genome and reflect correction in PMID:37212506. |
2023 | 37212506 | |||
161 | OMIA:000698-9796 | horse | New Forest Pony (Horse) | Myotonia | CLCN1 | missense | Naturally occurring variant | yes | EquCab3.0 | 4 | NC_009147.3:g.96518592A>C | XM_001915636.4:c.1775A>C | XP_001915671.3:p.(D592A) | c.1775A>C, Genbank acc. XM_001915636; p.D592A, Genbank acc. XP_001915671 (Wijnberg et al., 2014) | rs5334475185 | 2012 | 22197188 | (FN thanks Izabela De Assis Rocha, who provided genomic location in EquCab3.0 and the Genbank acc IDs, working under the supervision of Professor Ernie Bailey; 15 April 2020) Revised genomic location kindly provided by Cord Drögemüller; 21 May 2021 | |
1573 | OMIA:000698-9685 | domestic cat | Domestic Longhair | Myotonia | CLCN1 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | A2 | NC_018724.3:g.158967085_158967092del | NM_001305027.1:c.428_433+1del | NP_001291956.1:p.(L143Qfs3*) | published as chrA2:15897085‐15897092, coordinates in this table have been verified in Felis_catus_9.0 | 2022 | 35815860 | |||
1623 | OMIA:000698-9685 | domestic cat | Myotonia | CLCN1 | missense | Naturally occurring variant | yes | Felis_catus_9.0 | A2 | NC_018724.3:g.158976314G>C | NM_001305027.1:c.991G>C | NP_001291956.1:p.(A331P) | 2023 | 37668104 | |||||
408 | OMIA:000698-9685 | domestic cat | Myotonia | CLCN1 | splicing | Naturally occurring variant | yes | Felis_catus_9.0 | A2 | NC_018724.3:g.158986498G>T | NM_001305027.1:c.1930+1G>T | 2014 | 25356766 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||||
245 | OMIA:000698-9940 | sheep | Rasa Aragonesa, Spain (Sheep) | Myotonia | CLCN1 | missense | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 4 | NC_040255.1:g.115541101G>A | XM_004008136.4:c.277G>A | XP_004008185.4:p.(E93K) | Oar_v3.1 position is g.106140081G>A published as p.Gln93Lys. | rs401726021 | 2015 | 25744800 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | |
1365 | OMIA:000698-9823 | pig | Myotonia | CLCN1 | deletion, gross (>20) | Naturally occurring variant | yes | Sscrofa11.1 | 18 | NC_010460.4:g.6912538_6916702del | 2019 | 31666547 | |||||||
399 | OMIA:000698-89462 | water buffalo | Murrah (Buffalo) | Myotonia | CLCN1 | splicing | Naturally occurring variant | yes | UOA_WB_1 | 8 | NC_037552.1:g.106762128C>T | NM_001290916.1:c.396C>T | abnormal splicing associated with synonymous SNP (Ser132, c.396C>T) | 2013 | 23339992 | ||||
1678 | OMIA:000698-9615 | dog | French Bulldog (Dog) | Myotonia | CLCN1 | duplication | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 16 | NC_049237.1:g.6074128_6074135dup | NM_001003124.2:c.2423_2430dup | NP_001003124.1:p.(F811Lfs*39) | 2024 | 38473107 | ||||
1757 | OMIA:000698-9615 | dog | Mixed Breed (Dog) | Myotonia | CLCN1 | delins, small (<=20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 16 | NC_049237.1:g.[6080653T>A;6080658_6080661delinsCCCGTT] | NM_001003124.2:c.[1636_1639delinsAACGGG;1644A>T] | NP_001003124.1:p.(C546Nfs*5) | 2024 | 39559538 | ||||
210 | OMIA:001887-9913 | taurine cattle | Belgian Blue (Cattle) | Osteopetrosis with gingival hamartomas | CLCN7 | missense | Naturally occurring variant | yes | ARS-UCD1.2 | 25 | g.[1139611G>T; 1139613A>G] | c.[2248T>C;2250C>A] | p.(Y750Q) | 2014 | 24159188 | The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. | |||
648 | OMIA:001135-9913 | taurine cattle | Japanese Black, Japan (Cattle) | Renal dysplasia | CLDN16 | Type 1 | deletion, gross (>20) | Naturally occurring variant | yes | 1 | 37kb deletion of exons 1-4 | 2000 | 10810088 | ||||||
781 | OMIA:001135-9913 | taurine cattle | Japanese Black, Japan (Cattle) | Renal dysplasia | CLDN16 | Type 2 | deletion, gross (>20) | Naturally occurring variant | yes | 1 | "a 56-kb deletion that eliminates exons 1-4 and 21-bp of exon 5" 200922: g. info moved to here (g.77528017_?) until can be standardised | 2002 | 12047224 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||||
1669 | OMIA:002432-9913 | taurine cattle | Hereford (Cattle) | Retinal degeneration, CLN3-realted | CLN3 | delins, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.3 | 25 | NC_037352.1:g.26043843del | NM_001075174.2:c.1106del | NP_001068642.2:p.(P369Rfs*8) | NM_001075174.2; NP_001068642.2 | rs5377951844 | 2024 | 38516801 | ||
593 | OMIA:001482-9913 | taurine cattle | Devon (Cattle) | Neuronal ceroid lipofuscinosis, 5 | CLN5 | insertion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 12 | g.52112732_52112733insG | c.662_663insG | p.(R221Gfs*6) | 2006 | 16935476 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) 210909: after checking the genome assembly sequence, FN changed g.52461241insG to g.52461241_52461242insG; and c.662insG to c.662_663insG | |||
541 | OMIA:001482-9615 | dog | Golden Retriever (Dog) | Neuronal ceroid lipofuscinosis, 5 | CLN5 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 22 | g.30574953_30574954del | c.935_936del | p.(E312Vfs*6) | NM_001011556.1; NP_001011556.1,published as CLN5:c.934_935delAG; coordinates in the table have been updated to a recent reference genome and / or transcript | 2015 | 25934231 | Breed information obtained from Katz et al. (2017) Neurobiol Dis. doi: 10.1016/j.nbd.2017.08.017; Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn. | ||
279 | OMIA:001482-9615 | dog | Australian Cattle Dog (Dog) Border Collie (Dog) | Neuronal ceroid lipofuscinosis, 5 | CLN5 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 22 | NC_006604.3:g.30574637C>T | NM_001011556.1:c.619C>T | NP_001011556.1:p.(Q207*) | rs1152388418 | 2005 | 16033706 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool 30 Dec 2020: g. coordinate corrected, with thanks to Angelica K Kallenberg | ||
389 | OMIA:001482-9940 | sheep | Borderdale, New Zealand (Sheep) | Neuronal ceroid lipofuscinosis, 5 | CLN5 | splicing | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 10 | g.56313269G>A | c.571+1G>A | rs422165326 | 2008 | 17988881 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | |||
68 | OMIA:001443-9615 | dog | Australian Shepherd (Dog) | Neuronal ceroid lipofuscinosis, 6 | CLN6 | missense | Naturally occurring variant | yes | CanFam3.1 | 30 | NC_006612.3:g.32247875A>G | NM_001011888.1:c.829T>C | NP_001011888.1:p.(W277R) | alternative coordinates: ROS_Cfam_1.0:g.32443458A>G ENSCAFT00845033654.1:c.829T>C ENSCAFP00845026347.1:p.Trp277Arg | rs1152388420 | 2011 | 21234413 | ||
1703 | OMIA:001443-9615 | dog | Mixed Breed (Dog) | Neuronal ceroid lipofuscinosis, 6 | CLN6 | splicing | Naturally occurring variant | yes | Dog10K_Boxer_Tasha | 30 | NC_006612.4:g.32185406C>T | 2024 | 38927597 | ||||||
1213 | OMIA:001443-9685 | domestic cat | Domestic medium-haired | Neuronal ceroid lipofuscinosis, 6 | CLN6 | nonsense (stop-gain) | Naturally occurring variant | yes | Felis_catus_9.0 | B3 | g.39334330G>A | c.668G>A | p.(W223*) | ENSFCAT00000025909:c.668G>A; XM_003987007.5:c.668G>A (Katz et al. (2020) | rs5334475122 | 2020 | 32518081 | ||
671 | OMIA:001443-9940 | sheep | South Hampshire, New Zealand (Sheep) | Neuronal ceroid lipofuscinosis | CLN6 | deletion, gross (>20) | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 7 | deletion of exon 1 | 2013 | 23338040 | ||||||
234 | OMIA:001443-9940 | sheep | Merino (Sheep) | Neuronal ceroid lipofuscinosis, 6 | CLN6 | missense | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 7 | NC_040258.1:g.16039510G>A | NM_001040289.1:c.184C>T | NP_001035379.1:p.(R62C) | protein and cDNA position based on NP_001035379.1 and NM_001040289.1, respectively | rs399747319 | 2006 | 17046213 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | |
1702 | OMIA:001443-9615 | dog | Schapendoes (Dog) | Neuronal ceroid lipofuscinosis, 6 | CLN6 | missense | Naturally occurring variant | unknown | UU_Cfam_GSD_1.0 | 30 | NC_049251.1:g.32682554A>G | XM_038580811.1:c.386T>C | XP_038436739.1:p.(L129P) | 2024 | 38866396 | ||||
1030 | OMIA:001962-9542 | Japanese macaque | Neuronal ceroid lipofuscinosis, 7 | CLN7 | deletion, small (<=20) | Naturally occurring variant | yes | 4 | c.769delA | p.(I257Lfs*36) | 2018 | 30048804 | |||||||
690 | OMIA:001506-9615 | dog | Alpine Dachsbracke (Dog) | Neuronal ceroid lipofuscinosis, 8 | CLN8 | deletion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 37 | g.30852988_30902901del | c.-14679_*18669del | NM_001012343.1; a homozygous deletion encompassing the entire CLN8 gene | 2017 | 28024876 | g. information obtained from Katz et al. (2017) Neurobiol Dis. doi: 10.1016/j.nbd.2017.08.017 | |||
971 | OMIA:001506-9615 | dog | Saluki (Dog) | Neuronal ceroid lipofuscinosis, 8 | CLN8 | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 37 | g.30874636dupT | c.349dupT | p.(E117*) | "an insertion of 1 bp (T) in the CLN8 gene (Fig. S2) in a short T repeat, thereby changing the stretch of 9 T's to a stretch consisting of 10 T's. The exact position of the inserted base could obviously not be verified, given that this was an insertion of a single base in a stretch of nine repeats of the same base (CFA37:g.30874628–30874636). According to the recommended nomenclature, the T insertion was noted as a T duplication in the T farthest in the 3′ direction (g.30874636dupT; c.349dupT)" | 2018 | 29446145 | |||
69 | OMIA:001506-9615 | dog | English Setter (Dog) | Neuronal ceroid lipofuscinosis, 8 | CLN8 | missense | Naturally occurring variant | yes | CanFam3.1 | 37 | NC_006619.3:g.30874779T>C | NM_001012343.1:c.491T>C | NP_001012343.1:p.(L164P) | 2005 | 15629147 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
338 | OMIA:001506-9615 | dog | Australian Shepherd (Dog) German Shorthaired Pointer (Dog) | Neuronal ceroid lipofuscinosis, 8 | CLN8 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 37 | NC_006619.3:g.30883950G>A | NM_001012343.1:c.585G>A | NP_001012343.1:p.(W195*) | NM_001012343: c.585G>A (Guo et al., 2014) | 2014 | 24953404 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; confirmed by Guo et al. (2019, pages 3, 4, 5 and 6), assuming that the g. coordinate (g.30,895,648) in the abstract of Guo et al. (2019) is a typo. | ||
431 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | regulatory | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4934641C>T | published as C-371T | 2007 | 17553163 | ||||||
1432 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | regulatory | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4934795G>A | published as G-217A | 2007 | 17553163 | ||||||
430 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | insertion, small (<=20) | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4934941_4934942insAACGAGCAACCGAAGCTG | published as "an indel in the exon 1 5' UTR"; Delta-53; Felis_catus_9.0 represents the deletion allele | 2007 | 17553163 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | |||||
1431 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | missense | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4935345C>T | c.139C>T | p.(R47C) | NM_001244985.1; NP_001231914.1; published as c.136C>T | 2014 | 24697343 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | |||
118 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | missense | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4935348G>A | c.142G>A | p.(V48M) | NM_001244985.1; NP_001231914.1; initially reported as Felis_catus_6.2: B2:4587414G>A; c.139G>A; p.(V47M) | rs5334475157 | 2007 | 17553163 | The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770) | ||
