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69 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 | Inferred EVA rsID | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | ||||
| 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 | ||||||||||
| 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 | ||||||||
| 1490 | OMIA:002573-151761 | yellow-crowned parrot | Lewy body-like disease | CADPS2 | missense | Naturally occurring variant | yes | c.1675G>C | p.(V559L) | 2022 | 36086934 | |||||||||
| 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. | ||
| 399 | OMIA:000698-89462 | water buffalo | Murrah (Buffalo) | Myotonia | CLCN1 | splicing | Naturally occurring variant | yes | c.396C>T | 2013 | 23339992 | |||||||||
| 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 | ||||||||
| 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 | ||||||
| 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 | ||||||||||
| 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 | ||||||||||
| 148 | OMIA:000361-9783 | Asiatic elephant | Factor VII deficiency | F7 | missense | Naturally occurring variant | yes | c.202A>G | p.(R68G) | 2017 | 28118558 | |||||||||
| 559 | OMIA:000439-10036 | golden hamster | Hair, long | Fgf5 | deletion, small (<=20) | Naturally occurring variant | no | c.546delG | p.(R184GfsX6) | 2015 | 26481120 | |||||||||
| 517 | OMIA:000578-9544 | Rhesus monkey | Krabbe disease | GALC | deletion, small (<=20) | Naturally occurring variant | yes | c.387delAC | 1997 | 9192853 | ||||||||||
| 190 | OMIA:001473-9915 | indicine cattle (zebu) | Brahman (Cattle) | Dwarfism, growth-hormone deficiency | GH1 | missense | Naturally occurring variant | yes | c.641C>T | p.(T200M) | Bos indicus cDNA position based on AF034386, protein position based on AAB92549 | 2009 | 19524387 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||||
| 677 | OMIA:001920-27706 | largemouth bass | Abortion due to deletion in GHRH | GHRH | deletion, gross (>20) | Naturally occurring variant | yes | a 66bp deletion (c.-923_-858del) in the 5' flanking region of the GHRH gene in an autosomal recessive embryonic lethal | 2014 | 24697798 | ||||||||||
| 1178 | OMIA:001461-9217 | American flamingo | Tay-Sachs disease | HEXA | missense | Naturally occurring variant | yes | c.1406C>T | p.(P469L) | 2008 | 18693054 | |||||||||
| 1584 | OMIA:001243-9601 | Sumatran orangutan | Alkaptonuria | HGD | missense | Naturally occurring variant | yes | Susiae_PABv2/ponAbe3 | 3 | g.17314095G>A | c.1081G>A | p.(G361R) | 2023 | 37354891 | ||||||
| 789 | OMIA:002116-69293 | three-spined stickleback | Coat colour, albinism, oculocutaneous, HPS5-related | Hps5 | casper | insertion, small (<=20) | Naturally occurring variant | yes | "casper mutants have an insertion of a single nucleotide in the 6th exon of Hsp5, predicted to generate an early frameshift" | 2017 | 28739598 | |||||||||
| 331 | OMIA:001348-9544 | Rhesus monkey | Atrichia with papular lesions | HR | nonsense (stop-gain) | Naturally occurring variant | yes | MMUL_1 | 8 | g.22046679C>T | c.1831C>T | p.(R611*) | 2002 | 11831740 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||||
| 1622 | OMIA:002763-9541 | crab-eating macaque | Severe combined immunodeficiency disease | IL2RG | nonsense (stop-gain) | Base-editing | yes | Macaca_fascicularis_5.0 | X | g.68110639G>A | c.391C>T | p.(Q131*) | XM_005593892.2; XP_005593949.1 | 2023 | 37661226 | |||||
