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68 variant records found | [show instead phene records] |
By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.
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.
| OMIA ID(s) | Species Name | Breed(s) | Variant Phenotype | Gene | Allele | Type of Variant | Deleterious? | Reference Sequence | Chr. | g. or m. | c. or n. | p. | Verbal Description | EVA ID | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OMIA 000042-9031 | chicken | Wisconsin hypoalpha mutant (WHAM) | Analphalipoproteinaemia | ABCA1 | missense | yes | GalGal5 | Z | g.54792686G>A | c.265G>A | p.E89K | 2002 | 12364545 | Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool | |||
| OMIA 000702-9031 | chicken | Nanomelia | ACAN | nonsense (stop-gain) | yes | GalGal4 | 10 | g.12554157G>T | c.4537G>T | p.E1513* | 1994 | 7827752 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||
| OMIA 001622-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup C | BTN1A1 | nonsense (stop-gain) | no | GalGal4 | 28 | g.808011C>A | c.165C>A | p.C55* | rs735807319 | 2005 | 16051833 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000303-9031 | chicken | White Leghorn | Dwarfism, autosomal | C1H12ORF23 | nonsense (stop-gain) | yes | GalGal5 | 1 | g.53688583C>T | c.433G>A | p.Trp59∗ | Wu et al. (2018): "NM_001006244.1:c.433G > A . . . NP_001006244.1:p.(Trp59∗)" | 2018 | 29930570 | |||
| OMIA 001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | missense | no | c.120C>G | p.C40W | 2004 | 15564460 | ||||||||
| OMIA 001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | tva^r2 | insertion, small (<=20) | no | c.48insCTCG | 2004 | 15564460 | ||||||||
| OMIA 001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | deletion, small (<=20) | no | c.502_511delCGCTCACCCC | 2015 | 25873518 | |||||||||
| OMIA 001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | deletion, small (<=20) | no | c.502_516delCGCTCACCCCGCCCC | 2015 | 25873518 | |||||||||
| OMIA 001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | splicing | no | c.506-515del10 | 2012 | 22171251 | |||||||||
| OMIA 001299-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup A | CD320 | splicing | no | c.507-511del5 | 2012 | 22171251 | |||||||||
| OMIA 000102-9031 | chicken | Sex-linked extreme dilution | CDKN2A | B0 | complex rearrangement | 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 | |||||||
| OMIA 000102-9031 | chicken | Sex-linked dilution | CDKN2A | B2 | missense | no | GalGal5 | Z | g.78636802C>T | c.28C>T | p.R10C | 2010 | 20374521 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000102-9031 | chicken | Sex-linked barring | CDKN2A | B1 | missense | no | GalGal5 | Z | g.78636804T>A | c.26T>A | p.V9D | 2010 | 20374521 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000452-9031 | chicken | Golden Campine Sebright Bantam | Henny feathering | CYP19A1 | insertion, gross (>20) | no | GRCg6a | 10 | 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) 200922: g. info removed to here (g.9683879_9683880ins) until can be standardised | 1991 | 1939054 | Genomic location and size of the insertion provided by Li et al. (2019) | |||||