800 | OMIA:000119-9685 | domestic cat | 2019 TYPING PANEL | CMAH | missense | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4935385G>T | c.179G>T | p.(G60V) | NM_001244985.1; NP_001231914.1 | rs5334475140 | 2016 | 27755584 | The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770) | ||
801 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | missense | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4935393A>G | c.187A>G | p.(I63V) | NM_001244985.1; NP_001231914.1 | 2016 | 27755584 | ||||
119 | OMIA:000119-9685 | domestic cat | 2019 TYPING PANEL | CMAH | missense | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4938728T>A | c.268T>A | p.(Y90N) | NM_001244985.1; NP_001231914.1; published as c.265T>A (2007); revised designation of c.268T>A was reported by Kehl et al. (2019) | rs5334475138 | 2007 | 17553163 | The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770) | ||
1446 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | missense | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4947482C>A | c.327A>C | p.(E109D) | NM_001244985.1; NP_001231914.1; published as c.327A>C; variant is reported to be not causal for blood type B, but may impact Neu5GC levels (Omi et al.,2016). The Felis_catus_9.0 reference genome represents the C allele, while transcript NM_001244985.1 represents the A allele. | 2016 | 27171395 | ||||
799 | OMIA:000119-9685 | domestic cat | Ragdoll (Cat) | 2019 TYPING PANEL | CMAH | missense | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4947519C>T | c.364C>T | p.(P122S) | NM_001244985.1; NP_001231914.1 | rs5334475151 | 2016 | 27171395 | The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770) | |
1413 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | missense | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4953568G>A | c.773G>A | p.(R258Q) | NM_001244985.1; NP_001231914.1 | 2021 | 34589535 | ||||
1430 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | deletion, small (<=20) | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4955359del | c.933del | p.(A312Hfs*6) | NM_001244985.1; NP_001231914.1 | 2018 | 30235335 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | |||
1062 | OMIA:000119-9685 | domestic cat | Ragdoll (Cat) | 2019 TYPING PANEL | CMAH | deletion, small (<=20) | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4978934del | c.1322del | p.(L441*) | NM_001244985.1; NP_001231914.1; published as c.1322delT | 2018 | 30235335 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | ||
120 | OMIA:000119-9685 | domestic cat | Blood group system AB | CMAH | missense | Naturally occurring variant | no | Felis_catus_9.0 | B2 | g.4985762G>A | c.1603G>A | p.(D535N) | NM_001244985.1; NP_001231914.1; also published as c.1600G>A; p.(D534N) | rs5334475141 | 2007 | 17553163 | The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770) | ||
547 | OMIA:001977-9615 | dog | Shetland Sheepdog (Dog) | Progressive retinal atrophy, due to CNGA1 mutations | CNGA1 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 13 | g.43831897_43831900del | c.1752_1755del | p.(T585Sfs*7) | NM_001003222.1; published as c.1752_1755delAACT | 2015 | 26202106 | Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn | ||
548 | OMIA:001481-9615 | dog | Labrador Retriever (Dog) | Achromatopsia-2 | CNGA3 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 10 | g.44234198_44234200del | c.1931_1933del | p.(V644del) | NM_001301112.1; published as c.1931_1933delTGG | rs852784090 | 2015 | 26407004 | Genomic coordinates in CanFam3.1 and EVA ID provided by Robert Kuhn | |
97 | OMIA:001481-9615 | dog | German Shepherd Dog (Dog) | Achromatopsia-2 | CNGA3 | missense | Naturally occurring variant | yes | CanFam3.1 | 10 | NC_006592.3:g.44234861C>T | NM_001301112.1:c.1270C>T | NP_001288041.1:p.(R424W) | NM_001301112.1; NP_001288041.1 | 2015 | 26407004 | Genomic position in CanFam3.1 provided by Mateo Etcheveste. | ||
1016 | OMIA:001481-9940 | sheep | Awassi (Sheep) | Achromatopsia-2 (day blindness) | CNGA3 | missense | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 3 | NC_040254.1:g.108958871C>T | XM_027965914.1:c.1618G>A | XP_027821715.1:p.(G540S) | 2017 | 28282490 | Genomic coordinate on Oar_v4.0 (g.102602387G>A) kindly provided by Eyal Seroussi via Elisha Gootwine. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries. | |||
317 | OMIA:001481-9940 | sheep | Awassi (Sheep) | Achromatopsia-2 (day blindness) | CNGA3 | nonsense (stop-gain) | Naturally occurring variant | yes | Oori1 scaffold00739 | 3 | g.263324C>T | c.706C>T | p.(R236*) | In a pers. comm. to FN via Elisha Gootwine, Eyal Seroussi advises that the Oar_v4.0 assembly has errors in the region of of this mutation, such that it cannot be mapped onto that assembly. It can, however, be mapped on to the Ovis aries musimon sequence: "Exon 8 mutation is at position 263,324 in Ovis aries musimon unplaced genomic scaffold, alternate assembly Oori1 scaffold00739 (Sequence ID: NW_011942977.1 Length: 1056687)" | 2010 | 19874885 | |||
918 | OMIA:002723-9615 | dog | Papillon (Dog) Phalène (Dog) | Progressive retinal atrophy | CNGB1 | delins, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 2 | g.58622673_58622675delinsCTAGCTAC | c.2387_2389delinsCTAGCTAC | p.(Y796Sfs*7) | NM_001284462.1; NP_001271391.1; published as c.2685delA2687_2688insTAGCTA and p.(Y889Sfs*5); coordinates in the table have been updated to a recent reference genome and / or transcript and updated to HGVS recommendations | rs1152388403 | 2013 | 24015210 | ||
631 | OMIA:001365-9615 | dog | Alaskan Malamute (Dog) Miniature Australian Shepherd Dog (Dog) | Achromatopsia (cone degeneration, hemeralopia), AMAL | CNGB3 | cd^AMAL | deletion, gross (>20) | Naturally occurring variant | yes | 29 | "deletion removing all exons of canine CNGB3" | 2002 | 12140185 | ||||||
1400 | OMIA:001365-9913 | taurine cattle | Brown Swiss (Cattle) | Achromatopsia | CNGB3 | OH1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 14 | NC_037341.1:g.76011964G>A | XM_015474554.2:c.751G>A | XP_015330040.2:p.(D251N) | XM_015474554.2: c.751G>A, XP_015330040.2: p.Asp251Asn ENSBTAT00000065296.2:c.751G>A ENSBTAP00000054173.2:p.Asp251Asn | rs716218235 | 2021 | 34830323 | |
27 | OMIA:001365-9615 | dog | German Shorthaired Pointer (Dog) | Achromatopsia (cone degeneration, hemeralopia), GSPT | CNGB3 | cd^GSPT | missense | Naturally occurring variant | yes | CanFam3.1 | 29 | NC_006611.3:g.32837065C>T | NM_001003030.1:c.784G>A | NP_001003030.1:p.(D262N) | 2002 | 12140185 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool 30 Dec 2020 Chromosome corrected, thanks to Angelica K Kallenberg | ||
1502 | OMIA:002591-9615 | dog | Dalmatian (Dog) | Lysosomal storage disease, CNP-related | CNP | deletion, small (<=20) | Naturally occurring variant | yes | Dog10K_Boxer_Tasha | 9 | g.20350240del | c.1107del | p.(K370Nfs*11) | ENSCAFT00000102206 | 2022 | 35447247 | |||
1680 | OMIA:002591-9615 | dog | Weimaraner (Dog) | Lysosomal storage disease, CNP-related | CNP | missense | Naturally occurring variant | yes | Dog10K_Boxer_Tasha | 9 | NC_006591.4:g.20355460G>A | XM_844467.6:c.125C>T | XP_849560.2:p.(T42M) | XM_844467.6; XP_849560.2; NC_006591.4 | 2024 | 38397235 | |||
1273 | OMIA:002301-9615 | dog | Labrador Retriever (Dog) Leonberger (Dog) Pyrenean Shepherd (Dog) Saint Bernard (Dog) | Laryngeal paralysis and polyneuropathy | CNTNAP1 | LPPN3 | missense | Naturally occurring variant | yes | CanFam3.1 | 9 | NC_006591.3:g.20298261C>T | XM_548083.6:c.2810G>A | XP_548083.3:p.(G937E) | XM_548083.6:c.2810G>A; XP_548083.3:p.Gly937Glu; variant initially identified in Labrador Retriever, Leonberger and Saint Bernard and later reported in a Pyrenean Shepherd (PMID: 37582787) | rs24587752 | 2020 | 33261176 | |
172 | OMIA:001718-9823 | pig | Dwarfism, Schmid metaphyseal chondrodysplasia | COL10A1 | missense | Naturally occurring variant | yes | Sscrofa11.1 | 1 | NC_010443.5:g.81767089C>T | NM_001005153.1:c.1768G>A | NP_001005153.1:p.(G590R) | rs5334475171 | 2000 | 11130976 | The genomic and CDS position was determined by Stephanie Shields and the effect was confirmed with Ensembl VEP (27/05/2020) | |||
1657 | OMIA:002811-9615 | dog | Old English Sheepdog (Dog) | Multiocular defect | COL11A1 | missense | Naturally occurring variant | yes | CanFam3.1 | 6 | g.47611886T>C | c.1775T>C | p.(F1592S) | 2023 | 38153936 | ||||
78 | OMIA:001772-9615 | dog | Labrador Retriever (Dog) | Skeletal dysplasia 2 (SD2) | COL11A2 | missense | Naturally occurring variant | yes | CanFam3.1 | 12 | NC_006594.3:g.2652874C>G | XM_538855.5:c.143G>C | XP_538855.2:p.(R48P) | ROS_Cfam_1.0:g.2983602C>G ENSCAFT00845034709.1:c.143G>C ENSCAFP00845027184.1:p.Arg48Pro | rs851399084 | 2013 | 23527306 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
1634 | OMIA:002793-9685 | domestic cat | American Shorthair (Cat) | Epidermolysis bullosa, junctional, COL17A1-related | COL17A1 | splicing | Naturally occurring variant | yes | F.catus_Fca126_mat1.0 | D2 | g.62124169del | c.3019+1del | XM_006938156.5; variant reported in a single affected cat | 2023 | 37895184 | ||||
1635 | OMIA:002793-9685 | domestic cat | European Shorthair (Cat) | Epidermolysis bullosa, junctional, COL17A1-related | COL17A1 | splicing | Naturally occurring variant | yes | F.catus_Fca126_mat1.0 | D2 | g.62149308C>T | c.769+5G>A | p.([=,p.Val257Glyfs*82]) | XM_006938156.5; XP_006938218.3, variant described in a single affected cat | 2023 | 37895184 | |||
839 | OMIA:002127-9913 | taurine cattle | Simmental (Cattle) | Osteogenesis imperfecta, type II, COL1A1-related | COL1A1 | delins, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 19 | g.36470764_36470767delinsT | c.3145_3148delinsT | p.(A1049_P1050delinsS) | UMD3.1 position is g.37101299_37101302delinsT; cDNA position based on ENSBTAT00000017420.4 | rs876049195 | 2017 | 28904385 | The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. | |
1031 | OMIA:002127-9913 | taurine cattle | Red Angus (Cattle) | Osteogenesis imperfecta, type II, COL1A1-related | COL1A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 19 | NC_037346.1:g.36463798G>A | NM_001034039.2:c.1063G>A | NP_001029211.1:p.(G355S) | Petersen et al. (2019): "PolyPhen-2 predicted the mutation to be “probably damaging” with a score of 1.000 (sensitivity 0.00; specificity 1.00). Similarly, PROVEAN prediction classified the variant as “Deleterious” with a score of − 4.615, exceeding both the default (− 2.5) and stringent (− 4.1) thresholds for this classification." The genomic coordinate in the UMD3.1 assembly is g.37094333G>A (Petersen et al., 2019). The coding sequence coordinates are c.1063G>A (ENSBTAT00000017420.4) (Petersen, pers. comm.) | rs3423092630 | 2019 | 30788588 | ||
1289 | OMIA:002127-9913 | taurine cattle | Holstein (black and white) (Cattle) | Osteogenesis imperfecta, type II, COL1A1-related | COL1A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 19 | NC_037346.1:g.36473359T>A | NM_001034039.2:c.3917T>A | NP_001029211.1:p.(V1306E) | NM_001034039.2: c.3917T>A; XP_024835395.1: p.Val1306Glu (Jacinto et al., 2021) | rs5334474947 | 2021 | 33672767 | ||
1698 | OMIA:002127-9913 | taurine cattle | Normande (Cattle) | Osteogenesis imperfecta, type II, COL1A1-related | COL1A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 19 | NC_037346.1:g.36473965G>A | NM_001034039.2:c.4234G>A | NP_001029211.1:p.(D1412N) | 2024 | 38773368 | ||||