| 962 | OMIA:001675-61379 | black-footed cat | Cone-rod dystrophy 2 | IQCB1 | deletion, small (<=20) | Naturally occurring variant | yes | c.1282delCT | p.(L428*) | 2017 | 28322220 | |||||||||
| 1505 | OMIA:000449-452646 | American mink | Shadow coat colour | KIT | S^h | missense | Naturally occurring variant | unknown | NNQGG.v01 | NWR01000037.1 | g.6253028G>T | c.2374G>T | p.(D792Y) | 2022 | 35481560 | |||||
| 1556 | OMIA:000499-9544 | Rhesus monkey | Hypercholesterolaemia | LDLR | nonsense (stop-gain) | Naturally occurring variant | yes | 19 | p.(W284*) | G>A in exon 6 in position 914 of the human cDNA resulting in p.(W284*) | 1990 | 2326270 | ||||||||
| 1557 | OMIA:000499-9544 | Rhesus monkey | Hypercholesterolaemia | LDLR | missense | Naturally occurring variant | yes | 19 | c.245G>A | p.(C82Y) | 2023 | 37186395 | ||||||||
| 1672 | OMIA:002796-9541 | crab-eating macaque | Cardiomyopathy, dilated, LMNA-related | LMNA | splicing | Base-editing | yes | MFA1912RKSv2 | 1 | NC_052255.1:g.93546791T>C | XM_045371898.1:c.357-2A>G | 2024 | 38559624 | |||||||
| 518 | OMIA:000185-452646 | American mink | Chediak-Higashi syndrome | LYST | deletion, small (<=20) | Naturally occurring variant | yes | c.9468delC | 2013 | 22762706 | ||||||||||
| 249 | OMIA:000625-10141 | domestic guinea pig | Mannosidosis, alpha | Man2b1 | missense | Naturally occurring variant | yes | c.679C>T | p.(R227W) | 2002 | 11959458 | |||||||||
| 1287 | OMIA:002309-9646 | giant panda | Cataract | MIP | missense | Naturally occurring variant | yes | c.686G>A | p.(S229N) | 2021 | 33530927 | |||||||||
| 385 | OMIA:001401-10036 | golden hamster | Waardenburg syndrome, type 2A | MITF | splicing | Naturally occurring variant | yes | A T>A base substitution in intron 6 of MITF leads to the skipping of exon 7 and a premature termination. | 2003 | 12871913 | ||||||||||
| 505 | OMIA:000755-93934 | Japanese quail | Osteopetrosis | MITF | deletion, small (<=20) | Naturally occurring variant | yes | same MITF variant as for silver, as reported in 1998 | 2001 | 11169846 | ||||||||||
| 1205 | OMIA:001680-452646 | American mink | Hedlund | MITF | h | splicing | Naturally occurring variant | yes | MusPutFur1.0.86 | c.33+1G>A | GL896899.1:18635719 G/A (MITF-M C.33 + 1 G > A (Manakhov et al., 2017) | 2019 | 30872653 | |||||||
| 1209 | OMIA:001654-8932 | rock pigeon | Almond | MLANA | st | repeat variation | Naturally occurring variant | yes | "The CNV captures a 77-kb segment of the reference genome (ScoHet5_227: 5,181,467–5,259,256), with an additional increase in coverage in a nested 25-kb segment (ScoHet5_227: 5,201,091–5,226,635). Read-depth analysis confirmed 7 copies of the outer 77-kb segment and 14 copies of the inner 25-kb segment in the genomes of female (ZStW) Almond pigeons, which have an St locus on only one chromosome. We used PCR to amplify across the outer and inner CNV breakpoints of Almond pigeons and determined that the CNV consists of tandem repeats of the 77-kb and nested 25-kb segments (Fig 3)." (Bruders et al., 2020) | 2020 | 32433666 | |||||||||