| OMIA 001671-9031 | chicken | Ayam Cemani Black H'Mong Silky/Silkie Svarthöna (ohuslän-Dals Svarthöna) | Silky/Silkie pigmentation (Fibromelanosis) | EDN3 | FM | complex rearrangement | no | 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 | |||||||
| OMIA 001904-9031 | chicken | Feather colour, recessive white | EDNRB2 | mo^w | missense | no | c.1008G>T | p.C244F | 2014 | 24466053 | |||||||
| OMIA 001904-9031 | chicken | Feather colour, mottled | EDNRB2 | mo | missense | no | c.1272G>A | p.R332H | 2014 | 24466053 | |||||||
| OMIA 000296-9031 | chicken | Duplex comb | EOMES | duplication | no | "a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES)" | 2015 | 25789773 | |||||||||
| OMIA 000197-9031 | chicken | Cleft primary palate | ESRP2 | deletion, small (<=20) | yes | galGal5 | 11 | g.3384959delT | ss5200091912 | 2020 | 32162363 | ||||||
| OMIA 000889-9031 | chicken | Israeli experimental line Storrs, Connecticut (low line) UC Davis lines | Scaleless | FGF20 | nonsense (stop-gain) | yes | GalGal4 | 4 | g.62878803A>T | c.535A>T | p.R179* | 2012 | 22712610 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001360-9031 | chicken | Beijing You ISA Brown Lohmann Brown Marans Rhode Island Red TETRA Transylvanian naked neck | Trimethylaminuria (fishy taint) | FMO3 | missense | yes | c.1034A>T | p.T329S | 2005 | 15916878 | |||||||
| OMIA 001245-9031 | chicken | Rhode Island Red | Retinal degeneration I | GC1 | complex rearrangement | yes | This allele is characterised by an 81bp insertion adjacent to a 642bp deletion | 1998 | 9448321 | ||||||||
| OMIA 000701-9031 | chicken | Naked neck | GDF7 | insertion, gross (>20) | yes | a large insertion approximately 260kb downstream from the BMP12 gene (now known as GFD7), increasing the expression of this gene in embryonic skin | 2011 | 21423653 | |||||||||
| OMIA 000309-9031 | chicken | Connecticut (CT) strain S2 line | Dwarfism, sex-linked | GHR | deletion, gross (>20) | yes | Z | deletion of 1773 bp in the 3' end of the coding region of the growth hormone receptor gene | 1994 | 7964293 | |||||||
| OMIA 001368-9031 | chicken | Retinopathy globe enlarged | GNB3 | deletion, small (<=20) | yes | c.D153del | 2006 | 17065478 | |||||||||
| OMIA 000668-9031 | chicken | Huiyang Bearded | Muffs and beard | HOXB8 | complex rearrangement | no | "The Mb allele differs from the wild-type mb allele by three duplications, one in tandem and two that are translocated to that of the tandem repeat around 1.70 Mb on GGA27 | 2016 | 27253709 | ||||||||
| OMIA 000240-9031 | chicken | crested Polish Silky/Silkie | Crest | HOXC10 | duplication | no | GalGal6 | 33 | g.7587588_7587784dup | "a 197 bp duplication of an evolutionarily conserved sequence located in the intron of HOXC10 on chromosome 33" (Li et al., 2021) | 2021 | 33704432 | |||||
| OMIA 000006-9031 | chicken | Chinese Xingyi | Achondroplasia, creeper | IHH | deletion, gross (>20) | yes | 7 | g.21798705_21810600del | "a 11,896bp large deletion region (chr7: 21,798,705-21,810,600) covering the entire Indian hedgehog (IHH) gene" | 2016 | 27439785 | ||||||
| OMIA 000979-9031 | chicken | Talpid-3 | KIAA0586 | insertion, small (<=20) | yes | insT | 2006 | 16702409 | |||||||||
| OMIA 000394-9031 | chicken | Frizzle | KRT75 | deletion, gross (>20) | no | a 69 bp in-frame deletion in a conserved region of KRT75 | 2012 | 22829773 | |||||||||
