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155 variant records found |
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1499 | OMIA:002589-8839 | Mallard | Blue eggshell | ABCG2 | regulatory | Naturally occurring variant | no | BGI_duck1.0 | NW_004676534.1 | g.[3573054A>G;3573085A>G] | The BGI_duck1.0 reference genome represents the blue eggshell genotype. | 2020 | 33186356 | |||||||
| 1177 | OMIA:001089-9542 | Japanese macaque | Antigen B | ABO | haplotype | Naturally occurring variant | no | Allele B reflects the peptide haplotype p.266Met + p.268Ala | 2000 | 10984838 | ||||||||||
| 20 | OMIA:001089-9541 | crab-eating macaque | A antigen | ABO | haplotype | Naturally occurring variant | no | p.266L + p.268G | Allele A is reflected in the peptide haplotype p.266Leu + p.268Gly | 1998 | 9583803 | |||||||||
| 21 | OMIA:001089-9544 | Rhesus monkey | Antigen A | ABO | haplotype | Naturally occurring variant | no | p.266L + p.268G | Allele A is reflected in the peptide haplotype p.266Leu + p.268Gly | 1998 | 9583803 | |||||||||
| 1174 | OMIA:001089-9544 | Rhesus monkey | Antigen B | ABO | haplotype | Naturally occurring variant | no | p.266M + p.268A | Allele B is a reflection of the peptide haplotype p.266Met + p.268Ala | 1998 | 9583803 | |||||||||
| 1175 | OMIA:001089-9541 | crab-eating macaque | B antigen | ABO | haplotype | Naturally occurring variant | unknown | p.266M + p.268A | Allele B is a reflection of the peptide haplotype p.266Met + p.268Ala | 1998 | 9583803 | |||||||||
| 22 | OMIA:001089-9579 | agile gibbon | Alleles A and B | ABO | missense | Naturally occurring variant | no | c.2178C>A and c.2185G>C | Haplotype c.2178C + c.2185G is allele A; haplotype c.2178A + c.2185C is allele B | 2009 | 19298858 | |||||||||
| 23 | OMIA:001089-9580 | common gibbon | Blood group system ABO | ABO | missense | Naturally occurring variant | no | c.2178C>A and c.2185G>C | 2009 | 19298858 | ||||||||||
| 532 | OMIA:001089-9598 | chimpanzee | O (lack of antigen) | ABO | O^del | deletion, small (<=20) | Naturally occurring variant | no | c.514_522delGTGCTGGAG | p.(V172-E174del) | 1999 | 10380696 | ||||||||
| 24 | OMIA:001089-9598 | chimpanzee | O (lack of antigen) | ABO | O^x | missense | Naturally occurring variant | no | c.791A>C | p.(Y264C) | 1999 | 10380696 | ||||||||
| 665 | OMIA:000201-10042 | North American deer mouse | New Hampshire (Chicken) | Melanic (non-agouti) | ASIP | deletion, gross (>20) | Naturally occurring variant | no | "a 125-kb deletion, which includes the upstream regulatory region and exons 1 and 2 of Agouti, results in a loss of Agouti expression" | 2009 | 19649329 | |||||||||
| 1321 | OMIA:002200-9915 | zebu | Brahman (Cattle) Nellore, India (Sheep) | Darkness of hair coat | ASIP | delins, gross (>20) | Naturally occurring variant | unknown | 13 | 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons (Trigo et al.2021) | 2021 | 33910501 | ||||||||
| 251 | OMIA:000201-61386 | Kodkod | Melanism (black coat) | ASIP | missense | Naturally occurring variant | no | p.(C126Y) | 2015 | 25695801 | ||||||||||
| 252 | OMIA:000201-61406 | Colocolo | Melanism (black coat) | ASIP | missense | Naturally occurring variant | no | p.(R120C) | 2015 | 25695801 | ||||||||||
| 1119 | OMIA:000201-10141 | domestic guinea pig | Recessive black | Asip | deletion, small (<=20) | Naturally occurring variant | no | c.181_184delTTCA | MH026115: c.181_184delTTCA; the deletion leads to a truncated protein of 77 amino acids due to the premature stop codon. | 2019 | 30746725 | |||||||||