959 | OMIA:002126-9615 | dog | Golden Retriever (Dog) | Osteogenesis imperfecta, type III, COL1A1-related | COL1A1 | missense | Naturally occurring variant | yes | CanFam3.1 | 9 | NC_006591.3:g.26193593C>G | NM_001003090.1:c.1145G>C | NP_001003090.1:p.(G382A) | NM_001003090.1; NP_001003090.1; published as c.1276G>C, p.(G208A); coordinates in the table have been updated to a recent reference genome and / or transcript | rs1152388502 | 2000 | 11147834 | ||
762 | OMIA:002112-9615 | dog | Beagle (Dog) | Osteogenesis imperfecta, COL1A2-related | COL1A2 | delins, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 14 | g.(19918265_19918268delinsTGTCATTGG) | c.3656_3859delinsTGTCATTGG | p.(L1286Cfs*31) | NM_001003187.1; NP_001003187.1; "a mutation in which nucleotides 3991-3994 ("CTAG") were replaced with "TGTCATTGG." The first seven bases of the inserted sequence were identical to nucleotides 4002-4008 of the normal canine COL1A2 sequence. The resulting frameshift changed 30 amino acids and introduced a premature stop codon." The genomic information is presented in brackets as the variant was detected in cDNA and the genomic position is predicted. Coordinates in the table have been updated to a recent reference genome and or transcripts. | 2001 | 11393792 | |||
1114 | OMIA:002112-9615 | dog | Lagotto Romagnolo (Dog) | Osteogenesis imperfecta, COL1A2-related | COL1A2 | duplication | Naturally occurring variant | yes | CanFam3.1 | 14 | g.19898279_19898281dup | c.877_879dup | p.(P293dup) | NM_001003187.1; NP_001003187.1 | 2019 | 31468557 | |||
852 | OMIA:002112-9615 | dog | Chow Chow (Dog) | Osteogenesis imperfecta, COL1A2-related | COL1A2 | splicing | Naturally occurring variant | yes | CanFam3.1 | 14 | NC_006596.3:g.19898487G>A | NM_001003187.1:c.936+1G>A | 2018 | 29036614 | |||||
1275 | OMIA:001926-9913 | taurine cattle | Holstein Friesian (Cattle) | Bulldog calf | COL2A1 | deletion, gross (>20) | Naturally occurring variant | yes | ARS-UCD1.2 | 5 | g.32301911_32308589del | "Sanger sequencing revealed the precise breakpoints of the heterozygous deletion from position 32 301 911 located in intron 25 to 32 308 589 located within exon 45. The 6679 bp deletion includes the entire sequence of 18 exons (26–44) plus the first 36 nucleotides of exon 45" (Jacinto et al., 2020) | 2021 | 33316082 | |||||
1241 | OMIA:001926-9913 | taurine cattle | Holstein Friesian (Cattle) | Bulldog calf | COL2A1 | delins, gross (>20) | Naturally occurring variant | yes | ARS-UCD1.2 | 5 | g.32303127_32306640delinsTCTGGGGAGC | 2020 | 32894162 | ||||||
840 | OMIA:001926-9913 | taurine cattle | Charolais (Cattle) Salers (Cattle) | Bulldog calf | COL2A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 5 | NC_037332.1:g.32301746G>A | NM_001001135.3:c.1799G>A | NP_001001135.2:p.(G600D) | previously listed in OMIA as c.1791G>A, updated to reflect recent transcrupt inforamtion [03/09/2024] | rs5334474917 | 2017 | 28904385 | ||
842 | OMIA:001926-9913 | taurine cattle | Holstein Friesian (Cattle) | Bulldog calf | COL2A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 5 | NC_037332.1:g.32303739G>A | NM_001001135.3:c.2158G>A | NP_001001135.2:p.(G720S) | rs455596159 | 2017 | 28904385 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
414 | OMIA:001926-9913 | taurine cattle | Danish Holstein (Cattle) | bulldog calf | COL2A1 | splicing | Naturally occurring variant | yes | ARS-UCD1.3 | 5 | NC_037332.1:g.32305226G>A | NM_001001135.3:c.2463+1G>A | rs5334475095 | 2016 | 27296271 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
223 | OMIA:001926-9913 | taurine cattle | Holstein Friesian (Cattle) | Bulldog calf | COL2A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 5 | NC_037332.1:g.32307658G>A | NM_001001135.3:c.2878G>A | NP_001001135.2:p.(G960R) | rs3423194986 | 2014 | 25017103 | |||
841 | OMIA:001926-9913 | taurine cattle | Holstein Friesian (Cattle) | Bulldog calf | COL2A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 5 | NC_037332.1:g.32308008G>A | NM_001001135.3:c.2986G>A | NP_001001135.2:p.(G996S) | rs876243579 | 2017 | 28904385 | |||
1026 | OMIA:001926-9913 | taurine cattle | Holstein Friesian (Cattle) | Bulldog calf | COL2A1 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 5 | NC_037332.1:g.32308734G>A | NM_001001135.3:c.3166G>A | NP_001001135.2:p.(G1056S) | rs5334475093 | 2019 | 30378686 | |||
278 | OMIA:002618-9615 | dog | English Springer Spaniel (Dog) | Nephropathy | COL4A4 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 25 | NC_006607.3:g.39893376G>A | NM_001031818.1:c.2713C>T | NP_001026988.1:p.(Q905*) | NM_001031818.1; NP_001026988.1; published as c.2806C>T and p.(Q904*) | 2012 | 22369189 | |||
277 | OMIA:002618-9615 | dog | English Cocker Spaniel (Dog) | Nephropathy | COL4A4 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 25 | NC_006607.3:g.39953906T>A | NM_001031818.1:c.115A>T | NP_001026988.1:p.(K39*) | 2007 | 17552442 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
471 | OMIA:001112-9615 | dog | Navasota (mixed breed) (Dog) | Nephritis, X-linked | COL4A5 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | X | g.82134508_82134517del | c.513_522del | p.(N172Ifs) | XM_005640969.3; XP_005641026.1; a 10 base pair (TAATCCAGGA) deletion in exon 9 of COL4A5 | 2003 | 12879362 | |||
276 | OMIA:001112-9615 | dog | Samoyed (Dog) | Nephritis, X-linked | COL4A5 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | X | NC_006621.3:g.82196868G>T | NM_001002979.1:c.3079G>T | NP_001002979.1:p.(G1027*) | 1994 | 8171024 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
1124 | OMIA:002165-9615 | dog | Labrador Retriever (Dog) | Ehlers-Danlos syndrome, classic type, 1 | COL5A1 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 9 | NC_006591.3:g.50806169del | XM_022423936.1:c.3038del | XP_022279644.1:p.(G1013Vfs*260) | XM_022423936.1; XP_022279644.1; published as c.3038delG - "variant arose by a de novo mutation event during the development of the mother." (Bauer et al., 2019) | 2019 | 31546637 | |||
1125 | OMIA:002165-9615 | dog | Mixed Breed (Dog) | Ehlers-Danlos syndrome, classic type, 1 | COL5A1 | missense | Naturally occurring variant | yes | CanFam3.1 | 9 | NC_006591.3:g.50832936G>A | XM_022423936.1:c.4711G>A | XP_022279644.1:p.(G1571R) | XM_022423936.1,c.4711G>A; XP_022279644.1,p.(Gly1571Arg) | 2019 | 31546637 | |||
1722 | OMIA:002165-9615 | dog | Golden Retriever (Dog) | Ehlers-Danlos syndrome, classic type 1 | COL5A1 | nonsense (stop-gain) | Naturally occurring variant | yes | Dog10K_Boxer_Tasha | 9 | NC_006591.4:g.50091843C>T | XM_038615652.1:c.2512C>T | XP_038471580.1:p.(R838*) | ENSCAFT00000031582.6:c.2500C>T, p.(Arg834Ter) | 2024 | 39175162 | |||
1719 | OMIA:002165-9615 | dog | Mixed Breed (Dog) | Ehlers-Danlos syndrome, classic type 1 | COL5A1 | deletion, small (<=20) | Naturally occurring variant | yes | Dog10K_Boxer_Tasha | 9 | NC_006591.4:g.50109824del | XM_038615652.1:c.3371del | XP_038471580.1:p.(E1124Lfs*364) | ENSCAFT00000031582.6:c.3360del, p.(E1121Lfs*364) | 2024 | 39175162 | |||
1721 | OMIA:002165-9615 | dog | Dachshund, Miniature (Dog) | Ehlers-Danlos syndrome, classic type 1 | COL5A1 | duplication | Naturally occurring variant | yes | Dog10K_Boxer_Tasha | 9 | NC_006591.4:g.50111993dup | XM_038615652.1:c.3675dup | XP_038471580.1:p.(G1226Rfs*62) | Published as g.50111986insC, ENSCAFT00000031582.6:c.3663_3664insC, p.(Gly1222Argfs*62). Coordinates in this table have been adjusted in accordance with the HGVS recommendations. | 2024 | 39175162 | |||
1720 | OMIA:002165-9615 | dog | Scottish Terrier (Dog) | Ehlers-Danlos syndrome, classic type 1 | COL5A1 | deletion, small (<=20) | Naturally occurring variant | yes | Dog10K_Boxer_Tasha | 9 | NC_006591.4:g.50114284del | XM_038615652.1:c.3908del | XP_038471580.1:(P1303Rfs*186) | Published as g.50114279delC; ENSCAFT00000031582.6:c.3891del; p.(P1299Rfs*186). Coordinates in this table have been adjusted in accordance with the HGVS 3'rule. | 2024 | 39175162 | |||
1724 | OMIA:002165-9615 | dog | German Shepherd Dog (Dog) | Ehlers-Danlos syndrome, classic type 1 | COL5A1 | missense | Naturally occurring variant | yes | Dog10K_Boxer_Tasha | 9 | NC_006591.4:g.50116228G>A | XM_038615652.1:c.4117G>A | XP_038471580.1:p.(G1373R) | ENSCAFT00000031582.6:c.4105G>A, p.(Gly1369Arg) | 2024 | 39175162 | |||
1723 | OMIA:002165-9615 | dog | Beagle (Dog) | Ehlers-Danlos syndrome, classic type 1 | COL5A1 | deletion, small (<=20) | Naturally occurring variant | yes | Dog10K_Boxer_Tasha | 9 | NC_006591.4:g.50131170_50131172del | XM_038615652.1:c.5320_5322del | XP_038471580.1:p.G1774del | Published as chr9:50131166delGAG, ENSCAFT00000031582.6:c.5296_5298del, p.(Glu1766del). Coordinates in this table have been adjusted in accordance with the HGVS 3'rule. |
2024 | 39175162 | |||
1696 | OMIA:002165-9685 | domestic cat | Maine Coon (Cat) | classical Ehlers-Danlos syndrome | COL5A1 | deletion, gross (>20) | Naturally occurring variant | yes | F.catus_Fcat126_mat1.0 | D4 | NC_058380.1:g.93561989_93595728del | deletion of 33740 base pairs including the last two exons of COL5A1 | 2024 | 38745376 | |||||
1465 | OMIA:002165-9685 | domestic cat | Bombay (Cat) | classical Ehlers-Danlos syndrome | COL5A1 | nonsense (stop-gain) | Naturally occurring variant | yes | Felis_catus_9.0 | D4 | g.93209345T>A | c.3514A>T | p.(Lys1172*) | XM_023242950.1; XP_023098718.1 | 2022 | 35627182 | |||
1025 | OMIA:002165-9685 | domestic cat | Domestic Shorthair | classical Ehlers-Danlos syndrome | COL5A1 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | D4 | g.93210344del | c.3420del | p.(L1141Sfs*134) | XM_023242951.1; XP_023098719.1; published as c.3420delG | 2018 | 30246406 | |||
1466 | OMIA:002165-9685 | domestic cat | Domestic Shorthair | classical Ehlers-Danlos syndrome | COL5A1 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | D4 | g.93215496del | c.3066del | p.(Gly1023Valfs*50) | XM_023242950.1; XP_023098718.1 | 2022 | 35627182 | |||
1609 | OMIA:002165-9685 | domestic cat | Domestic medium-haired | classical Ehlers-Danlos syndrome | COL5A1 | splicing | Naturally occurring variant | yes | Felis_catus_9.0 | D4 | g.93290016T>G | c.501-2A>C | XM_023242950.1 | 2023 | 37594181 | ||||
1464 | OMIA:002165-9685 | domestic cat | Bengal (Cat) | classical Ehlers-Danlos syndrome | COL5A1 | deletion, gross (>20) | Naturally occurring variant | yes | Felis_catus_9.0 | D4 | g.93331577_93331598del | c.112_118+15del | r.spl? | XM_023242950.1 | 2022 | 35627182 | |||
1263 | OMIA:002295-9913 | taurine cattle | Holstein (black and white) (Cattle) | Ehlers-Danlos syndrome, classic type, 2 | COL5A2 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 2 | NC_037329.1:g.7331916G>T | XM_024979774.1:c.2366G>T | XP_024835542.1:p.(G789V) | XM_024979774.1: c.2366G>T; XP_024835542.1: p.Gly789Val (Jacinto et al., 2020) | rs5334475045 | 2020 | 33143196 | ||
1460 | OMIA:002295-9615 | dog | Chihuahua (Dog) | Ehlers-Danlos syndrome, classic type, 2 | COL5A2 | deletion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 36 | g.30548697_30548723del | c.3388_3414del | p.(Lys1130_Asp1138del) | XM_005640393.3; XP_005640450.1 | 2022 | 35627319 | |||
340 | OMIA:001967-9615 | dog | Landseer (Dog) | Muscular dystrophy, Ullrich type | COL6A1 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 31 | NC_006613.3:g.39303964G>T | XM_003434001.5:c.289G>T | XP_003434049.2:p.(E97*) | XM_003434001.5; XP_003434049.2; previously incorrectly listed in this table as c.289C>T; p.(Q97*) - corrected 8/2/2022 | 2015 | 26438297 | |||