| OMIA 001612-9031 | chicken | Silky/Silkie | Oligozeugodactyly | LMBR1 | deletion, gross (>20) | yes | "a large deletion in LMBR1-intron 5, eliminating most of the limb-specific enhancer conserved sequence." | 2011 | 21509895 | ||||||||
| OMIA 000810-9031 | chicken | Polydactyly | LMBR1 | regulatory | yes | GalGal5 | 2 | g.8500245G>T | rs80659072 | 2010 | 20064842 | ||||||
| OMIA 000344-9031 | chicken | Fayoumi eplipeptic strain | Epilepsy | LOC430486 | splicing | yes | c581-4CC>TG | 2011 | 22046416 | ||||||||
| OMIA 000374-9031 | chicken | Feather colour, extended black | MC1R | regulatory | no | 11 | c.-37C>T | 5 prime UTR variant | rs733919322 | 2017 | 28699279 | ||||||
| OMIA 000374-9031 | chicken | Feather colour, extended black | MC1R | E | missense | no | 11 | c.212T>C | p.Met71Thr | rs312264213 | 2017 | 28699279 | |||||
| OMIA 000374-9031 | chicken | Feather colour, extended black | MC1R | E | missense | no | 11 | c.274G>A | p.E92K | rs314881228 | 2003 | 12873211 | |||||
| OMIA 000374-9031 | chicken | Mie-Jidori | Feather colour, wheaten-like | MC1R | e^m | missense | no | 11 | c.644A>C | p.(His215Pro) | rs735789743 | 2020 | 31977074 | ||||
| OMIA 000374-9031 | chicken | Feather colour, buttercup | MC1R | missense | no | 11 | c.644A>C | p.H215P | rs735789743 | 2003 | 12873211 | ||||||
| OMIA 002108-9031 | chicken | Fayoumi | barring, autosomal | MC1R | E*R(Fay), Pg | missense | no | GalGal5.0 | 11 | g.19084979T>A | c.398T>A | p.(L133Q) | rs737523889 | 2021 | 33793042 | ||
| OMIA 001445-9031 | chicken | Five gray | MLPH | missense | no | 7 | g.4727070A>G | c.1909A>G | 2016 | 27173258 | |||||||
| OMIA 001445-9031 | chicken | Feather colour, lavender | MLPH | missense | no | GalGal5 | 7 | g.4795061C>T | c.103C>T | p.R35W | 2008 | 18197963 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||
| OMIA 000884-9031 | chicken | Rose comb | MNR2 | inversion | no | a 7.38 Mb inversion | 2012 | 22761584 | |||||||||
| OMIA 001366-9031 | chicken | Retinal dysplasia and degeneration | MPDZ | nonsense (stop-gain) | yes | GalGal4 | Z | g.30882785C>T | c.1372C>T | p.R458* | 2011 | 21862650 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||
| OMIA 001534-9031 | chicken | Resistance to myxovirus | MX1 | missense | no | GalGal5 | 1 | g.108941567G>A | c.1892G>A | p.S631N | rs313590198 | 2002 | 11932243 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001101-9031 | chicken | Polymorphic Nucleolar (PNU) strain | Ribosomal RNA deficiency | NOR | deletion, gross (>20) | yes | "Embryos exhibiting a nucleolar phenotype of one large and one very small nucleolus (Pp) are heterozygous for a reduced rDNA cluster (+/p1) and were shown in the present study to contain about 66% of the complement of rRNA genes in normal individuals (+/+) that show two large equal-sized nucleoli (PP)" | 1994 | 8014461 | ||||||||
| OMIA 000913-9031 | chicken | Silky/Silkie | Silky/Silkie feathering | PDSS2 | PDSS2(-103C-G) | regulatory | unknown | GalGal5 | 3 | g.68009144C>G | c.-103C>G | Feng et al. (2014): "a C to G transversion at 70,486,623 bp (ss666793747)" "The ss666793747 mutation is 103 bp upstream of the initiator codon ATG of PDSS2". The reported location was with respect to the galGal2 assembly. In the intervening years, ss666793747 has become rs316090093, from which the present location is taken. | rs316090093 | 2014 | 25166907 | ||