| 330 | OMIA:000201-10042 | North American deer mouse | Alaska, United States of America (North American deer mouse) | Melanic (non-agouti) | ASIP | nonsense (stop-gain) | Naturally occurring variant | no | c.193?>? | p.(Q65*) | 2009 | 19649329 | ||||||||
| 333 | OMIA:000201-9691 | leopard | Black panther | ASIP | nonsense (stop-gain) | Naturally occurring variant | no | c.333C>A | p.(C111*) | 2012 | 23251368 | |||||||||
| 1219 | OMIA:000201-9858 | Western roe deer | Melanistic (black) | ASIP | missense | Naturally occurring variant | no | c.33G>T | p.(L11F) | 2020 | 32545389 | |||||||||
| 149 | OMIA:000201-9793 | ass | No light points | ASIP | NLP | missense | Naturally occurring variant | no | c.349T>C | p.(C117R) | 2015 | 25887951 | ||||||||
| 253 | OMIA:000201-61455 | Asiatic golden cat | Black | ASIP | missense | Naturally occurring variant | no | c.384C>G | p.(C128W) | 2012 | 23251368 | |||||||||
| 1010 | OMIA:000201-9838 | Arabian camel | Black and dark-brown coat colour | ASIP | haplotype | Naturally occurring variant | no | c.[23delT;c.25G>A] | KU179868; c.[23delT;c.25G>A]. As described by Almathen et al. (2018), this haplotype comprises "a 1-bp deletion (23delT/T) and a SNP (25G/A) in exon 2 of ASIP". | 2018 | 29893870 | |||||||||
| 1270 | OMIA:000213-89462 | water buffalo | White | ASIP | insertion, gross (>20) | Naturally occurring variant | no | UOA_WB_1 | 14 | "2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene" (Liang et al. (2020) | 2021 | 33212507 | ||||||||
| 667 | OMIA:000201-9627 | red fox | Dark Standard Silver | ASIP | deletion, gross (>20) | Naturally occurring variant | no | VulVul2.2 | NW_020356514.1 | A 16.5-kb deletion resulting in "a 166-nt deletion in the Standard Silver fox cDNA, spanning the second exon ... .This deletion removes the start codon and entire signal peptide" | 1997 | 9054949 | ||||||||
| 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 | ||||||||
| 1375 | OMIA:002466-48883 OMIA:002466-48882 OMIA:002466-87173 OMIA:002466-48884 OMIA:002466-48885 OMIA:002466-48886 OMIA:002466-1553461 | medium ground-finch | Beak colour, yellow | BCO2 | synonymous | Naturally occurring variant | no | 24 | g.6166878G>A | p.(V?V) | synonymous change 32 bp into exon 4 | 2021 | 34687609 | |||||||
| 1490 | OMIA:002573-151761 | yellow-crowned parrot | Lewy body-like disease | CADPS2 | missense | Naturally occurring variant | yes | c.1675G>C | p.(V559L) | 2022 | 36086934 | |||||||||
| 516 | OMIA:001416-9612 | gray wolf | Coat colour, dominant black | CBD103 | K^B | deletion, small (<=20) | Naturally occurring variant | no | 3bp deletion of the CBD103 gene | 2009 | 19197024 | |||||||||
| 520 | OMIA:001416-9614 | coyote | Coat colour, dominant black | CBD103 | deletion, small (<=20) | Naturally occurring variant | no | 3bp deletion of the CBD103 gene | 2009 | 19197024 | ||||||||||
| 1340 | OMIA:002386-9544 | Rhesus monkey | OKT4 epitope deficiency | CD4 | missense | Naturally occurring variant | unknown | 11 | c.C793T | p.(A265W) | 2021 | 33893743 | ||||||||
| 863 | OMIA:001890-198806 | ruff | Male body size/courtship behaviour | CENPN | inversion | Naturally occurring variant | unknown | "a 4.5Mb inversion on the ruff orthologue of chicken chromosomr GGA11 which, due to the well-known lethality of recombinants within an inversion, has created a supergene determining male breeding behaviour, body size and plumage colour" | 2016 | 26569123 | ||||||||||