1184 | OMIA:002260-9913 | taurine cattle | Holstein Friesian (Cattle) | de novo mutation in an AI sire | COL6A3 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 3 | NC_037330.1:g.116826597G>A | XM_024990262.1:c.5675C>T | XP_024846030.1:p.(T1892M) | Bourneuf et al. (2017) detected COL6A3 g.117453719G>A; p.T1894M as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Holstein AI bull. No information was provided on the descendants of this bull. p. coordinates have been updated to reflect recent NCBI transcript [29/08/2024]. | rs5334475059 | 2017 | 28904385 | ||
1625 | OMIA:002274-9615 | dog | American Staffordshire Terrier (Dog) | Muscular dystrophy, COL6A3-related | COL6A3 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 25 | g.48005972del | c.6398del | p.(P2133Rfs*109) | NM_001103215.1; NP_001096685.1; published as g.48287602CG>C in CanFam4 | 2023 | 37706358 | |||
1208 | OMIA:002274-9615 | dog | Labrador Retriever (Dog) | Muscular dystrophy, COL6A3-related | COL6A3 | splicing | Naturally occurring variant | yes | CanFam3.1 | 25 | NC_006607.3:g.48007994C>T | NM_001103215.1:c.6210+1G>A | NM_001103215.1; CanFam3.1 chr25:48,007,994C > T; NM_001103215.1 c.6210 + 1G > A (Bolduc et al., 2020) | 2020 | 32439203 | ||||
1207 | OMIA:002274-9615 | dog | Labrador Retriever (Dog) | Muscular dystrophy, COL6A3-related | COL6A3 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 25 | NC_006607.3:g.48014962G>A | NM_001103215.1:c.4726C>T | NP_001096685.1:p.(R1576*) | NM_001103215.1; NP_001096685.1; CanFam3.1 chr25:48,014,962G > A; NM_001103215.1 c.4726C > T, p.R1576* (Bolduc et al., 2020) | 2020 | 32439203 | |||
292 | OMIA:000341-9913 | taurine cattle | Rotes Höhenvieh, Germany (Cattle) Vorderwälder, Germany (Cattle) | Epidermolysis bullosa, dystrophic | COL7A1 | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.2 | 22 | g.51301158C>T | c.4762C>T | p.(R1588*) | rs876174537 | 2012 | 22715415 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed and some variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
1276 | OMIA:000341-9615 | dog | Basset Hound (Dog) | Epidermolysis bullosa, dystrophic | COL7A1 | complex rearrangement | Naturally occurring variant | yes | CanFam3.1 | 20 | g.[40524302_40524308del;40524267_40524380dup] | c.[2028_2034del;1993_2050+56dup] | p.(V677Sfs*11) | NM_001002980.1; NP_001002980.1; complex duplication event spanning parts of exon 15 and intron 15 of the COL7A1 gene, starting at position 40,524,267 and ending at 40,524,380 on chromosome 20 (CanFam3.1 assembly) (Garcia et al., 2020). | 2020 | 33291836 | |||
357 | OMIA:000341-9615 | dog | Central Asian Shepherd Dog (Dog) | Epidermolysis bullosa, dystrophic | COL7A1 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 20 | NC_006602.3:g.40532043C>T | XM_022406202.1:c.4579C>T | XP_022261910.1:p.(R1527*) | 2017 | 28493971 | Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool | |||
38 | OMIA:000341-9615 | dog | Golden Retriever (Dog) | Epidermolysis bullosa, dystrophic | COL7A1 | missense | Naturally occurring variant | yes | CanFam3.1 | 20 | NC_006602.3:g.40538034G>A | XM_022406202.1:c.5716G>A | XP_022261910.1:p.(G1906S) | rs1152388417 | 2003 | 12874109 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
641 | OMIA:001523-9615 | dog | Samoyed (Dog) | Oculoskeletal dysplasia 2 | COL9A2 | deletion, gross (>20) | Naturally occurring variant | yes | 15 | a 1,267 bp deletion that eliminates part of the 5’UTR, all of exon 1 and part of intron 1 | 2010 | 20686772 | |||||||
581 | OMIA:001522-9615 | dog | Labrador Retriever (Dog) | Oculoskeletal dysplasia 1 | COL9A3 | insertion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 24 | g.46653422_46653423insG | c.10_11insG | p.(A4Gfs*46) | NM_001197171.1; NP_001184100.1; published as "a 1-base insertion (guanine) in exon 1 that changes a string of four guanines (CFA24: 49,699,847–49,699,850; CanFam2) to a string of five guanines (c.7–10insG). ... (p.A4GX46)" Goldstein et al. (2010). Information in this table has been changed in accordance to HGVS 3'rule and updated to the current reference genome. | 2010 | 20686772 | |||
1092 | OMIA:001522-9615 | dog | Northern Inuit Dog (Dog) | Oculoskeletal dysplasia 1 | COL9A3 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 24 | NC_006606.3:g.46660067C>T | NM_001197171.1:c.700C>T | NP_001184100.1:p.(R234*) | 2019 | 31415586 | ||||
944 | OMIA:001621-9685 | domestic cat | Devon Rex (Cat) Sphynx (Cat) | Muscular dystrophy-dystroglycanopathy (limb-girdle) | COLQ | missense | Naturally occurring variant | yes | Felis_catus_9.0 | C2 | g.135068287C>T | c.1190G>A | p.(C397Y) | rs869320615 | 2015 | 26327126 26374066 | Genomic location obtained via Ensembl's VEP | ||
643 | OMIA:001988-9615 | dog | Bedlington Terrier (Dog) | Wilson disease, COMMD1 type | COMMD1 | deletion, gross (>20) | Naturally occurring variant | yes | 10 | deletion "breakpoints were positioned at 65.3091 and 65.3489 Mb of dog chromosome 10, in intron 1 and intron 2 of COMMD1 respectively, a deletion of 39.7 kb" | 2005 | 16293123 | |||||||
1545 | OMIA:002667-9031 | chicken | Feather colour, Inhibitor of gold | COMTD1 | IG | insertion, small (<=20) | Naturally occurring variant | no | GRCg6a | 6 | g.15675521_15675522insCT | c.747_748insCT | p.(Q250fs) | XM_015288295.1; XP_015143781.1 | 2023 | 37068079 | |||
215 | OMIA:001529-9913 | taurine cattle | Holstein Friesian (Cattle) | Dominant red | COPA | DR^DR | missense | Naturally occurring variant | no | ARS-UCD1.3 | 3 | NC_037330.1:g.9361962C>T | NM_001105645.1:c.478C>T | NP_001099115.1:p.(R160C) | rs3423151160 | 2017 | 28904385 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
1506 | OMIA:001274-452646 | American mink | Coat colour, black crystal | COPA | missense | Naturally occurring variant | unknown | NNQGG.v01 | FNWR01000261.1 | g.4876673G>A | c.478C>T | p.(R160C) | 2022 | 35729186 | |||||
1012 | OMIA:002159-9694 | tiger | Golden tiger | CORIN | missense | Naturally occurring variant | no | c.1759C>T | p.(H587Y) | 2017 | 28281538 | ||||||||
1463 | OMIA:002159-9685 | domestic cat | British Shorthair (Cat) | Copper (British recessive wideband) | CORIN | vwb^BSH | nonsense (stop-gain) | Naturally occurring variant | no | Felis_catus_9.0 | B1 | c.2425C>T | p.(R809*) | ON640807 | 2022 | 35703390 | |||
1456 | OMIA:002159-9685 | domestic cat | Siberian (Cat) | Extreme sunshine (Siberian recessive extreme wideband) | CORIN | vwb^eSIB | missense | Naturally occurring variant | no | Felis_catus_9.0 | B1 | g.167737406G>A | c.839G>A | p.(C280Y) | XM_019829549.2; XP_019685108.1; reported as Genbank ID ON355336 | 2022 | 35574714 | ||
1313 | OMIA:002159-9685 | domestic cat | Siberian (Cat) | Sunshine (golden) | CORIN | vwb^SIB | missense | Naturally occurring variant | no | Felis_catus_9.0 | B1 | g.167809720C>T | c.2383C>T | p.(R795C) | XM_019829551.2; XP_019685110.1 | 2021 | 33970502 | Genomic position in Felis_catus_9.0 provided by Joshua Khamis. | |
358 | OMIA:002111-9913 | taurine cattle | Holstein (red and white) (Cattle) | Cataract, recessive, CPAMD8-related | CPAMD8 | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.3 | 7 | NC_037334.1:g.6073556C>T | XM_015471929.2:c.220C>T | XP_015327415.2:p.(Q74*) | rs5334474964 | 2017 | 28683140 | |||
1418 | OMIA:002519-9913 | taurine cattle | Brown Swiss (Cattle) | Haplotype with homozygous deficiency BH24 | CPT1C | BH24 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 18 | NC_037345.1:g.56098048G>A | XM_002695120.5:c.158G>A | XP_002695166.2:p.(G53D) | XM_002695120.5 | rs719328437 | 2021 | 34915862 | |
1428 | OMIA:002533-9685 | domestic cat | Domestic Shorthair | Osteogenesis imperfecta | CREB3L1 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | D1 | g.100436508_100436509del | c.370_371del | p.(C124Lfs) | XM_003993204.4; XP_003993253.1; published as c.370_371delTG | 2022 | 35168412 | |||
916 | OMIA:000881-9685 | domestic cat | Abyssinian (Cat) | Rod-cone dysplasia | CRX | Rdy | deletion, small (<=20) | Naturally occurring variant | yes | F.catus_Fca126_mat1.0 | E2 | g.9492897del | c.546del | p.(P185Lfs*2) | XM_045045412.1; XP_044901347.1; published as CRX: n.546delC; in the Felis_catus_9.0 assembly the CRX gene is duplicated and genomic coordinates in this table are given for a more recent reference genome | 2010 | 20053974 | ||
1491 | OMIA:001643-10036 | golden hamster | duper | Cry1 | deletion, small (<=20) | Naturally occurring variant | unknown | c.578del | p.(P193fs) | published as c.578delC | 2022 | 35471909 | |||||||
1176 | OMIA:000168-10141 | domestic guinea pig | Cataract | Cryz | splicing | Naturally occurring variant | yes | "a 102-bp deletion towards the 3' end of the coding region. This deletion does not interfere with the reading frame but results in a protein 34 amino acids shorter." (Rodriguez et al., 1992) | 1992 | 1390943 | |||||||||
692 | OMIA:000852-9925 | goat | Casein, alpha-S1, reduced concentration | CSN1S1 | insertion, gross (>20) | Naturally occurring variant | no | 6 | "a 457-bp insertion within exon 19 (last untranslated exon). This insert is a truncated long interspersed repeated element (LINE) containing part of the ORF-2, the 3' UTR and the poly(A) tail of the original retroposon." | 1994 | 7926797 | ||||||||
907 | OMIA:001623-9925 | goat | Casein, alpha-S2, absence | CSN1S2 | nonsense (stop-gain) | Naturally occurring variant | no | ARS1.2 | 6 | NC_030813.1:g.86085134G>A | NM_001285585.1:c.374G>A | NP_001272514.1:p.W125* | published as as AJ131465 c.763G>A and p.(T110*), publication identifies that the codon changed is 'TGG' coding for tryptophan (W) - information in the table updated to recent transcript [04/10/2024] | rs268293093 | 2001 | 11419340 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | ||
220 | OMIA:002033-9913 | taurine cattle | A2 milk | CSN2 | A2 | missense | Naturally occurring variant | no | ARS-UCD1.2 | 6 | g.85451298T>G | c.245A>C | p.(H82P) | Note that cattle cannot be genotyped for the A2 allele solely on the basis of the c.245A>C variant because this variant is common to 4 other alleles; see Table 2 of Caroli et al. (2009) J. Dairy Sci. 92, 5335-5352 (Matt McClure, pers. comm.) | rs43703011 | 2013 | 23102962 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
1312 | OMIA:001424-9925 | goat | Absence of β‐casein | CSN2 | CSN2^0 | deletion, small (<=20) | Naturally occurring variant | no | ARS1.2 | 6 | NC_030813.1:g.86008404del | XM_013964699.2:c.295del | XP_013820153.1:p.I99Sfs*10 | Changed from g.86008401del to g.86008404del to adhere to the HGVS 3’rule [22/01/10]' previously listed as ENSCHIT00000032661.1:c.175del ENSCHIP00000024801.1:p.Ile59SerfsTer10; update to NCBI transcript information [04/10/24]; Persuy et al. (1999): "allele CSN2^O had a one-nucleotide deletion in the 5' end of exon 7, which introduces a premature stop codon. The open reading frame of allele CSN2^O encodes a shortened polypeptide of 72 amino acids, compared to 223 amino acids for caprine pre beta-casein A." | rs645737170 | 1999 | 10612234 | ||
1311 | OMIA:001424-9925 | goat | Absence of β‐casein | CSN2 | CSN2^01 | regulatory | Naturally occurring variant | no | ARS1.2 | 6 | NC_030813.1:g.86015651A>G | Cosenza et al. (2016): "nucleotide C .... negatively affects the promoter activity of the CSN2 gene" Synonyms: dbSNP ss1245869815 | rs654545998 | 2007 | 17931404 | The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries | |||
1186 | OMIA:002262-9913 | taurine cattle | Montbéliarde (Cattle) | de novo mutation in an AI sire | CSNK1G2 | missense | Naturally occurring variant | yes | ARS-UCD1.2 | 7 | g.44265842G>C | p.(D164H) | Bourneuf et al. (2017) detected Chr7 CSNK1G2 g.45885860G>C; p.D164H as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Montbéliarde AI bull. No information was provided on the descendants of this bull. | rs5334475073 | 2017 | 28904385 | |||