| 1014 | OMIA:002145-9544 | Rhesus monkey | Colorectal cancer, MLH1-related | MLH1 | nonsense (stop-gain) | Naturally occurring variant | yes | 2 | c.1029C<G | p.(Y343*) | Dray et al. (2018): "a de novo stop codon in the coding region of MLH1. This de novo stop codon occurs in exon 11 out of 19 in the MLH1 gene, and thus would produce a dramatically truncated and possibly non-functional protein". Ozirmak Lermi et al. (2022) reported the c. and p. coordinates of this variant. | 2018 | 30108684 | |||||||
| 1013 | OMIA:002145-9544 | Rhesus monkey | Colorectal cancer, hereditary nonpolyposis, MLH1-related | MLH1 | deletion, small (<=20) | Naturally occurring variant | yes | 2 | g.99561829_99561830del | Brammer et al. (2018): "a heterozygous deletion in the putative promoter region of the MLH1 gene (rheMac2: 2:99,561,829– 99,561,830; hg19: ∼3:37,034,780; c.−258_259)" | 2018 | 29490919 | ||||||||
| 1015 | OMIA:002160-9544 | Rhesus monkey | Colorectal cancer, hereditary nonpolyposis, MSH6-related | MSH6 | missense | Naturally occurring variant | unknown | Dray et al. (2018): "a heterozygous missense mutation in MSH6 that has a CADD score of 22.8, indicating that it would be among the <1% most deleterious mutations possible in the human genome (if that variant occurred in the human MSH6 gene" | 2018 | 30108684 | ||||||||||
| 519 | OMIA:001342-8790 | emu | Mucopolysaccharidosis IIIB | NAGLU | deletion, small (<=20) | Naturally occurring variant | yes | c.1098_1099delGG | 2001 | 11414757 | ||||||||||
| 316 | OMIA:000545-93934 | Japanese quail | Hypotrophic axonopathy | NEFL | nonsense (stop-gain) | Naturally occurring variant | yes | c.352C>T | p.(Q114*) | 1993 | 8468353 | |||||||||
| 1602 | OMIA:002130-9544 | Rhesus monkey | Coat colour, oculocutaneous albinism | OCA2 | missense | Naturally occurring variant | yes | c.2363C>T | p.(S788L) | 2020 | 32259106 | |||||||||
| 1022 | OMIA:002163-9544 | Rhesus monkey | Cone dystrophy 4, PDE6C-related | PDE6C | missense | Naturally occurring variant | yes | Mmul_8.0.1 | 9 | p.(R565Q) | 2019 | 30667376 | ||||||||
| 1507 | OMIA:000944-447135 | Bank vole | Susceptibility to atypical scrapie | PRNP | missense | Naturally occurring variant | yes | p.(M109I) | 2022 | 35731839 | ||||||||||
| 1621 | OMIA:002763-9541 | crab-eating macaque | Severe combined immunodeficiency disease | RAG1 | nonsense (stop-gain) | Base-editing | yes | Macaca_fascicularis_5.0 | 14 | g.30840789G>T | c.181C>T | p.(Q61*) | XM_005578172.2; XP_005578229.1 | 2023 | 37661226 | |||||
| 1427 | OMIA:002531-74940 | Chinook salmon | XY female | sdY | missense | Naturally occurring variant | yes | p.(I183N) | 2022 | 35100376 | ||||||||||
| 651 | OMIA:000162-10036 | golden hamster | Cardiomyopathy, dilated | SGCD | deletion, gross (>20) | Naturally occurring variant | yes | genomic deletion was found to be located at 6.1 kb 5' upstream of the second exon of δ-SG gene, and its 5' upstream region of more than 27.4 kb, including the authentic first exon of δ-SG gene, was deleted | 1997 | 9391120 | ||||||||||
| 652 | OMIA:002211-10036 | golden hamster | Cardiomyopathy, hypertrophic | SGCD | deletion, gross (>20) | Naturally occurring variant | yes | a large deletion in the delta-SG gene | 1997 | 9097966 | ||||||||||
| 386 | OMIA:000370-93934 | Japanese quail | Feather colour, albinism, sex-linked, imperfect | SLC45A2 | splicing | Naturally occurring variant | yes | a splice-site mutation in the SLC45A2 gene: "a G → T transversion at the splice acceptor site just preceding exon 4" | 2007 | 17151254 | ||||||||||