| OMIA 002270-9031 | chicken | Feathered shanks | PITX1 | deletion, gross (>20) | no | GRCg6a | 13 | g.16089993_16107660del | a 17.7kb deletion upstream of PITX1. | 2020 | 32344431 32344429 | ||||||
| OMIA 000373-9031 | chicken | Feather colour, dominant white | PMEL | I | insertion, small (<=20) | no | a 9-bp (3aa) insertion (WAP) after amino acid 610 in exon 10 | 2004 | 15579702 | ||||||||
| OMIA 000373-9031 | chicken | Feather colour, Dun | PMEL | deletion, small (<=20) | no | "a deletion of five amino acids in the transmembrane region" | 2004 | 15579702 | |||||||||
| OMIA 000373-9031 | chicken | Feather colour, Smoky | PMEL | deletion, small (<=20) | no | “The Smoky allele shared the 9-bp insertion in exon 10 with Dominant white, as expected from its origin, but also had a deletion of 12 nucleotides in exon 6, eliminating four amino acids from the mature protein†| 2004 | 15579702 | |||||||||
| OMIA 000380-9031 | chicken | Feathering, Z-linked | PRLR | duplication | no | The tandem duplication of this region results in the partial duplication of two genes; the prolactin receptor and the gene encoding sperm flagellar protein 2. | 2008 | 18713476 | |||||||||
| OMIA 001547-9031 | chicken | Wingless-2 | RAF1 | nonsense (stop-gain) | yes | galGal6a | 12 | g.5374854G>A | c.175C>T | p.Arg59Ter | NC_006099.5:g.5374854G>A ENSGALT00000033956.3:c.175C>T ENSGALP00000033314.3:p.Arg59Ter | rs314452077 | 2019 | 31075853 | |||
| OMIA 000876-9031 | chicken | Riboflavinuria | RBP | splicing | yes | A "deletion in the rd ribBP cDNA correspond[ing] precisely to an exon. The splice site following this exon contains a G-->A mutation at position 1 of the downstream 5'-splice donor sequence. | 1993 | 8226844 | |||||||||
| OMIA 000915-9031 | chicken | Sex-linked imperfect albinism | SLC45A2 | S*AL | deletion, small (<=20) | no | c.106delT | 2007 | 17151254 | ||||||||
| OMIA 000915-9031 | chicken | Feather colour, silver | SLC45A2 | S*S | missense | no | GalGal5 | Z | g.10336663C>A | c.1039C>A | p.L347M | rs314509501 | 2007 | 17151254 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 000915-9031 | chicken | White Leghorn | Feather colour, silver | SLC45A2 | S*S | missense | no | GalGal5 | Z | g.10340976A>G | c.830A>G | p.Y277C | rs315357427 | 2007 | 17151254 | Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool | |
| OMIA 000142-9031 | chicken | Araucana | Blue eggshell | SLCO1B3 | insertion, gross (>20) | no | A different location for the same insertion: "a ~4.2 kb [retroviral] EAV-HP insertion in the 5' flanking region of SLCO1B3" but 23bp upstream of where the insertion occurs in Chinese breeds Dongxiang and Lushi | 2013 | 23359636 | ||||||||
| OMIA 000142-9031 | chicken | Dongxiang Lushi | Blue eggshell | SLCO1B3 | insertion, gross (>20) | no | "a ~4.2 kb [retroviral] EAV-HP insertion in the 5' flanking region of SLCO1B3" | 2013 | 23359636 | ||||||||
| OMIA 001569-9031 | chicken | Feather colour, dark brown | SOX10 | deletion, gross (>20) | no | "an 8.3-kb deletion upstream of SOX10" | 2011 | 21210960 | |||||||||