66 | OMIA:001505-9615 | dog | American Bulldog (Dog) | Neuronal ceroid lipofuscinosis, 10 | CTSD | missense | Naturally occurring variant | yes | CanFam3.1 | 18 | NC_006600.3:g.46013354C>T | NM_001025621.1:c.597G>A | NP_001020792.1:p.(M199I) | 2006 | 16386934 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
905 | OMIA:001505-9940 | sheep | Roslagsfår, Sweden (Sheep) | Neuronal ceroid lipofuscinosis, 10 | CTSD | missense | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 21 | NC_040272.1:g.51583020G>A | XM_027959254.1:c.883G>A | XP_027815055.1:p.(D295N) | published as c.934G>A; protein and cDNA positions in this table based on XP_027815055.1 and XM_027959254.1, respectively | 2000 | 10856224 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | ||
1517 | OMIA:002607-9685 | domestic cat | Domestic Longhair | Pyknodysostosis | CTSK | nonsense (stop-gain) | Naturally occurring variant | yes | Felis_catus_9.0 | C1 | g.105945826G>A | c.724C>T | p.(R242*) | ENSFCAT00000003643; variant is reported in a single affected cat | 2022 | 36532681 | |||
529 | OMIA:001786-9615 | dog | Beagle (Dog) | Intestinal cobalamin malabsorption due to CUBN mutation | CUBN | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 2 | NC_006584.3:g.19796293del | NM_001003148.1:c.786del | NP_001003148.1:p.(D262Efs*47) | NM_001003148.1; NP_001003148.1; deletion C | rs1152388404 | 2014 | 24164695 | ||
447 | OMIA:001786-9615 | dog | Border Collie (Dog) | Intestinal cobalamin malabsorption due to CUBN mutation | CUBN | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 2 | NC_006584.3:g.19974334del | NM_001003148.1:c.8392del | NP_001003148.1:p.(Q2798Rfs*3) | NM_001003148.1; NP_001003148.1; deletion C | 2013 | 23613799 | |||
1036 | OMIA:001786-9615 | dog | Komondor (Dog) | Intestinal cobalamin malabsorption, CUBN-related | CUBN | splicing | Naturally occurring variant | yes | CanFam3.1 | 2 | NC_006584.3:g.19981457G>A | NM_001003148.1:c.8746+1G>A | NM_001003148.1 | 2018 | 30591068 | ||||
287 | OMIA:001697-9913 | taurine cattle | Jersey (Cattle) | Abortion due to haplotype JH1 | CWC15 | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.3 | 15 | NC_037342.1:g.15449431C>T | NM_001046399.2:c.163C>T | NP_001039864.1:p.(R55*) | UMD3.1 position is g.15707169C>T, cDNA and protein positions based on XM_005215764.2 | rs1115118696 | 2013 | 23349982 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. | |
850 | OMIA:002131-9615 | dog | Mixed Breed (Dog) | Methaemoglobinaemia, CYB5R3-related | CYB5R3 | missense | Naturally occurring variant | yes | CanFam3.1 | 10 | g.22832962G>A | c.227G>A | p.(G72S) | NM_001048084.1; NP_001041549.1; published as g.22832963G>A, c.214G>A - coordinates updated based on Table 1, Jaffey et al. (2020), reported in a single dog | 2017 | 28963729 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
1700 | OMIA:002131-9615 | dog | Mixed Breed (Dog) | Methaemoglobinaemia, CYB5R3-related | CYB5R3 | missense | Naturally occurring variant | yes | CanFam3.1 | 10 | NC_006592.3:22836975A>G | NM_001048084.1:c.604A>C | NP_001041549.1:p.(T202A) | reported in a single dog | 2020 | 33293645 | |||
1699 | OMIA:002131-9615 | dog | American Pit Bull Terrier (Dog) Mixed Breed (Dog) | Methaemoglobinaemia, CYB5R3-related | CYB5R3 | missense | Naturally occurring variant | yes | CanFam3.1 | 10 | NC_006592.3:22841895G>C | NM_001048084.1:c.656G>C | NP_001041549.1:p.(R219P) | 2020 | 33293645 | ||||
967 | OMIA:002131-9615 | dog | Chihuahua (Dog) Mixed Breed (Dog) Pomeranian (Dog) Rat Terrier (Dog) | Methaemoglobinaemia, CYB5R3-related | CYB5R3 | missense | Naturally occurring variant | yes | CanFam3.1 | 10 | NC_006592.3:g.22836951A>C | NM_001048084.1:c.580A>C | NP_001041549.1:p.(I194L) | NM_001048084.1; NP_001041549.1 | 2018 | 29356095 | Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn. | ||
1548 | OMIA:002131-9685 | domestic cat | Domestic Shorthair | Methaemoglobinaemia, CYB5R3-related | CYB5R3 | splicing | Naturally occurring variant | yes | F.catus_Fca126_mat1.0 | B4 | g.135605715C>T | c.226+5G>A | XM_045062469.1; two transcripts were observed in the cat with the splice variant resulting in two predicted protein variants: XP_044918404.1:p.(G76_Q77insERSPDPARVEPG) and XP_044918404.1:p.(V52Afs*58), | 2023 | 37048064 | ||||
1155 | OMIA:002131-9685 | domestic cat | Domestic Shorthair | Methaemoglobinaemia, CYB5R3-related | CYB5R3 | missense | Naturally occurring variant | yes | Felis_catus_9.0 | B4 | g.137967506C>T | c.625G>A | p.(G209S) | Jaffey e al. (2019): "p.Gly209Ser amino acid change in transcript CYB5R3-202 (ENSFCAT00000056925) at position B4:137967506" | 2019 | 31650629 | |||
1156 | OMIA:002131-9685 | domestic cat | Domestic Shorthair | Methaemoglobinaemia, CYB5R3-related | CYB5R3 | splicing | Naturally occurring variant | yes | Felis_catus_9.0 | B4 | g.137970815C>G | c.232-1G>C | Jaffey et al. (2019): "a putative loss of function splice acceptor variant at c.232-1G>C in the CYB5R3-202 transcript (ENSFCAT00000056925) at position B4:137970815 that is in the acceptor site for exon 4, which likely affects downstream translation of the protein." | 2019 | 31650629 | ||||
629 | OMIA:000017-9986 | rabbit | Adrenal hyperplasia, congenital | CYP11A1 | deletion, gross (>20) | Naturally occurring variant | yes | "a large deletion mutation in the P450scc gene" | 1993 | 7682938 | |||||||||
1751 | OMIA:000017-8128 | Nile tilapia | Steroid hormone-deprived sex reversal, CYP11A1-related | cyp11a1 | deletion, gross (>20) | Genome-editing (CRISPR-Cas9) | yes | 22 bp deletion in exon 4 | 2024 | 39284885 | |||||||||
117 | OMIA:001661-9685 | domestic cat | Adrenal hyperplasia, congenital, due to 11-beta hydroxylase deficiency | CYP11B1 | missense | Naturally occurring variant | yes | Felis_catus_9.0 | F2 | g.84247412G>A | c.1151G>A | p.(R384Q) | XM_004000154.3; XP_004000203.1 published as "a guanosine-to-adenosine mutation in exon 7 that results in an arginine to glutamine amino acid substitution; this latter mutation results in 11β-hydroxylase deficiency-associated CAH in people [Parajes et al. (2010) J Clin Endocrinol Metab 95:779–788]. | 2012 | 22827537 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | |||
720 | OMIA:000452-9031 | chicken | Campine (Chicken) Sebright Bantams, United Kingdom of Great Britain and Northern Ireland (Chicken) | Henny feathering | CYP19A1 | insertion, gross (>20) | Naturally occurring variant | no | GRCg6a | 10 | g.9683879_9683880insN[7524] | The insertion is 7524bp and "contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains, suggesting a recent integration. The ERV 3’LTR, containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the CYP19A1 5′ untranslated region" (Li et al., 2019) | 1991 | 1939054 | Genomic location and size of the insertion provided by Li et al. (2019) | ||||
274 | OMIA:001405-9615 | dog | Beagle (Dog) | Metabolizer of a cognitive enhancer | CYP1A2 | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | 30 | NC_006612.3:g.37821686C>T | NM_001008720.1:c.1117C>T | NP_001008720.1:p.(R373*) | rs852922442 | 2004 | 15564884 | Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool | ||
1251 | OMIA:002288-9913 | taurine cattle | Hereford (Cattle) | Mandibulofacial dysostosis | CYP26C1 | missense | Naturally occurring variant | yes | ARS-UCD1.2 | 26 | g.14404993T>C | c.563T>G | p.(L188P) | ENSBTAT00000056396.3:c.563T>G; ENSBTAP00000050244.2:p.Leu188Arg | rs431913023 | 2020 | 33105751 | ||
502 | OMIA:000837-9685 | domestic cat | Vitamin D-deficiency rickets, type I | CYP27B1 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | B4 | g.86180281del | c.731del | p.(R244Pfs*32) | XM_003988966.3; XP_003989015.1; published as c.731delG | 2009 | 19138382 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | |||
315 | OMIA:000837-9685 | domestic cat | Siamese (Cat) | Vitamin D-deficiency rickets, type I | CYP27B1 | nonsense (stop-gain) | Naturally occurring variant | yes | Felis_catus_9.0 | B4 | g.86180375C>A | c.637G>T | p.(E213*) | XM_003988966.3; XP_003989015.1; | rs5334475145 | 2012 | 22553308 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
656 | OMIA:000837-9823 | pig | Vitamin D-deficiency rickets, type I | CYP27B1 | deletion, gross (>20) | Naturally occurring variant | yes | Sscrofa11.1 | 5 | NM_213995.1:c.952_1124del | the first of two deletions (173 bp or 329 bp) in the cDNA for cytochromome P450C1 (otherwise known as CYP27B1), | 2003 | 12915218 | ||||||
657 | OMIA:000837-9823 | pig | Vitamin D-deficiency rickets, type I | CYP27B1 | deletion, gross (>20) | Naturally occurring variant | yes | Sscrofa11.1 | 5 | NM_213995.1:c.952_1279del | the second of two deletions (173 bp or 329 bp) in the cDNA for cytochromome P450C1 (otherwise known as CYP27B1) | 2003 | 12915218 | ||||||
1576 | OMIA:000837-9615 | dog | Pug (Dog) | Vitamin D-deficiency rickets, type IA | CYP27B1 | nonsense (stop-gain) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 10 | NC_049231.1:g.2182971G>T | XM_038549826.1:c.261C>A | XP_038405754.1:p.(Y87*) | XM_038549826.1; XP_038405754.1 | 2023 | 37293695 | |||
1411 | OMIA:002508-9913 | taurine cattle | Simmental (Cattle) | Haplotype with homozygous deficiency SH8 | CYP2B6 | SH8 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 18 | NC_037345.1:g.50296371A>T | NM_001075173.1:c.938T>A | NP_001068641.1:p.(I313N) | NM_001075173.1 | rs5352006042 | 2021 | 34944310 | |
1137 | OMIA:002221-9685 | domestic cat | Domestic Shorthair | Vitamin D-deficiency rickets, type Ib | CYP2R1 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | D1 | g.72977336del | c.1386del | p.(F462Lfs*20) | XM_003993015.5; XP_003993064.1; genomic position in accordance with HGVS 3'-rule | 2019 | 30777056 | Genomic position in Felis_catus_9.0 provided by Joshua Khamis. | ||
52 | OMIA:002684-9615 | dog | Australian Cattle Dog (Dog) Shetland Sheepdog (Dog) | Leucodystrophy | CYTB | missense | Naturally occurring variant | yes | CanFam3.1 | M | m.14474G>A | c.14474G>A | p.(V98M) | 2006 | 16026996 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
1743 | OMIA:002894-10036 | golden hamster | Dcaf17 deficiency | Dcaf17 | deletion, small (<=20) | Genome-editing (CRISPR-Cas9) | yes | BCM_Maur_2.0 | NW_024429189.1:g.39589667_39589671del | XM_040745545.1:c.71_75del | XP_040601479.1:p.(D24Gfs*24) | 2024 | 39239833 | ||||||
784 | OMIA:001986-9823 | pig | Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation | DCLRE1C | splicing | Naturally occurring variant | yes | Sscrofa11.1 | 10 | NC_010452.4:g.46845535G>A | XM_021063988.1:c.678+1G>A | rs5334475180 | 2015 | 26320255 | |||||
785 | OMIA:001986-9823 | pig | Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation | DCLRE1C | nonsense (stop-gain) | Naturally occurring variant | yes | Sscrofa11.1 | 10 | NC_010452.4:g.46851262G>A | XM_021063988.1:c.800G>A | XP_020919647.1:p.(Trp267*) | rs5334475181 | 2015 | 26320255 | ||||
167 | OMIA:000735-9796 | horse | Belgian Draft (Horse) Connemara Pony (Horse) Haflinger (Horse) Rocky Mountain, United States of America (Bighorn sheep) Welsh Pony (Horse) | Ocular squamous cell carcinoma | DDB2 | missense | Naturally occurring variant | yes | EquCab3.0 | 12 | NC_009155.3:g.11726667C>T | XM_023654000.1:c.1013C>T | XP_023509768.1:p.(T338M) | The EquCab2 coordinates, obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool, are g.11608667, c.1013C>T and p.T338M | rs1139682898 | 2017 | 28425625 | The EquCab3 g. coordinates were provided by by Meredith O’Connell, working under the guidance of Professor Ernie Bailey, 5 March 2019. Breed information updated based on PMID: 38600096 | |