| 399 | OMIA:000698-89462 | water 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 | ||||||
| 1012 | OMIA:002159-9694 | tiger | Golden tiger | CORIN | missense | Naturally occurring variant | no | c.1759C>T | p.(H587Y) | 2017 | 28281538 | |||||||||
| 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 | ||||||||||
| 1335 | OMIA:002377-8845 | swan goose | Lion Head (Goose (domestic)) Sichuan White, China (Goose (domestic)) | Knob, basal | DIO2 | missense | Naturally occurring variant | no | AnsCyg_PRJNA183603_v1.0 | NW_013185827.1 | g.642923G>A | p.(P265L) | 2021 | 34193033 | ||||||
| 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 | ||||||||||
| 1164 | OMIA:001252-8843 | domestic goose | Gang, China (Goose (domestic)) | Feather colour, recessive white | EDNRB2 | insertion, small (<=20) | Naturally occurring variant | no | AnsCyg_PRJNA183603_v1.0 | g.750748_750735insCACAGGTGAGCTCT | "NW_013185915.1: g. 750,748-750,735 insertion. CACAGGTGAGCTCT" (Xi et al., 2020) | 2020 | 32066369 | |||||||
| 1 | OMIA:000240-8932 | rock pigeon | Crest | EPHB2 | cr | missense | Naturally occurring variant | no | c.???C>T | p.(R758C) | 2013 | 23371554 | ||||||||
| 148 | OMIA:000361-9783 | Asiatic elephant | Factor VII deficiency | F7 | missense | Naturally occurring variant | yes | c.202A>G | p.(R68G) | 2017 | 28118558 | |||||||||
| 983 | OMIA:000439-9844 | llama | Long hair | FGF5 | complex rearrangement | Naturally occurring variant | no | A "a single base deletion (c.348delA), [and] a 12-bp insertion (c.351_352insCATATAACATAG)" that comprise a single likely causal variant | 2017 | 29024003 | ||||||||||
| 347 | OMIA:000439-9793 | ass | Hair, long | FGF5 | nonsense (stop-gain) | Naturally occurring variant | no | c.245G>A | 2014 | 25927731 | ||||||||||
| 982 | OMIA:000439-10141 | domestic guinea pig | Long hair | Fgf5 | nonsense (stop-gain) | Naturally occurring variant | no | c.403C>T | p.(R135*) | "The data were submitted to the European Variation Archive (accession no. PRJEB24997)" | 2018 | 29603294 | ||||||||
| 560 | OMIA:000439-9793 | ass | Hair, long | FGF5 | deletion, small (<=20) | Naturally occurring variant | no | c.433_434delAT | 2014 | 25927731 | ||||||||||
| 984 | OMIA:000439-9844 | llama | Long hair | FGF5 | nonsense (stop-gain) | Naturally occurring variant | no | c.499C>T | 2017 | 29024003 | ||||||||||
| 1343 | OMIA:000439-9838 | Arabian camel | Long hair | FGF5 | missense | Naturally occurring variant | no | CamDro3 | 2 | g.76625546C>T | c.779C>T | p.(P260L) | cDNA and protein positions based on transcript ENSCDRT00005003721.1 | 2021 | 34432312 | |||||
| 517 | OMIA:000578-9544 | Rhesus monkey | Krabbe disease | GALC | deletion, small (<=20) | Naturally occurring variant | yes | c.387delAC | 1997 | 9192853 | ||||||||||
| 190 | OMIA:001473-9915 | 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 | |||||||||
| 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 | |||||
| 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 | |||||||||
| 1525 | OMIA:001652-9627 | red fox | Platinum coat colour | KIT | splicing | Naturally occurring variant | yes | G>A variant in the first nucleotide of KIT intron 17 causes skipping of exon 17 | 2015 | 25662789 | ||||||||||
| 566 | OMIA:001737-9838 | Arabian camel | Coat colour, white spotting, KIT-related | KIT | deletion, small (<=20) | Naturally occurring variant | no | c.1842delG | p.(M614Ifs*5) | 2017 | 28282952 | |||||||||
