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39 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | ||||
| 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 | |||||
| 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 | rs735807319 | 2005 | 16051833 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| 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. | |||
| 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) | |||||
| 1169 | OMIA:002543-9031 | chicken | Cleft primary palate | ESRP2 | deletion, small (<=20) | Naturally occurring variant | yes | GRCg6a | 11 | g.3284041del | ss5200091912 | ❌ rs3386590816 | 2020 | 32162363 | ||||||
| 327 | OMIA:000889-9031 | chicken | Israeli experimental line, Israel (Chicken) Storrs Connecticut scaleless low line, United States of America (Chicken) UC Davis line, United States of America (Chicken) | Scaleless | FGF20 | nonsense (stop-gain) | Naturally occurring variant | yes | GRCg6a | 4 | g.63270401A>T | c.535A>T | p.(R179*) | 2012 | 22712610 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||
| 860 | OMIA:001360-9031 | chicken | Beijing You, China (Chicken) Commercial strain- layer- ISA Brown (Chicken) Commercial strain- layer- Lohmann Brown (Chicken) Marans (Chicken) Rhode Island Red (Chicken) TETRA strain, United States of America (Chicken) Transylvanian Naked Neck (Chicken) | Trimethylaminuria (fishy taint) | FMO3 | missense | Naturally occurring variant | yes | 8 | c.1034A>T | p.(T329S) | 2005 | 15916878 | |||||||
| 744 | OMIA:001245-9031 | chicken | Rhode Island Red (Chicken) | Retinal degeneration I | GC1 | complex rearrangement | Naturally occurring variant | yes | 26 | This allele is characterised by an 81bp insertion adjacent to a 642bp deletion | 1998 | 9448321 | ||||||||
| 721 | OMIA:000701-9031 | chicken | Naked neck | GDF7 | insertion, gross (>20) | Naturally occurring variant | yes | 3 | 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 | |||||||||
| 660 | OMIA:000309-9031 | chicken | Connecticut (CT) strain, United States of America (Chicken) S2 line, China (Chicken) | Dwarfism, sex-linked | GHR | deletion, gross (>20) | Naturally occurring variant | yes | Z | deletion of 1773 bp in the 3' end of the coding region of the growth hormone receptor gene | 1994 | 7964293 | ||||||||
| 515 | OMIA:001368-9031 | chicken | Retinopathy globe enlarged | GNB3 | deletion, small (<=20) | Naturally occurring variant | yes | 1 | c.D153del | 2006 | 17065478 | |||||||||
| 751 | OMIA:000668-9031 | chicken | Huiyang Bearded, China (Chicken) | Muffs and beard | HOXB8 | complex rearrangement | Naturally occurring variant | no | 27 | "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 | ||||||||
| 687 | OMIA:000006-9031 | chicken | Chinese Xingyi bantam, China (Chicken) | Achondroplasia, creeper | IHH | deletion, gross (>20) | Naturally occurring variant | yes | Gallus_gallus-4.0 | 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 | ||||||
| 604 | OMIA:000979-9031 | chicken | Talpid-3 | KIAA0586 | insertion, small (<=20) | Naturally occurring variant | yes | 5 | insT | 2006 | 16702409 | |||||||||
| 662 | OMIA:000394-9031 | chicken | Frizzle | KRT6A | deletion, gross (>20) | Naturally occurring variant | no | GRCg6a | 33 | g.5251413_5251496del | p.(V311_K333del) | NM_001001313.2; NP_001001313.2; published as a 84bp deletion that covers positions −24 of exon 5 to +59 of intron 5 of KRT6A (called KRT75 in an earlier genome assembly); the deletion activates a cryptic splice site resulting in a 69 bp in-frame deletion in mRNA after splicing and a deletion of 23-amino acids (position 311–333) | 2012 | 22829773 | ||||||
| 663 | OMIA:001612-9031 | chicken | Silkie (Chicken) | Oligozeugodactyly | LMBR1 | deletion, gross (>20) | Naturally occurring variant | yes | 2 | "a large deletion in LMBR1-intron 5, eliminating most of the limb-specific enhancer conserved sequence." | 2011 | 21509895 | ||||||||
| 393 | OMIA:000344-9031 | chicken | Fayoumi (Chicken) | Epilepsy | LOC430486 | splicing | Naturally occurring variant | yes | 25 | c581-4CC>TG | 2011 | 22046416 | ||||||||
| 1433 | OMIA:000884-9031 | chicken | Rose comb | MNR2 | R2 | complex rearrangement | Naturally occurring variant | no | galGal3 | 7 | g.16499781_16499782ins[23881384_23790414inv;16499583–16499781] | predicted to be the result of a recombination event between the wild-type allele and the R1 allele: "R2 does not carry the entire inversion but instead has two duplicated segments, one 91 kb fragment (23,790,414–23,881,384 bp) that represents a remaining fragment of the inverted region together with a small duplicated fragment of 198 bp (16,499,583–16,499,781 bp)" | 2012 | 22761584 | ||||||