1624 | OMIA:002582-9913 | taurine cattle | Japanese Black, Japan (Cattle) | Hepatic fibrinogen storage disease | DGKG | missense | Genome-editing (CRISPR-Cas9) | yes | ARS-UCD1.3 | 1 | NC_037328.1:g.81082187C>T | XM_002684869.5:c.2162C>T | XP_002684915.3:p.T721I | XM_002684869.5; XP_002684915.3 | 2023 | 37681469 | |||
1335 | OMIA:002377-8845 | swan goose | Lion Head (Goose (domestic)) Sichuan White, China (Goose (domestic)) | Knob, basal | DIO2 | missense | Naturally occurring variant | no | AnsCyg_PRJNA183603_v1.0 | NW_013185827.1 | g.642923G>A | p.(P265L) | 2021 | 34193033 | |||||
565 | OMIA:002095-9615 | dog | Rhodesian Ridgeback (Dog) | Epilepsy, generalized myoclonic, with photosensitivity | DIRAS1 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 20 | g.56474668_56474671del | c.564_567del | p.(D189Afs*11) | XM_005633100.3; XP_005633157.1; published as DIRAS1:c.564_567delAGAC | 2017 | 28223533 | Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn | ||
1412 | OMIA:002505-9913 | taurine cattle | Simmental (Cattle) | Haplotype with homozygous deficiency SH5 | DIS3 | SH5 | insertion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 12 | g.47511687_47511687insT | c.2032dup | p.(I678N*2) | NP_025000110.1, XM_025000110.1 | 2021 | 34944310 | ||
1308 | OMIA:001484-9685 | domestic cat | Abyssinian (Cat) Burmese (Cat) Maine Coon (Cat) Oriental Shorthair (Cat) | Ticked | DKK4 | Ti^CK | missense | Naturally occurring variant | no | Felis_catus_9.0 | B1 | g.42620835C>T | c.53C>T | p.(A18V) | rs5334475164 | 2021 | 33780570 | ENSFCAT00000034752:c.53C>T; XM_023252567.1:c53C>T | |
1307 | OMIA:001484-9685 | domestic cat | Abyssinian (Cat) | Ticked | DKK4 | Ti^A | missense | Naturally occurring variant | no | Felis_catus_9.0 | B1 | g.42621481G>A | c.188G>A | p.(C63Y) | published as g.41621481G>A | rs785541575 | 2021 | 33780570 | (XM_023252567.1; ENSFCAT00000034752: c.188G>A) |
914 | OMIA:001354-9940 | sheep | Rambouillet (Sheep) | Muscular hypertrophy (double muscling), Callipyge | DLK1 | regulatory | Naturally occurring variant | unknown | Oar_rambouillet_v1.0 | 18 | g.66187430A>G | "a single A/G polymorphism located at position 103,894 of GenBank AF354168 and position 267 of the GenBank STS AF401294" (Freking et al., 2002) "the CLPG mutation, an A to G transition in a highly conserved dodecamer motif located in the 90-Kb intergenic region separating the Delta-like 1 homologue (DLK1) and Gene trap locus 2 (GTL2) genes in the eponymous imprinted domain" (Xu et al., 2015; PubMed 26474044) In relation to the Oar_v4.0/oviAri4 genome assembly, the location of the causative SNP is OAR18:g.64294536A>G (Ross Tellam, pers. comm. to FN 5 Nov 2020) | rs10721113 | 2002 | 12368241 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries. | |||
615 | OMIA:002109-9913 | taurine cattle | Brown Swiss (Cattle) | Tricho-dento-osseous-like syndrome | DLX3 | insertion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 19 | g.36665831_36665832insGGAGCACA | c.584_585insGGAGCACAGG | p.(S198Rfs*99) | NM_001081622 position is g.37298375_37298376insGGAGCACA | rs5334475096 | 2017 | 28670783 | The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. | |
728 | OMIA:001919-9615 | dog | Nova Scotia Duck Tolling Retriever (Dog) | Cleft palate 1 | DLX6 | insertion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | 14 | g.22068082_22068083insN[2056] | "2056 bp insertion [including LINE1] . . within a highly conserved region of DLX6 intron 2 at cfa14.25016716"[CanFam2.0] | 2014 | 24699068 | |||||
922 | OMIA:001081-9685 | domestic cat | Domestic Shorthair | Muscular dystrophy, Duchenne type | DMD | deletion, gross (>20) | Naturally occurring variant | yes | X | A deletion of the muscle promoter and first exon and the Purkinje neuronal first exon of the DMD gene | 1994 | 7881288 | |||||||
923 | OMIA:001081-9685 | domestic cat | Domestic Shorthair | Muscular dystrophy, Duchenne type | DMD | deletion, gross (>20) | Naturally occurring variant | yes | X | A large deletion that "involved regions of the dystrophin gene that are poorly characterized, including the cortical neuronal promoter and its first exon and the skeletal neuronal promoter and its first exon" | 2014 | 24446404 | |||||||
1395 | OMIA:001081-9823 | pig | Duchenne muscular dystrophy | DMD | DMD^ex52del | delins, gross (>20) | Transgenesis via somatic cell nuclear transfer (SCNT) | yes | X | gene targeting and somatic cell nuclear transfer was used to replace DMD exon 52 with a neomycin resistance cassette | 2013 | 23784375 | |||||||
680 | OMIA:001081-9615 | dog | German Shorthaired Pointer (Dog) | Muscular dystrophy, Duchenne type | DMD | deletion, gross (>20) | Naturally occurring variant | yes | X | a "deletion encompassing the entire dystrophin [DMD] gene" | 1999 | 10407848 | |||||||
536 | OMIA:001081-9615 | dog | Cocker Spaniel (Dog) | Muscular dystrophy, Duchenne type | DMD | deletion, small (<=20) | Naturally occurring variant | yes | X | deletion of four nucleotides in exon 65, with a reading frame shift predicting a premature stop codon at the site of the deletion | 2012 | 22218699 | |||||||
681 | OMIA:001081-9615 | dog | Tibetan Terrier (Dog) | Muscular dystrophy, Duchenne type | DMD | deletion, gross (>20) | Naturally occurring variant | yes | X | "a large deletion of exons 8-29" | 2012 | 22218699 | |||||||
729 | OMIA:001081-9615 | dog | Labrador Retriever (Dog) | Muscular dystrophy, Duchenne type | DMD | insertion, gross (>20) | Naturally occurring variant | yes | X | "184 nucleotide [pseudoexon] insertion between exon 19 and exon 20, which results in a premature stop codon at the next codon downstream of the insertion" | 2012 | 22218699 Reference not in PubMed; see OMIA 001081-9615 for reference details | |||||||
957 | OMIA:001081-9615 | dog | Rottweiler (Dog) | Muscular dystrophy, Duchenne type | DMD | nonsense (stop-gain) | Naturally occurring variant | yes | X | "nonsense mutation in exon 58" | 1994 | Reference not in PubMed; see OMIA 001081-9615 for reference details | |||||||
989 | OMIA:001081-9615 | dog | Poodle, Miniature (Dog) | Muscular dystrophy, Duchenne type | DMD | deletion, gross (>20) | Naturally occurring variant | yes | X | "a >5 Mb deletion on the X chromosome, encompassing the entire DMD gene" | 2018 | 29474464 | |||||||
562 | OMIA:001081-9615 | dog | Cavalier King Charles Spaniel (Dog) | Muscular dystrophy, Duchenne type | DMD | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | X | g.27442996_27443002del | c.6057_6063del | p.(N2021Pfs) | NM_001003343.1; NP_001003343.1; published as c.6051_6057delTCTCAAT based on different transcript | 2016 | 28028563 | |||
542 | OMIA:001081-9615 | dog | Norfolk Terrier (Dog) | Muscular dystrophy, Duchenne type | DMD | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | X | g.27606021del | c.3084delG | p.(G1029Nfs*30) | 2015 | 26401335 | ||||
1249 | OMIA:001081-9615 | dog | Jack Russell Terrier (Dog) | Duchenne-type muscular dystrophy | DMD | deletion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | X | g.27615280_27982912del | c.94-10346_2807-6207del | XM_005641029.1 | 2020 | 33049940 | ||||
1234 | OMIA:001081-9615 | dog | Labrador Retriever (Dog) | Labrador Retriever muscular dystrophy (LRMD) | DMD | inversion | Naturally occurring variant | yes | CanFam3.1 | X | g.27622834_29823788inv | c.-1490357_2626-947inv | XM_005641029.1 | 2020 | 32767978 | ||||
1235 | OMIA:001081-9615 | dog | Border Collie (Dog) | Muscular dystrophy, Duchenne | DMD | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | X | g.27626466del | c.2841delT | 2018 | 29843823 | |||||
750 | OMIA:001081-9615 | dog | Japanese Spitz (Dog) | Muscular dystrophy, Duchenne type | DMD | inversion | Naturally occurring variant | yes | CanFam3.1 | X | g.27631972_33069482inv | c.-4736051_2384-5339inv | XM_005641029.1; "an inversion of a 5.4-Mb fragment of the X chromosome, with one break point (BP1) in the DMD gene . . . and a second break point (BP2) in a gene farther toward the centromere, the RPGR gene". | 2015 | 25644216 | ||||
708 | OMIA:001081-9615 | dog | Pembroke Welsh Corgi (Dog) | Muscular dystrophy, Duchenne type | DMD | insertion, gross (>20) | Naturally occurring variant | yes | CanFam3.1 | X | g.27721607_27721608insN[(4800)] | "a long interspersed repetitive element-1 (LINE-1) insertion in intron 13, which introduced a new exon containing an in-frame stop codon" | 2011 | 20714321 | |||||
1492 | OMIA:001081-9615 | dog | Labrador Retriever (Dog) | Muscular dystrophy, Duchenne type | DMD | duplication | Naturally occurring variant | yes | CanFam3.1 | X | g.27851768_28247504dup | Shelton et al. (2022): "chrX:27,851,768-27,852,122 bp position (Intron 7 . . .) and chrX:28,247,150-28,247,504 bp position (Intron 1 . . .)" | 2022 | 36041985 | |||||
367 | OMIA:001081-9615 | dog | Cavalier King Charles Spaniel (Dog) | Muscular dystrophy, Duchenne type | DMD | splicing | Naturally occurring variant | yes | CanFam3.1 | X | NC_006621.3:g.26956239G>A | NM_001003343.1:c.7294+5G>T | NM_001003343.1; NP_001003343.1; experimentally confirmed splice defect; a single nucleotide variant in the 5'-splice site of intron 51 that results in skipping of exon 50 in mRNA transcripts and a predicted premature truncation of the translated protein | 2010 | 20072625 | ||||
1236 | OMIA:001081-9615 | dog | Australian Labradoodle (Dog) | Australian Labradoodle dystrophinopathy | DMD | nonsense (stop-gain) | Naturally occurring variant | yes | CanFam3.1 | X | NC_006621.3:g.27621845G>A | NM_001003343.1:c.2668C>T | NP_001003343.1:p.(R890*) | NM_001003343.1; NP_001003343.1; "a C to T transition at base pair 43 in exon 21 of the dystrophin gene" (Shrader et al., 2018) | 2018 | 30286978 | |||
366 | OMIA:001081-9615 | dog | Golden Retriever (Dog) | Muscular dystrophy, Duchenne type | DMD | splicing | Naturally occurring variant | yes | CanFam3.1 | X | NC_006621.3:g.27926946T>C | NM_001003343.1:c.531-2A>G | NM_001003343.1; a point mutation in the consensus splice acceptor site in exon 6 , such that exon 7 is skipped | rs1152388423 | 1992 | 1577476 | |||
1656 | OMIA:001081-9685 | domestic cat | Domestic Shorthair | Muscular dystrophy, Duchenne type | DMD | nonsense (stop-gain) | Naturally occurring variant | yes | F.catus_Fca126_mat1.0 | X | g.27949145C>T | c.4849C>T | p.(Q1617*) | XM_023249210.1 | 2024 | 38180235 | |||
1510 | OMIA:001081-9685 | domestic cat | Maine Coon (Cat) | Muscular dystrophy, Duchenne type | DMD | nonsense (stop-gain) | Naturally occurring variant | yes | F.catus_Fca126_mat1.0 | X | g.28208148G>A | c.1180C>T | p.(R394*) | XM_045050794.1; XP_044906729.1 | 2022 | 36359052 | |||
1531 | OMIA:001888-9685 | domestic cat | Maine Coon (Cat) | Becker muscular dystrophy | DMD | missense | Naturally occurring variant | yes | F.catus_Fca126_mat1.0 | X | NC_058386.1:g.27988938G>A | XM_045050787.1:c.4186C>T | XP_044906722.1:p.(H1396Y) | 2023 | 36834603 | ||||
1684 | OMIA:001888-9685 | domestic cat | Kinkalow (Cat) | Muscular dystrophy, X-linked | DMD | nonsense (stop-gain) | Naturally occurring variant | yes | Felis_catus_9.0 | X | NC_018741.3:g.27350268G>A | XM_023249210.1:c.8467C>T | XP_023104978.1:p.(Q2823*) | likely de novo mutation reported in a single cat | 2024 | 38613437 | |||