| 403 | OMIA:000209-494514 | Arctic fox | Coat colour, dominant white | KIT | splicing | Naturally occurring variant | no | c.1867+1G>T | 2013 | 24308634 | ||||||||||
| 405 | OMIA:001737-9793 | ass | Coat colour, white spotting, due to KIT | KIT | Ws | splicing | Naturally occurring variant | no | c.1978+2T>A | 2015 | 25818843 | |||||||||
| 1102 | OMIA:000209-30538 | alpaca | Classic grey coat colour | KIT | missense | Naturally occurring variant | no | c.376G>A | p.(G126R) | 2019 | 31297861 | |||||||||
| 150 | OMIA:000209-9793 | ass | Coat colour, dominant white | KIT | W | missense | Naturally occurring variant | no | c.662A>C | p.(Y221S) | 2015 | 25818843 | ||||||||
| 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 | |||||
| 1152 | OMIA:002237-8090 | Japanese medaka | Few melanophore | kitlga | insertion, gross (>20) | Naturally occurring variant | no | Otsuki et al. (2020): "the phenotype of fm medaka is attributable to insertion of a Tcb1-like transposon at the kitlga locus" | 2020 | 31757930 | ||||||||||
| 1046 | OMIA:001701-13146 | budgerigar | Feater colour, blue | LOC101880715 | missense | Naturally occurring variant | no | 1 | p.(R644W) | 2017 | 28985565 | |||||||||
| 605 | OMIA:001721-32536 | cheetah | Coat colour, king | LVRN | insertion, small (<=20) | Naturally occurring variant | no | p.(N977Kfs*110) | 2012 | 22997338 | ||||||||||
| 518 | OMIA:000185-452646 | American mink | Chediak-Higashi syndrome | LYST | deletion, small (<=20) | Naturally occurring variant | yes | c.9468delC | 2013 | 22762706 | ||||||||||
| 1359 | OMIA:002449-94885 | corn snake | Skin colour, lavender | LYST | nonsense (stop-gain) | Naturally occurring variant | no | c.9508C>T | p.(Q3169*) | 2020 | 33020272 | |||||||||
| 249 | OMIA:000625-10141 | domestic guinea pig | Mannosidosis, alpha | Man2b1 | missense | Naturally occurring variant | yes | c.679C>T | p.(R227W) | 2002 | 11959458 | |||||||||
| 674 | OMIA:001199-30640 | gray squirrel | Melanism (black) | MC1R | E^B | deletion, gross (>20) | Naturally occurring variant | no | MC1RΔ24 allele E^B ["at amino acid positions 87-94"] | 2009 | 19643815 | |||||||||
| 1007 | OMIA:001199-10141 | domestic guinea pig | Brown coat colour | MC1R | e (MC1R*4) | deletion, gross (>20) | Naturally occurring variant | no | Vidal (2018): "a deletion of 2760 bp, including the entire MC1R coding region" | 2018 | 30101449 | |||||||||
| 250 | OMIA:001199-46844 | Geoffroy's cat | Melanism (black coat) | MC1R | missense | Naturally occurring variant | no | p.(C125R) | 2015 | 25695801 | ||||||||||
| 1002 | OMIA:002156-46218 | Chinese painted quail | Feather colour, Blue Face | MC1R | missense | Naturally occurring variant | no | p.(E92K) | 2018 | 29974967 | ||||||||||
| 1328 | OMIA:000374-495946 | Eleonora's falcon | Feather colour, extended black | MC1R | deletion, small (<=20) | Naturally occurring variant | no | p.(M114_V117del) | 2011 | 21696477 | ||||||||||
| 1100 | OMIA:000374-57662 | red-footed booby | White plumage | MC1R | haplotype | Naturally occurring variant | no | p.(M85V) + p.(R207H) | 2007 | 17602182 | ||||||||||
| 1003 | OMIA:002155-46218 | Chinese painted quail | Feather colour, Red Breasted | MC1R | missense | Naturally occurring variant | no | p.(P292L) | 2018 | 29974967 | ||||||||||
| 1173 | OMIA:001199-37349 | woolly mammoth | Light hair colour | MC1R | missense | Naturally occurring variant | no | p.(R67C) | 2006 | 16825562 | ||||||||||