| 746 | OMIA:001821-8090 | Japanese medaka | Coat colour, albinism, oculocutaneous type IV | slc45a2 | complex rearrangement | Naturally occurring variant | yes | an inversion of 167 bp, an insertion of 48 bp, and a deletion of 172 bp | 2008 | 18245373 | ||||||||||
| 259 | OMIA:000370-93934 | Japanese quail | Feather colour, cinnamon | SLC45A2 | missense | Naturally occurring variant | no | c.287C>A | p.(A72D) | 2007 | 17151254 | |||||||||
| 861 | OMIA:001821-9593 | western gorilla | Coat colour, albinism, oculocutaneous type IV | SLC45A2 | missense | Naturally occurring variant | yes | gorGor3.1 | 17 | g.59753498G>C | c.1552G>C | p.(G518R) | 2013 | 23721540 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||||
| 1438 | OMIA:002537-9541 | crab-eating macaque | Encephalopathy, STXBP1-related | STXBP1 | missense | Base-editing | yes | Macaca_fascicularis5.0 | 15 | g.101106196C>T | c.875G>A | p.(R292H) | XM_005582167.2; XP_005582224.1 | 2022 | 35283272 | |||||
| 670 | OMIA:001617-9694 | tiger | Sweet taste, lack | TAS1R2 | deletion, gross (>20) | Naturally occurring variant | yes | "a 247-base pair microdeletion in exon 3 and stop codons in exons 4 and 6" | 2005 | 16103917 | ||||||||||
| 668 | OMIA:001617-32536 | cheetah | Sweet taste, lack | TAS1R2 | deletion, gross (>20) | Naturally occurring variant | yes | "a 247-base pair microdeletion in exon 3 and stop codons in exons 4 and 6" | 2005 | 16103917 | ||||||||||
| 1620 | OMIA:000240-8839 | Mallard | Crest cushion | TAS2R40 | regulatory | Naturally occurring variant | unknown | 1 | published as variant in the 5′UTR of TAS2R40 (123272114_c. G78A) | 2023 | 37652165 | |||||||||
| 397 | OMIA:000162-9103 | turkey | Cardiomyopathy, dilated | TNNT2 | splicing | Naturally occurring variant | yes | delGGGCTCCTC | 2002 | 11886865 | ||||||||||
| 1538 | OMIA:001472-9541 | crab-eating macaque | Neuronal ceroid lipofuscinosis, 2 | TPP1 | deletion, small (<=20) | Naturally occurring variant | yes | c.42delC | p.(L15Sfs*33) | 2023 | 36918063 | |||||||||
| 666 | OMIA:000202-9669 | domestic ferret | Coat colour, albinism | TYR | deletion, gross (>20) | Naturally occurring variant | yes | "deletion of exon 4" | 2007 | 17655555 | ||||||||||
| 1304 | OMIA:000202-476259 | Japanese raccoon dog | Albinism | TYR | complex rearrangement | Naturally occurring variant | yes | Mae et al. (2020): "the third exon was removed due to a deletion ... :two separate regions of 3.8 kb and 7.3 kb had been removed, but a segment of 0.3 kb between these two regions was retained, though was present in the reverse orientation." | 2020 | 32783776 | ||||||||||
| 1027 | OMIA:000202-9773 | humpback whale | Migaloo, the white whale | TYR | deletion, small (<=20) | Naturally occurring variant | yes | "(264 del C) at codon 88" | 2012 | 22140253 | ||||||||||
| 723 | OMIA:000202-8090 | Japanese medaka | Skin colour, albinism | tyr | i1 | insertion, gross (>20) | Naturally occurring variant | yes | a 1.9 kb fragment, corresponding to a novel transposable element (Tol1), has been inserted in exon 1 of the gene for tyrosinase | 1995 | 8552044 | |||||||||
| 1555 | OMIA:000202-8090 | Japanese medaka | Skin colour, albino (weak) | tyr | i(b) | insertion, gross (>20) | Naturally occurring variant | yes | a 4.7-kb insertion in the 5' untranslated region (Tol2) | 2004 | 15016305 | |||||||||
