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39 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.

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%