| 1101 | OMIA:000374-70340 | Lesser snow goose | Blue plumage | MC1R | missense | Naturally occurring variant | no | p.(V85M) | 2004 | 15031505 | ||||||||||
| 262 | OMIA:001199-494514 | Arctic fox | Blue coat colour | MC1R | Ed | missense | Naturally occurring variant | no | p.[(G5C);(F280C)] | The blue (Ed) allele is a haplotype comprising two missense variants (p.Gly5Cys and p.Phe280Cys) (Våge et al., 2005) | 2005 | 15982782 | ||||||||
| 1271 | OMIA:001199-30532 | fallow deer | White coat colour | MC1R | missense | Naturally occurring variant | no | c.143T>C | p.(L48P) | NM_174108.2:c.143T>C; NP_776533.1:p.(L48P) | 2020 | 33213385 | ||||||||
| 180 | OMIA:001199-9870 | reindeer | Coat colour, extension | MC1R | missense | Naturally occurring variant | no | c.218T>C | p.(M73T) | 2014 | 25039753 | |||||||||
| 1350 | OMIA:001199-9915 | zebu | Guzerat (Cattle) | Red | MC1R | deletion, small (<=20) | Naturally occurring variant | no | c.311delT | p.(G104Vfs*) | 2021 | 34555208 | ||||||||
| 18 | OMIA:001494-9103 | turkey | Feather colour, dominant black | MC1R | missense | Naturally occurring variant | no | c.364A>T | p.(I122F) | 2010 | 20634512 | |||||||||
| 1329 | OMIA:000374-120794 | gyrfalcon | Feather colour, extended black | MC1R | missense | Naturally occurring variant | no | c.376A>G | p.(I126V) | 2012 | 22497627 | |||||||||
| 996 | OMIA:001199-9793 | ass | Âne normand, France (Ass) Miniature, United States of America (Ass) | Red coat colour | MC1R | e | missense | Naturally occurring variant | no | c.629T>C | p.(M210T) | 2014 | 25155046 | |||||||
| 1006 | OMIA:001199-10141 | domestic guinea pig | Brown coat colour | MC1R | e (MC1R*2) | missense | Naturally occurring variant | no | c.749T>C | p.(L250Q) | 2018 | 30101449 | ||||||||
| 181 | OMIA:001199-9870 | reindeer | Coat colour, extension | MC1R | missense | Naturally occurring variant | no | c.839T>G | p.(F280C) | 2014 | 25039753 | |||||||||
| 1351 | OMIA:001199-9915 | zebu | Sahiwal (Cattle) | Red | MC1R | missense | Naturally occurring variant | no | c.844C>A | p.(T281 N) | 2021 | 33512595 | ||||||||
| 1346 | OMIA:001199-37190 | antarctic fur seal | Hypopigmentation (blond) | MC1R | missense | Naturally occurring variant | unknown | c.872C>T | p.(S291F) | 2016 | 27547348 | |||||||||
| 19 | OMIA:001494-9103 | turkey | Feather colour, black-wing bronze | MC1R | missense | Naturally occurring variant | no | c.887C>T | p.(A296V) | 2010 | 20634512 | |||||||||
| 1009 | OMIA:001199-9838 | Arabian camel | White coat colour | MC1R | missense | Naturally occurring variant | no | c.901C>T | p.(R301C) | KU179867; c.901C>T; p.R301C | 2018 | 29893870 | ||||||||
| 328 | OMIA:001494-9103 | turkey | Bronze feathers | MC1R | nonsense (stop-gain) | Naturally occurring variant | no | c.96G>A | 2010 | 20634512 | ||||||||||
| 115 | OMIA:001199-9627 | red fox | Coat colour, extension | MC1R | E^A | missense | Naturally occurring variant | no | VulVul2.2 | NW_020356486.1 | g.6101019T>C | c.373T>C | p.(C125R) | XM_026005028.1; XP_025860813.1 | 1997 | 9054949 | ||||
| 1287 | OMIA:002309-9646 | giant panda | Cataract | MIP | missense | Naturally occurring variant | yes | c.686G>A | p.(S229N) | 2021 | 33530927 | |||||||||
| 341 | OMIA:000214-89462 | water buffalo | Swamp buffalo (Buffalo) | White spotting | MITF | nonsense (stop-gain) | Naturally occurring variant | no | c.328C>T | p.(R110*) | 2015 | 26417640 | ||||||||