1667 | OMIA:001888-9685 | domestic cat | Domestic Shorthair | Muscular dystrophy, X-linked | DMD | nonsense (stop-gain) | Naturally occurring variant | yes | Felis_catus_9.0 | X | NC_018741.3:g.27361452C>T | XM_023249210.1:c.8333G>A | XP_023104978.1:p.(W2778*) | F.catus_Fca126_mat1.0 coordinates are g.27110574G>A | 2024 | 38415938 | |||
1714 | OMIA:001081-9615 | dog | Border Collie (Dog) | Muscular dystrophy, X-linked | DMD | insertion, gross (>20) | Naturally occurring variant | unknown | ROS_Cfam_1.0 | X | NC_051843.1:g.26431863_26431864insN[162] | NM_001003343.1:c.9271_9272insN[162] | NP_001003343.1:p.(Ala3091fs*21) | likely de-novo variant present in a single affected dog | 2024 | 39152696 | |||
1457 | OMIA:001888-9823 | pig | Becker muscular dystrophy | DMD | insertion, gross (>20) | Naturally occurring variant | yes | Sscrofa11.1 | X | Aihara et al. (2022): "Analysis of dystrophin mRNA showed a 62 base pair insertion between exons 26 and 27. The insertion was derived from intron 26." | 2022 | 35220848 | |||||||
179 | OMIA:001685-9823 OMIA:001888-9823 | pig | Stress syndrome | DMD | missense | Naturally occurring variant | yes | Sscrofa11.1 | X | g.28309227G>A | c.5872C>T | p.(R1958W) | Ensembl VEP was used to identify cDNA position in transcript ENSSSCT00000089893.1, SIFT score 0.01 | rs196952080 | 2012 | 22691118 | |||
1615 | OMIA:001081-9615 | dog | Brittany Spaniel (Dog) | Muscular dystrophy, Duchenne | DMD | insertion, gross (>20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | X | RSPYR1 retrogene insertion in intron 20; reported in a single dog; reported in a single dog | 2023 | 37628610 | ||||||
1616 | OMIA:001081-9615 | dog | French Bulldog (Dog) | Muscular dystrophy, Duchenne | DMD | insertion, small (<=20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | X | g.27774668_27774669insT | c.3371_3372insA | p.(F1125fs) | NM_001003343.1; NP_001003343.1; published as p.(F1125*), reported in a single dog | 2023 | 37628610 | |||
1614 | OMIA:001081-9615 | dog | Brittany Spaniel (Dog) | Muscular dystrophy, Duchenne | DMD | nonsense (stop-gain) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | X | NC_049260.1:g.26939052G>A | NM_001003343.1:c.8059C>T | NP_001003343.1:p.(Q2687*) | NM_001003343.1; NP_001003343.1; reported in 2 related dogs | 2023 | 37628610 | |||
1744 | OMIA:001081-9615 | dog | Entlebucher Mountain Dog (Dog) | Muscular dystrophy, Duchenne type | DMD | duplication | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | X | NC_049260.1:g.27027497_27,036112dup8616 | NM_001003343.1:c.7528-4048_7645+4450dup | NP_001003343.1:p.(I2549Sfs*3) | 2024 | 39307576 | ||||
908 | OMIA:001542-9940 | sheep | Corriedale (Sheep) | Hypophosphatemic rickets, autosomal recessive, 1 | DMP1 | nonsense (stop-gain) | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 6 | NC_040257.1:g.112910614C>T | XM_012180327.3:c.433C>T | XP_012035717.1:p.(R145*) | Published as g.112213795C>T / c.250C>T. Protein and cDNA positions in this table are based on XP_012035717.1 and XM_012180327.3. | 2011 | 21747952 | The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. | ||
321 | OMIA:001715-9796 | horse | American Trotter (Horse) Bhotia Pony, India (Horse) Chakouyi, China (Horse) French Trotter (Horse) Icelandic Horse (Horse) Kentucky Mountain Saddle, United States of America (Horse) Missouri Fox Trotting Horse (Horse) Morgan (Horse) Paso Fino (Horse) Peruvian Paso (Horse) Quarter Horse (Horse) Rocky Mountain Horse (Horse) Scandinavian Coldblood Trotter (Horse) Spiti Pony, India (Horse) Tennessee Walking Horse (Horse) Thoroughbred (Horse) Zaniskari Pony (Horse) | Gaitedness | DMRT3 | nonsense (stop-gain) | Naturally occurring variant | no | EquCab3.0 | 23 | NC_009166.3:g.22391254C>A | NM_001317265.1:c.902C>A | NP_001304194.1:p.(S301*) | rs1150690013 | 2012 | 22932389 | Breed information updated based PMID:39571791 on PMID:38600096 and PMID:37149793 | ||
1352 | OMIA:002442-9823 | pig | Large White (Pig) | Sperm flagella defect | DNAH17 | deletion, small (<=20) | Naturally occurring variant | yes | Sscrofa11.1 | 12 | NC_010454.4:g.3556402_3556414del | Nosková et al. (2021): "intronic 13-bp deletion ... causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17" | rs5334475172 | 2021 | 33724408 | ||||
1687 | OMIA:002847-9615 | dog | Portuguese Water Dog (Dog) | Microphthalmos with hematopoietic defects, congenital | DNAJC21 | insertion, gross (>20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 4 | NC_049225.1:g.74274883ins[T70]TGCTGCTTGGATT | 2024 | 38682429 | ||||||
39 | OMIA:001466-9615 | dog | Boykin Spaniel (Dog) Chesapeake Bay Retriever (Dog) Curly Coated Retriever (Dog) Labrador Retriever (Dog) Pembroke Welsh Corgi (Dog) | Exercise-induced collapse | DNM1 | missense | Naturally occurring variant | yes | CanFam3.1 | 9 | NC_006591.3:g.55282762C>A | NM_001131049.1:c.767G>T | XP_001124521.1:p.(R256L) | ROS_Cfam_1.0:g.56204742C>A ENSCAFT00845051951.1:c.767G>T ENSCAFP00845040760.1:p.Arg256Leu | rs852832685 | 2008 | 18806795 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
1434 | OMIA:002534-9615 | dog | Border Collie (Dog) | Centronuclear myopathy 1 | DNM2 | missense | Naturally occurring variant | yes | CanFam3.1 | 20 | NC_006602.3:g.50423497G>A | XM_005632882.3:c.1393C>T | XP_005632939.1.:p.(R465W) | XM_005632882.3; XP_005632939.1. | 2022 | 35244154 | |||
125 | OMIA:001776-9685 | domestic cat | Dihydropyrimidinase deficiency | DPYS | missense | Naturally occurring variant | yes | Felis_catus_9.0 | F2 | g.52064442C>T | c.1303G>A | p.(G435R) | XM_023248231.1; XP_023103999.1 | 2012 | 23430934 | Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley. | |||
1194 | OMIA:002266-9615 | dog | Rottweiler (Dog) | Hyperkeratosis, palmoplantar, DSG1-related | DSG1 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 7 | g.58163636_58163640del | c.2541_2545del | p.(G848Wfs*2) | NM_001002939.1; NP_001002939.1; published as c.2541_2545delGGGCT | 2020 | 32344723 | |||
1392 | OMIA:002452-9685 | domestic cat | Domestic Shorthair | Hair shaft dysplasia | DSG4 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | D3 | g.55315010del | c.76del | p.(I26Lfs*4) | XM_019815116.1; XP_019670675.1 | 2022 | 34878611 | |||
1393 | OMIA:002452-9685 | domestic cat | Domestic Shorthair | Hair shaft dysplasia | DSG4 | deletion, small (<=20) | Naturally occurring variant | yes | Felis_catus_9.0 | D3 | g.55336127del | c.1777del | p.(H593Tfs*23) | XM_019815116.1; XP_019670675.1 | 2022 | 34878611 | |||
1408 | OMIA:002243-9913 | taurine cattle | Highland (Cattle) | Ichthyosis, DSP-related | DSP | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 23 | NC_037350.1:g.47826600G>T | NM_001192368.2:c.6893C>A | NP_001179297.1:p.(A2298D) | NM_001192368.2; NP_001179297.1 | rs5385033307 | 2022 | 34996433 | ||
1710 | OMIA:002243-9615 | dog | Poodle, Miniature (Dog) | Ichthyosis, syndromic | DSP | deletion, small (<=20) | Naturally occurring variant | unknown | UU_Cfam_GSD_1.0 | 35 | NC_049256.1:g.8804542_8804544del | XM_038584124.1:c.1821_1823del | XP_038440052.1:p.(N608del) | de novo variant in one dog | 2024 | 39136317 | |||
1115 | OMIA:002210-9823 | pig | Bama Xiang Zhu, China (Pig) | Congenital hypothyroidosis | DUOX2 | missense | Naturally occurring variant | yes | Sscrofa11.1 | 1 | NC_010443.5:g.126625620A>G | NM_213999.2:c.1226A>G | NP_999164.2:p.(D409G) | ENU mutagenesis was used to create these pigs, the mutation is located within an exonic splicing enhancer motif and causes aberrant splicing of DUOX2 transcripts (Cao et al., 2019) | rs5334475175 | 2019 | 30651277 | ||
1056 | OMIA:002186-9615 | dog | Boston Terrier (Dog) Bulldog (Dog) French Bulldog (Dog) | Screw tail | DVL2 | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | 5 | g.32195051del | c.2051del | p.(P684Lfs*26) | XM_005619960.3; XP_005620017.1; published as g.32195043_32195044del; c.2044delC and changed to HGVS nomenclature in this table | 2018 | 30521570 | |||
1739 | OMIA:000543-103695 | central bearded dragon | Scaleless | EDA | Sca | deletion, gross (>20) | Naturally occurring variant | unknown | "in-frame deletion of 14 amino acids in a highly conserved tumor necrosis factor (TNF) motif of the EDA protein" | 2016 | 28439533 | ||||||||
711 | OMIA:000543-9913 | taurine cattle | Danish Holstein (Cattle) | Anhidrotic ectodermal dysplasia | EDA | HED6 | insertion, gross (>20) | Naturally occurring variant | yes | X | "a LINE1-derived pseudoexon between EDA exons 1 and 2. The 161-bp-long pseudoexon introduces a shift in reading frame and a premature stop codon early in EDA exon 2" | 2011 | 22034998 | Allele id was copied from Table 1 of Capuzzello et al. (2022) | |||||
645 | OMIA:000543-9913 | taurine cattle | Deutsche Holstein Schwarzbunt, Germany (Cattle) | Anhidrotic ectodermal dysplasia | EDA | HED1 | deletion, gross (>20) | Naturally occurring variant | yes | X | c.397_502del | p.(M133Vfs*111) | a large deletion including exon 3 in the gene for ectodysplasin (ED1; now called EDA) 200922: g. info moved to here (g.85821470) until it can be standardised | 2001 | 11591646 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 Allele id and p. information were copied from Table 1 of Capuzzello et al. (2022) | |||
1120 | OMIA:000543-9913 | taurine cattle | Holstein Friesian (Cattle) | Generalized hypohidrotic ectodermal dysplasia | EDA | HED8 | inversion | Naturally occurring variant | yes | ARS-UCD1.2 | X | g.77174882_80737442inv | Escouflaire et al. (2019): The "first breakpoint . . . [is] between positions 82,271,052 and 82,271,053 bp on chromosome X . . . The second breakpoint is situated at position 86,034,441 bp within the EDA intron 1" | 2019 | 31533624 | Allele id was copied from Table 1 of Capuzzello et al. (2022). | |||
1293 | OMIA:000543-9913 | taurine cattle | Red Angus-Simmental cross | Hypohidrotic ectodermal dysplasia | EDA | HED9 | deletion, gross (>20) | Naturally occurring variant | yes | ARS-UCD1.2 | X | g.80382423_80435202del | GCF_002263795.1 (O'Toole et al., 2021) | 2021 | 33801223 | Allele id was copied from Table 1 of Capuzzello et al. (2022). | |||
1484 | OMIA:000543-9913 | taurine cattle | British Blue x Holstein-Friesian cross | Anhidrotic ectodermal dysplasia, EDA-related | EDA | HED10 | deletion, gross (>20) | Naturally occurring variant | yes | ARS-UCD1.2 | X | g.80516615_80538514del | c.397_502del | p.(M133Vfs*111) | NM_001081743.2; NP_001075212.1 | 2022 | 36068608 | Allele id was copied from Table 1 of Capuzzello et al. (2022). | |
586 | OMIA:000543-9913 | taurine cattle | Japanese Black, Japan (Cattle) | Anhidrotic ectodermal dysplasia | EDA | HED7 | insertion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | X | g.80802800_80802801insCCCT | c.280_281insAGGG | p.(G94Qfs*49) | rs5334475024 | 2012 | 22497423 | The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Allele id was copied from Table 1 of Capuzzello et al. (2022). | |
1665 | OMIA:000543-9913 | taurine cattle | Fleckvieh-Simmental, Germany (Cattle) | Hypohidrotic ectodermal dysplasia, X-linked | EDA | missense | Naturally occurring variant | yes | ARS-UCD1.3 | X | g.80417567C>T | c.679G>A | p.(G227R) | NM_001081743.2; NP_001075212.1; published as g.85716041G>A in ARS-UCD2.0 | rs1114816375 | 2023 | 38275590 | ||
