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59 variant records found

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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 Gallus_gallus-5.0 Z g.54792686 c.265G>A p.E89K 2002 12364545 Variant coordinates obtained from or confirmed by EBI's Some 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 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: "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 Gallus_gallus-5.0 Z g.78636802 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 Gallus_gallus-5.0 Z g.78636804 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 the terminal repeat sequence of a retrovirus that has been inserted into the 5' promoter region of the aromatase gene. 1991 1939054
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, mottling EDNRB2 missense no c.1008G>T p.C244F 2014 24466053
OMIA 001904-9031 chicken Feather colour, mottling EDNRB2 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 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 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 Gallus_gallus-5.0 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 c.-37C>T ss2137510513 2017 28699279
OMIA 000374-9031 chicken Feather colour, extended black MC1R missense no c.212T>C p.Met71Thr ss2727686851 2017 28699279
OMIA 000374-9031 chicken Feather colour, extended black MC1R missense no c.274G>A p.E92K ss2727686852 2003 12873211
OMIA 000374-9031 chicken Feather colour, buttercup MC1R missense no c.644A>C p.H215P ss2727686853 2003 12873211
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 Gallus_gallus-5.0 7 g.4795061 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 Gallus_gallus-5.0 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 Gallus_gallus-5.0 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 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 insertion, gross (>20) 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 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 Gallus_gallus-5.0 Z g.10336663 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 Gallus_gallus-5.0 Z g.10340976 c.830A>G p.Y277C rs315357427 2007 17151254 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
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 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 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 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 Gallus_gallus-5.0 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 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 Gallus_gallus-5.0 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 59
Variants with genomic location 15 (25.4% )
Variants in a variant database, i.e. with rs ID 11 (18.6%)
Variant Type Count Percent
complex rearrangement 4 6.8%
deletion, gross (>20) 6 10.2%
deletion, small (<=20) 7 11.9%
duplication 1 1.7%
insertion, gross (>20) 6 10.2%
insertion, small (<=20) 3 5.1%
inversion 1 1.7%
missense 18 30.5%
nonsense (stop-gain) 5 8.5%
regulatory 3 5.1%
repeat variation 1 1.7%
splicing 4 6.8%
Year First Reported Count Percent
1991 1 1.7%
1992 0 0.0%
1993 1 1.7%
1994 3 5.1%
1995 1 1.7%
1996 0 0.0%
1997 0 0.0%
1998 1 1.7%
1999 0 0.0%
2000 1 1.7%
2001 0 0.0%
2002 3 5.1%
2003 2 3.4%
2004 5 8.5%
2005 2 3.4%
2006 3 5.1%
2007 3 5.1%
2008 4 6.8%
2009 1 1.7%
2010 4 6.8%
2011 6 10.2%
2012 5 8.5%
2013 2 3.4%
2014 3 5.1%
2015 3 5.1%
2016 3 5.1%
2017 2 3.4%