| 409 | OMIA:000214-89462 | water buffalo | Swamp buffalo (Buffalo) | White spotting | MITF | splicing | Naturally occurring variant | no | c.840+2T>A | 2015 | 26417640 | |||||||||
| 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 | ||||||||
| 672 | OMIA:000031-452646 | American mink | Coat colour, silver-blue | MLPH | deletion, gross (>20) | Naturally occurring variant | no | deletion of exon 8 | 2013 | 23747352 | ||||||||||
| 1204 | OMIA:000031-452646 | American mink | Silverblue | MLPH | p | splicing | Naturally occurring variant | no | MusPutFur1.0.86 | g.662639G>A | c.901+1G>A | GL896909.1:662639 G/A (MLPH C.901 + 1 G > A) (Manakhov et al., 2019) | 2019 | 30872653 | ||||||
| 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 | ||||||||||
| 1064 | OMIA:002189-8932 | rock pigeon | Barless | NDP | c | start-lost | Naturally occurring variant | no | Cliv_1.0 | Vickrey et al. (2018): "a nonsynonymous protein-coding change at the start codon of NDP". | 2018 | 30014848 | ||||||||
| 747 | OMIA:001771-7091 | domestic silkworm | "Ming" lethal egg | NEWENTRY | complex rearrangement | Naturally occurring variant | yes | an ~1.9 kb region from the 3' untranslated region of BmVMP23 to the forepart of BmEP80 was replaced by a >100 kb DNA fragment | 2013 | 23262333 | ||||||||||
| 865 | OMIA:002130-94885 | corn snake | Coat colour, oculocutaneous albinism, OCA2-related | OCA2 | insertion, gross (>20) | Naturally occurring variant | yes | LTR retrotransposon in the 11th intron | 2015 | 26597053 | ||||||||||
| 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 | ||||||||
| 1212 | OMIA:002270-8932 | rock pigeon | Feathered shank | PITX1 | deletion, gross (>20) | Naturally occurring variant | no | "a 44-kb deletion (from 6.719–6.763 Mb)" (Domyan et al., 2016) | 2016 | 26977633 | ||||||||||
| 540 | OMIA:001545-30521 | domestic yak | Coat colour, dilution | PMEL | deletion, small (<=20) | Naturally occurring variant | no | c.50_52del | p.(L18del) | 2014 | 24989079 | |||||||||
| 845 | OMIA:000483-30521 | domestic yak | Polled, Mongolian allele | POLLED | P[sub]M or P[sub]219ID | complex rearrangement | Naturally occurring variant | no | "a complex 219-bp duplication-insertion (P219ID) beginning at 1,976,128 bp and a 7-bp deletion and 6-bp insertion (P1ID) located 621 bp upstream of this position . . . . This rearrangement results in duplication of an 11-bp motif (5'-AAAGAAGCAAA-3') that is entirely conserved among Bovidae . . . and that is also duplicated in the 80-kb duplication responsible for Friesian polledness" | 2017 | 28135247 | |||||||||
| 977 | OMIA:000380-9103 | turkey | Feathering, Z-linked | PRLR | deletion, small (<=20) | Naturally occurring variant | unknown | Turkey_5.1 | Z | g.9426018_9426022delTTGGT | p.(E726Dfs*7) | 2018 | 29566646 | |||||||
| 1507 | OMIA:000944-447135 | Bank vole | Susceptibility to atypical scrapie | PRNP | missense | Naturally occurring variant | yes | p.(M109I) | 2022 | 35731839 | ||||||||||
| 1256 | OMIA:002292-452646 | American mink | Moyle coat colour | RAB38 | deletion, small (<=20) | Naturally occurring variant | no | NNQGG.v01 | 1 | g.16075438_16075453del | c.574-589del | "We identified a homozygous 16-bp deletion [FNWR01000007.1:16075438–16075453del (RAB38:c.574-589del)], hereinafter referred to as RAB383del, in the Moyle sample, at the third exon of RAB38 gene. We found a homozygous 2-bp duplication NWR01000007.1:16132224_16132225dupCT (RAB38:c.20-21dup)], hereinafter referred to as RAB381dup, in the Violet sample, at the first exon of the RAB38 gene. Both mutations potentially resulted in the loss of function of RAB38 protein" (Manakhov et al., 2020) | 2020 | 32985525 | ||||||