373 | OMIA:000543-9913 | taurine cattle | Deutsche Holstein Schwarzbunt, Germany (Cattle) | Anhidrotic ectodermal dysplasia | EDA | HED2 | splicing | Naturally occurring variant | yes | ARS-UCD1.3 | X | NC_037357.1:g.80411671A>C | NM_001081743.2:c.924+2T>G | c.DNA position is based on NM_001081743.2 | rs5334474632 | 2002 | 12021844 | The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Allele id was copied from Table 1 of Capuzzello et al. (2022) | |
1661 | OMIA:000543-9913 | taurine cattle | Limousin (Cattle) | Hypohidrotic ectodermal dysplasia, X-linked | EDA | HED11 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | X | NC_037357.1:g.80411716T>C | NM_001081743.2:c.881A>G | NP_001075212.1:p.(E294G) | NM_001081743.2; NP_001075212.1 | rs439722471 | 2024 | 38252617 | |
1295 | OMIA:000543-9913 | taurine cattle | Holstein Friesian (Cattle) | Anhidrotic ectodermal dysplasia | EDA | HED5 | splicing | Naturally occurring variant | yes | ARS-UCD1.3 | X | NC_037357.1:g.80411795C>A | NM_001081743.2:c.802C>A | "a single nucleotide polymorphism (SNP) G/A at the 9th base of exon 8 [GenBank: AJ278907.1 position 30.549] ... Sequencing of the RT-PCR products revealed that the amplified fragment of the affected animals lacked ... exon 8. At the protein level, the exon skipping leads to a frameshift and consequently to a premature stop codon." (Gargani et al., 2011) | rs5334475058 | 2011 | 21740563 | Allele id and c. information were copied from Table 1 of Capuzzello et al. (2022) | |
1294 | OMIA:000543-9913 | taurine cattle | Red Angus-Charolais-Simmental cross | Anhidrotic ectodermal dysplasia | EDA | HED3 | nonsense (stop-gain) | Naturally occurring variant | yes | ARS-UCD1.3 | X | NC_037357.1:g.80415626G>A | NM_001081743.2:c.730C>T | NP_001075212.1:p.(R244*) | rs5334474792 | 2007 | 17616058 Reference not in PubMed; see OMIA 000543-9913 for reference details | The g. coordinate for the named reference genome assembly, together with the c. coordinate, were kindly provided by Tosso Leeb (22 March 2021). Allele id was copied from Table 1 of Capuzzello et al. (2022). | |
482 | OMIA:000543-9913 | taurine cattle | Holstein Friesian (Cattle) | Anhidrotic ectodermal dysplasia | EDA | HED4 | deletion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.3 | X | NC_037357.1:g.80803015_80803033del | NM_001081743.2:c.48_66del | NP_001075212.1:p.(A16S22fs*55) | "a 19-bp deletion at nucleotides c.48_66 in exon 1 ... . This mutation is predicted to generate a truncated 49 aa protein." | rs5334474984 | 2011 | 21410470 | Allele id and p. information were copied from Table 1 of Capuzzello et al. (2022) |
1458 | OMIA:000543-9615 | dog | Mixed Breed (Dog) | X-linked hypohidrotic ectodermal dysplasia | EDA | splicing | Naturally occurring variant | yes | CanFam3.1 | X | r.385_487del | p.M129fs*112 | NM_001014770.2; NP_001014770.1; EDA transcript lacks 103 nucleotides encoded by exon 2, exon skipping is likely to be caused by an intronic splice variant | 2016 | 27449516 | ||||
1017 | OMIA:000543-9615 | dog | Dachshund (Dog) | X-linked hypohidrotic ectodermal dysplasia | EDA | deletion, small (<=20) | Naturally occurring variant | yes | CanFam3.1 | X | g.54509504del | c.842delT | p.(L281Hfs*22) | 2018 | 30276836 | ||||
361 | OMIA:000543-9615 | dog | German Shepherd Dog (Dog) | Anhidrotic ectodermal dysplasia | EDA | splicing | Naturally occurring variant | yes | CanFam3.1 | X | NC_006621.3:g.54511433G>A | NM_001014770.2:c.910-1G>A | NM_001014770.2 | rs1152388425 | 2005 | 16151697 | Genomic coordinates in CanFam3.1 und EVA Id provided by Zoe Shmidt and Robert Kuhn. | ||
1705 | OMIA:000543-9685 | domestic cat | Domestic Shorthair | Hypohidrotic ectodermal dysplasia | EDA | missense | Naturally occurring variant | yes | F.catus_Fca126_mat1.0 | X | NC_058386.1:g.57148944G>A | XM_011291781.3:c.1042G>A | XP_011290083.1:p.(A348T) | reported in a single cat | 2024 | 39062633 | |||
724 | OMIA:001695-8090 | Japanese medaka | Reduced scale-3 | edar | insertion, gross (>20) | Naturally occurring variant | yes | "several kb of extra sequence in the 5' UTR that . . . contains out-of-frame start codons and stop codons, [and consequently] the mutant transcript is likely to result in premature initiation and termination of translation and, as a result, the EDAR protein is not synthesized" | 2001 | 11516953 | |||||||||
843 | OMIA:002128-9913 | taurine cattle | Charolais (Cattle) | Anhidrotic ectodermal dysplasia, EDAR-related | EDAR | insertion, small (<=20) | Naturally occurring variant | yes | ARS-UCD1.2 | 11 | g.44599876_44599877insC | p.(P161Rfs*97) | UMD3.1 position is g.44462236_44462237insC | 2017 | 28904385 | The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. | |||
1550 | OMIA:002687-9940 | sheep | Fleece variation, wool density | EDAR | regulatory | Naturally occurring variant | no | Oar_v4.0 | 3 | g.61927840T>C | the T allele is associated denser wool production in fine wool sheep | rs408766096 | 2024 | 37137429 | |||||
1738 | OMIA:002887-94885 | corn snake | Scaleless | EDARADD | scl | deletion, small (<=20) | Naturally occurring variant | unknown | UNIGE_PanGut_3.0 | Super-Scaffold_423 | NW_023010793.1:g.39572203_39572204del | XM_034428296.1:c.545_546del | XP_034284187.1:p.C182* | 2023 | 37315141 | ||||
1474 | OMIA:002560-9913 | taurine cattle | Lidia, Spain (Cattle) | Growth and respiratory lethal syndrome | EDN2 | missense | Naturally occurring variant | yes | ARS-UCD1.2 | 3 | g.104701617G>A | c.149G>A | p.(C50Y) | ENSBTAG00000021434; ENSBTAT00000028571.3 | 2022 | 35912509 | |||
1747 | OMIA:002901-8296 | axolotl | Skin colour, white | EDN3 | d | not known | no | cDNA from animals with the white phenotype lack exon 2 | 2017 | 28127056 | |||||||||
722 | OMIA:001671-9031 | chicken | Bohuslän - Dals svarthöna, Sweden (Chicken) H'mong, Viet Nam (Chicken) Kedu, Indonesia (Chicken) Silkie (Chicken) | Silky/Silkie pigmentation (Fibromelanosis) | EDN3 | FM | complex rearrangement | Naturally occurring variant | no | 20 | the FM mutation actually involves "the duplication of two genomic regions, each larger than 100 kb and separated by 417 kb on wild-type [GGA20] chromosomes" | 2011 | 22216010 | ||||||
760 | OMIA:002164-9925 | goat | Coat colour, white spotting, EDNRA-related | EDNRA | repeat variation | Naturally occurring variant | no | 17 | "a 1Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats" | 2016 | 27329507 | ||||||||
160 | OMIA:000629-9796 | horse | American Paint (Horse) Miniature Horse (Horse) Quarter Horse (Horse) Thoroughbred (Horse) | Megacolon | EDNRB | frame overo | delins, small (<=20) | Naturally occurring variant | yes | EquCab3.0 | 17 | NC_009160.3:g.50503041_50503042delinsCT | NM_001081837.2:c.353_354delinsAG | NP_001075306.2:p.(I118K) | NM_001081837.2; NP_001075306.2 | 1998 | 9530628 | ||
930 | OMIA:001765-9940 | sheep | West African Dwarf (Sheep) | Waardenburg syndrome, type 4A | EDNRB | deletion, gross (>20) | Naturally occurring variant | yes | Oar_rambouillet_v1.0 | 10 | "a deletion of about 110 kb on sheep chromosome [OAR]10, comprising the entire EDNRB gene" | 2012 | 23300849 | ||||||
1632 | OMIA:000375-8932 | rock pigeon | Piebald | EDNRB2 | Group 4 | duplication | Naturally occurring variant | yes | tandem duplication of a 37-kb region spanning from intron 1 of VAMP7 to just 5’ of EDNRB2 | 2023 | 37546953 | ||||||||
1631 | OMIA:000375-8932 | rock pigeon | Piebald | EDNRB2 | Group2 | missense | Naturally occurring variant | yes | p.(A42E) | 2023 | 37546953 | ||||||||
1630 | OMIA:000375-8932 | rock pigeon | Piebald | EDNRB2 | Group1 | missense | Naturally occurring variant | yes | p.(R290C) | 2023 | 37546953 | ||||||||
1562 | OMIA:002701-51751 | ball python | Skin colour, EDNRB2-related | EDNRB2 | yellowbelly | deletion, small (<=20) | Naturally occurring variant | unknown | c.1646del | OP589186.1; 1-bp deletion introduces a frameshift, which removes or alters three of the seven transmembrane helices | 2023 | 37191439 | |||||||
1563 | OMIA:002701-51751 | ball python | Skin colour, EDNRB2-related | EDNRB2 | yellowbelly | deletion, small (<=20) | Naturally occurring variant | unknown | c.1747_1763del | OP589186.1; "17-bp deletion introduces a frameshift into the transcript, which removes or alters two of the seven transmembrane helices" | 2023 | 37191439 | |||||||
1564 | OMIA:002701-51751 | ball python | Skin colour, EDNRB2-related | EDNRB2 | specter | missense | Naturally occurring variant | unknown | c.2601G>C | p.(R315P) | OP589186.1 | 2023 | 37191439 | ||||||
1567 | OMIA:002701-51751 | ball python | Skin colour, EDNRB2-related | EDNRB2 | asphalt | splicing | Naturally occurring variant | unknown | c.3118G>A | OP589186.1; G-to-A substitution in the sixth splice donor for the sixth intron | 2023 | 37191439 | |||||||
1565 | OMIA:002701-51751 | ball python | Skin colour, EDNRB2-related | EDNRB2 | spark | missense | Naturally occurring variant | unknown | c.481G>C | p.(L152F) | OP589186.1 | 2023 | 37191439 | ||||||
1566 | OMIA:002701-51751 | ball python | Skin colour, EDNRB2-related | EDNRB2 | gravel | splicing | Naturally occurring variant | unknown | c.499G>A | OP589186.1; G-to-A substitution at the splice donor for the first intron | 2023 | 37191439 | |||||||
257 | OMIA:000375-93934 | Japanese quail | Feather colour, panda/dotted white | EDNRB2 | missense | Naturally occurring variant | no | c.995G>A | p.(R332H) | 2007 | 17313575 | ||||||||
1633 | OMIA:001252-8932 | rock pigeon | Recessive white and bull eye | EDNRB2 | missense | Naturally occurring variant | no | 4A | g.11167700C>T | c.766G>A | p.(E256K) | 2023 | 37546953 | ||||||
1164 | OMIA:001252-8843 | domestic goose | Gang, China (Goose (domestic)) | Feather colour, recessive white | EDNRB2 | insertion, small (<=20) | Naturally occurring variant | no | AnsCyg_PRJNA183603_v1.0 | NW_013185915.1:g.750748_750735insCACAGGTGAGCTCT | 2020 | 32066369 | |||||||
16 | OMIA:001904-9031 | chicken | Feather colour, recessive white | EDNRB2 | mo^w | missense | Naturally occurring variant | no | GRCg6a | 4 | g.11164302G>T | c.731G>T | p.(C244F) | NM_204120.1; NP_989451.1; published as c.1008G>T and p.(C244F); coordinates in the table have been updated to a recent reference genome and / or transcript | 2014 | 24466053 | Genomic position in GRCg6a provided by Joshua Khamis. | ||
17 | OMIA:001904-9031 | chicken | Feather colour, mottled | EDNRB2 | mo | missense | Naturally occurring variant | no | GRCg6a | 4 | g.11166001G>A | c.999G>A | p.(R332H) | NM_204120.1; NP_989451.1; published as c.1272G>A and p.(R332H); coordinates in the table have been updated to a recent reference genome and / or transcript | 2014 | 24466053 | Genomic position in GRCg6a provided by Joshua Khamis. | ||
1481 | OMIA:002564-9615 | dog | English Springer Spaniel (Dog) | Dyserythropoietic anemia and myopathy syndrome (DAMS) | EHBP1L1 | deletion, small (<=20) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 18 | g.52123541delG | c.3120delC | p.(F1041Sfs*30) | XM_038563927.1; XP_038419855.1 | 2022 | 36140701 | |||
1483 | OMIA:002564-9615 | dog | Labrador Retriever (Dog) | Congenital dyserythropoietic anemia and polymyopathy | EHBP1L1 | nonsense (stop-gain) | Naturally occurring variant | yes | UU_Cfam_GSD_1.0 | 18 | NC_049239.1:g.52128140G>A | XM_038563927.1:c.388C>T | XP_038419855.1:p.(R130*) | XM_038563927.1; | 2022 | 36011338 | |||
1753 | OMIA:002904-9913 | taurine cattle | Angus (Cattle) | Male subfertility, EML5-related | EML5 | missense | Naturally occurring variant | yes | ARS-UCD1.3 | 10 | NC_037337.1:g.100310158G>A | NM_001206576.1:c.4960C>T | NP_001193505.1:p.(R1654W) | rs380547429 | 2022 | 35478957 | |||
452 | OMIA:001805-9615 | dog | It |