| 745 | OMIA:000884-9031 | chicken | Rose comb | MNR2 | R1 | inversion | Naturally occurring variant | no | galGal3 | 7 | g.16499782_23881391delins23881384_16499781 | published as a 7.38 Mb inversion | 2012 | 22761584 | ||||||
| 326 | OMIA:001366-9031 | chicken | Retinal dysplasia and degeneration | MPDZ | nonsense (stop-gain) | Naturally occurring variant | yes | GRCg6a | Z | g.31023848G>A | c.1372C>T | p.(R458*) | 2011 | 21862650 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||||
| 14 | OMIA:001534-9031 | chicken | Resistance to myxovirus | MX1 | missense | Naturally occurring variant | no | GRCg6a | 1 | g.110260061G>A | c.1892G>A | p.(S631N) | rs313590198 | rs313590198 | 2002 | 11932243 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| 664 | OMIA:001101-9031 | chicken | Polymorphic Nucleolar [PNU] strain, United States of America (Chicken) | Ribosomal RNA deficiency | NOR | deletion, gross (>20) | Naturally occurring variant | 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 | |||||||||
| 719 | OMIA:000380-9031 | chicken | Feathering, Z-linked | PRLR | duplication | Naturally occurring variant | no | Z | 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 | |||||||||
| 1123 | OMIA:001547-9031 | chicken | Wingless-2 | RAF1 | nonsense (stop-gain) | Naturally occurring variant | yes | GRCg6a | 12 | g.5374854G>A | c.175C>T | p.(R59*) | NC_006099.5:g.5374854G>A ENSGALT00000033956.3:c.175C>T ENSGALP00000033314.3:p.Arg59Ter | rs314452077 | rs314452077 | 2019 | 31075853 | |||
| 913 | OMIA:000876-9031 | chicken | Riboflavinuria | RBP | splicing | Naturally occurring variant | yes | 8 | 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 | |||||||||
| 836 | OMIA:000810-9031 | chicken | Polydactyly | SHH | regulatory | Naturally occurring variant | yes | GRCg6a | 2 | g.8553470G>T | published as "single SNP in a highly conserved cis-regulatory region of Sonic Hedgehog was significantly associated with polydactyly" | rs80659072 | rs80659072 | 2010 | 20064842 | |||||
| 1047 | OMIA:000303-9031 | chicken | White Leghorn (Chicken) | Dwarfism, autosomal | TMEM263 | nonsense (stop-gain) | Naturally occurring variant | yes | GRCg6a | 1 | g.53638233C>T | c.433G>A | p.(W59*) | Wu et al. (2018): "NM_001006244.1:c.433G > A . . . NP_001006244.1:p.(Trp59∗)" | 2018 | 29930570 | ||||
| 13 | OMIA:001302-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup B | TNFRSF10B | missense | Naturally occurring variant | no | 22 | c.G>C | p.(C125S) | 2008 | 18094190 | ||||||||
| 324 | OMIA:001302-9031 | chicken | Resistance to avian sarcoma and leukosis viruses, subgroup B | TNFRSF10B | nonsense (stop-gain) | Naturally occurring variant | no | GRCg6a | 22 | g.1418711C>T | c.172C>T | p.(Q58*) | rs736008824 | rs736008824 | 2002 | 12097608 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| 718 | OMIA:000369-9031 | chicken | Feather colour, recessive white | TYR | C*C | insertion, gross (>20) | Naturally occurring variant | no | 1 | a retroviral insertion in the tyrosinase gene | 2006 | 16457736 | ||||||||
| 513 | OMIA:000369-9031 | chicken | Feather colour, albinism | TYR | C*A | deletion, small (<=20) | Naturally occurring variant | yes | 1 | c.817_822del6 | p.(D237_W238del) | 2000 | 10685888 | |||||||
| 15 | OMIA:000865-9031 | chicken | Restricted ovulator | VLDLR | missense | Naturally occurring variant | yes | Z | c.G>C | p.(C682S) | 1995 | 7568242 | ||||||||
| 11 | OMIA:000679-9031 | chicken | New Hampshire (Chicken) | Muscular dystrophy | WWP1 | missense | Naturally occurring variant | yes | GRCg6a | 2 | g.123014353G>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 | 39 |
| Variants with genomic location | 19 (48.7% ) |
| Variants in a variant database, i.e. with rs ID | 6 (15.4%) |
| Variant Type | Count | Percent |
|---|---|---|
| complex rearrangement | 3 | 7.7% |
| deletion, gross (>20) | 5 | 12.8% |
| deletion, small (<=20) | 5 | 12.8% |
| duplication | 1 | 2.6% |
| insertion, gross (>20) | 3 | 7.7% |
| insertion, small (<=20) | 2 | 5.1% |
| inversion | 1 | 2.6% |
| missense | 7 | 17.9% |
| nonsense (stop-gain) | 7 | 17.9% |
| regulatory | 1 | 2.6% |
| splicing | 4 | 10.3% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1991 | 1 | 2.6% |
| 1992 | 0 | 0.0% |
| 1993 | 1 | 2.6% |
| 1994 | 3 | 7.7% |
| 1995 | 1 | 2.6% |
| 1996 | 0 | 0.0% |
| 1997 | 0 | 0.0% |
| 1998 | 1 | 2.6% |
| 1999 | 0 | 0.0% |
| 2000 | 1 | 2.6% |
| 2001 | 0 | 0.0% |
| 2002 | 3 | 7.7% |
| 2003 | 0 | 0.0% |
| 2004 | 2 | 5.1% |
| 2005 | 2 | 5.1% |
| 2006 | 3 | 7.7% |
| 2007 | 0 | 0.0% |
| 2008 | 3 | 7.7% |
| 2009 | 0 | 0.0% |
| 2010 | 1 | 2.6% |
| 2011 | 4 | 10.3% |
| 2012 | 6 | 15.4% |
| 2013 | 0 | 0.0% |
| 2014 | 0 | 0.0% |
| 2015 | 2 | 5.1% |
| 2016 | 2 | 5.1% |
| 2017 | 0 | 0.0% |
| 2018 | 1 | 2.6% |
| 2019 | 1 | 2.6% |
| 2020 | 1 | 2.6% |