| OMIA 000782-9031 | chicken | Japanese game fowl | Pea comb | SOX5 | repeat variation | no | "Pea-comb is caused by a massive amplification of a duplicated sequence located near evolutionary conserved non-coding sequences in intron 1 of the gene encoding the SOX5 transcription factor." The pea-comb mutant phenotype results from large-scale amplification of this duplication: pea comb alleles typically have 20-40 copies of the duplicated sequence, which must be sufficient to interfere with transcription. | 2009 | 19521496 | ||||||||
| OMIA 000839-9031 | chicken | Feathered shanks | TBX5 | regulatory | no | GRCg6a | 15 | g.12573054T>C | This SNP is 25kb upstream of the gene TBX5 (Bortoluzzi et al., 2020; Li et al. 2020) | 2020 | 32344431 32344429 | ||||||
| OMIA 001302-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup B | TNFRSF10B | missense | no | c.G>C | p.C125S | 2008 | 18094190 | ||||||||
| OMIA 001302-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup B | TNFRSF10B | nonsense (stop-gain) | no | GalGal5 | 22 | g.1281321C>T | c.172C>T | p.Q58* | rs736008824 | 2002 | 12097608 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000369-9031 | chicken | Feather colour, recessive white | TYR | C*C | insertion, gross (>20) | no | a retroviral insertion in the tyrosinase gene | 2006 | 16457736 | ||||||||
| OMIA 000369-9031 | chicken | Feather colour, albinism | TYR | C*A | deletion, small (<=20) | yes | c.817_822del6 | p.237-238delDW | 2000 | 10685888 | |||||||
| OMIA 001259-9031 | chicken | Orpington Wyandotte | Chocolate feathered | TYRP1 | missense | no | galGal5 | Z | g.30830367C>A | c.640C>A | p.His214Asn | 2019 | 30457703 | ||||
| OMIA 000865-9031 | chicken | Restricted ovulator | VLDLR | missense | yes | c.G>C | p.C682S | 1995 | 7568242 | ||||||||
| OMIA 000679-9031 | chicken | NH-413 strain OPN strain | Muscular dystrophy | WWP1 | missense | yes | GalGal5 | 2 | g.123640033G>A | c.1322G>A | p.R441Q | 2008 | 18501710 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool |
| Overall Statistics | |
|---|---|
| Total number of variants | 68 |
| Variants with genomic location | 24 (35.3% ) |
| Variants in a variant database, i.e. with rs ID | 15 (22.1%) |
| Variant Type | Count | Percent |
|---|---|---|
| complex rearrangement | 4 | 5.9% |
| deletion, gross (>20) | 7 | 10.3% |
| deletion, small (<=20) | 8 | 11.8% |
| duplication | 3 | 4.4% |
| insertion, gross (>20) | 5 | 7.4% |
| insertion, small (<=20) | 3 | 4.4% |
| inversion | 1 | 1.5% |
| missense | 21 | 30.9% |
| nonsense (stop-gain) | 7 | 10.3% |
| regulatory | 4 | 5.9% |
| repeat variation | 1 | 1.5% |
| splicing | 4 | 5.9% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1991 | 1 | 1.5% |
| 1992 | 0 | 0.0% |
| 1993 | 1 | 1.5% |
| 1994 | 3 | 4.4% |
| 1995 | 1 | 1.5% |
| 1996 | 0 | 0.0% |
| 1997 | 0 | 0.0% |
| 1998 | 1 | 1.5% |
| 1999 | 0 | 0.0% |
| 2000 | 1 | 1.5% |
| 2001 | 0 | 0.0% |
| 2002 | 3 | 4.4% |
| 2003 | 2 | 2.9% |
| 2004 | 5 | 7.4% |
| 2005 | 2 | 2.9% |
| 2006 | 3 | 4.4% |
| 2007 | 3 | 4.4% |
| 2008 | 4 | 5.9% |
| 2009 | 1 | 1.5% |
| 2010 | 4 | 5.9% |
| 2011 | 6 | 8.8% |
| 2012 | 5 | 7.4% |
| 2013 | 2 | 2.9% |
| 2014 | 3 | 4.4% |
| 2015 | 3 | 4.4% |
| 2016 | 3 | 4.4% |
| 2017 | 2 | 2.9% |
| 2018 | 1 | 1.5% |
| 2019 | 2 | 2.9% |
| 2020 | 4 | 5.9% |
| 2021 | 2 | 2.9% |