| 1554 | OMIA:000202-8090 | Japanese medaka | Skin colour, albino (quasi-albino) | tyr | i4 | insertion, gross (>20) | Naturally occurring variant | yes | a 4.7-kb insertion in exon 5 (Tol2-tyr) | 1996 | 8779712 | |||||||||
| 1599 | OMIA:000202-9544 | Rhesus monkey | Coat colour, golden | TYR | missense | Naturally occurring variant | no | 14 | p.(H256Q) | 2023 | 37522525 | |||||||||
| 332 | OMIA:000202-452646 | American mink | Albinism | TYR | nonsense (stop-gain) | Naturally occurring variant | yes | c.138T>A | p.(C46*) | 2008 | 18822100 | |||||||||
| 329 | OMIA:000202-89462 | water buffalo | Albinism | TYR | nonsense (stop-gain) | Naturally occurring variant | yes | c.1431G>A | p.(W477*) | 2012 | 22817390 | |||||||||
| 260 | OMIA:000202-452646 | American mink | Himalayan | TYR | missense | Naturally occurring variant | no | c.1835C>G | p.(H420Q) | 2009 | 19308642 | |||||||||
| 1600 | OMIA:000202-9544 | Rhesus monkey | Coat colour, oculocutaneous albinism | TYR | nonsense (stop-gain) | Naturally occurring variant | yes | 14 | c.552C>A | p.(S184*) | 2000 | 10751629 | ||||||||
| 355 | OMIA:000202-9515 | Tufted capuchin | Coat colour, albinism | TYR | nonsense (stop-gain) | Naturally occurring variant | yes | c.64C>T | p.(R22*) | 2017 | 28476152 | |||||||||
| 1303 | OMIA:000202-31143 | Japanese ratsnake | Coat colour, oculocutaneous albinism | TYR | albino - pet trade | nonsense (stop-gain) | Naturally occurring variant | yes | c.895C>T | p.(R299X) | 2018 | 30158334 | ||||||||
| 1601 | OMIA:000202-9544 | Rhesus monkey | Coat colour, oculocutaneous albinism | TYR | missense | Naturally occurring variant | yes | 14 | c.934C>A | p.(L312I) | 2020 | 32259106 | ||||||||
| 1118 | OMIA:000202-9627 | red fox | Albinism | TYR | insertion, small (<=20) | Naturally occurring variant | yes | VulVul2.2 | NW_020356544.1 | g.7130732dup | c.365dup | p.(N122Kfs4*) | XM_026015193.1; XP_025870978.1; published as c.365dupA | 2019 | 31246286 |
| Overall Statistics | |
|---|---|
| Total number of variants | 69 |
| Variants with genomic location | 15 (21.7% ) |
| Variants in a variant database, i.e. with rs ID | 0 (0.0%) |
| Variant Type | Count | Percent |
|---|---|---|
| complex rearrangement | 2 | 2.9% |
| deletion, gross (>20) | 6 | 8.7% |
| deletion, small (<=20) | 12 | 17.4% |
| insertion, gross (>20) | 5 | 7.2% |
| insertion, small (<=20) | 3 | 4.3% |
| missense | 21 | 30.4% |
| nonsense (stop-gain) | 11 | 15.9% |
| regulatory | 1 | 1.4% |
| repeat variation | 1 | 1.4% |
| splicing | 7 | 10.1% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1990 | 1 | 1.4% |
| 1991 | 0 | 0.0% |
| 1992 | 1 | 1.4% |
| 1993 | 1 | 1.4% |
| 1994 | 0 | 0.0% |
| 1995 | 1 | 1.4% |
| 1996 | 1 | 1.4% |
| 1997 | 3 | 4.3% |
| 1998 | 0 | 0.0% |
| 1999 | 0 | 0.0% |
| 2000 | 1 | 1.4% |
| 2001 | 3 | 4.3% |
| 2002 | 5 | 7.2% |
| 2003 | 1 | 1.4% |
| 2004 | 1 | 1.4% |
| 2005 | 2 | 2.9% |
| 2006 | 0 | 0.0% |
| 2007 | 3 | 4.3% |
| 2008 | 3 | 4.3% |
| 2009 | 2 | 2.9% |
| 2010 | 0 | 0.0% |
| 2011 | 0 | 0.0% |
| 2012 | 2 | 2.9% |
| 2013 | 3 | 4.3% |
| 2014 | 1 | 1.4% |
| 2015 | 1 | 1.4% |
| 2016 | 0 | 0.0% |
| 2017 | 4 | 5.8% |
| 2018 | 6 | 8.7% |
| 2019 | 4 | 5.8% |
| 2020 | 4 | 5.8% |
| 2021 | 1 | 1.4% |
| 2022 | 6 | 8.7% |
| 2023 | 7 | 10.1% |
| 2024 | 1 | 1.4% |