| 1257 | OMIA:002292-452646 | American mink | Moyle coat colour | RAB38 | duplication | Naturally occurring variant | no | NNQGG.v01 | 1 | g.16132224_16132225dupCT | c.20-21dup | "We identified a homozygous 16-bp deletion [FNWR01000007.1:16075438–16075453del (RAB38:c.574-589del)], hereinafter referred to as RAB383del, in the Moyle sample, at the third exon of RAB38 gene. We found a homozygous 2-bp duplication NWR01000007.1:16132224_16132225dupCT (RAB38:c.20-21dup)], hereinafter referred to as RAB381dup, in the Violet sample, at the first exon of the RAB38 gene. Both mutations potentially resulted in the loss of function of RAB38 protein" (Manakhov et al., 2020) | 2020 | 32985525 | ||||||
| 1099 | OMIA:002209-7950 | Atlantic herring | Adaptation to a red-shifted light environment | rho | missense | Naturally occurring variant | no | p.(F261Y) | 2019 | 31451650 | ||||||||||
| 1349 | OMIA:001308-8932 | rock pigeon | Short beak | ROR2 | Ku2 | missense | Naturally occurring variant | no | Cliv_2.1 | c.1087C>T | Genomic position on scaffold ScoHet5_445.1:6568443; non-reference allele causes an arginine-to-cysteine substitution in the seventh exon of ROR2 (Boer et al., 2021) | 2021 | 34551284 | |||||||
| 1427 | OMIA:002531-74940 | Chinook salmon | XY female | sdY | missense | Naturally occurring variant | yes | p.(I183N) | 2022 | 35100376 | ||||||||||
| 1298 | OMIA:002416-8932 | rock pigeon | Pearl-eye | SLC2A11B | tr | nonsense (stop-gain) | Naturally occurring variant | no | AKCR02000030.1 | g.1895934G>A | p.(W49X) | Andrade et al. (2021): "This mutation creates a premature STOP codon in exon 3 of the likely canonical SLC2A11B transcript." | 2021 | 33621224 | ||||||
| 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 | ||||||||||
| 1530 | OMIA:002628-215402 | northern snakehead | Skin colour, yellow | SLC45A2 | YM | nonsense (stop-gain) | Naturally occurring variant | no | 19 | c.383G>A | p.(W128*) | 2023 | 36789536 | |||||||
| 254 | OMIA:000213-74535 | Bengal tiger | Coat colour, white | SLC45A2 | missense | Naturally occurring variant | no | C>T | p.(A477V) | 2013 | 23707431 | |||||||||
| 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 | |||||
| 1537 | OMIA:002651-499056 | Asian vine snakes | Skin colour, yellow | SMARCE1 | missense | Naturally occurring variant | no | 4 | g.43233281C>T | c.58C>T | p.(P20S) | 2023 | 36895044 | |||||||
| 1065 | OMIA:002190-8932 | rock pigeon | Recessive red | SOX10 | e^1 | deletion, gross (>20) | Naturally occurring variant | no | Domyan et al. (2014) reported a 7.5kb deletion that spans "a conserved enhancer element that drives Sox10 expression in melanocytes" | 2014 | 24508169 | |||||||||
| 1066 | OMIA:002190-8932 | rock pigeon | Recessive red | SOX10 | e^2 | deletion, gross (>20) | Naturally occurring variant | no | Domyan et al. (2014) reported a 2.5kb deletion that spans "a conserved enhancer element that drives Sox10 expression in melanocytes" | 2014 | 24508169 | |||||||||
| 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 | |||||
| 1348 | OMIA:002431-9694 | tiger | Pseudomelamism | Taqpep | missense | Naturally occurring variant | no | PanTig1.0 | A1 | c.1360C>T | p.H454Y | Sagar et al. (2021): "[Assembly PanTig1.0(GCF_000464555.1)]. . . . (Taqpep c.1360C > T); XP_007086933.1) of the protein (Taqpep p.H454Y)" | 2021 | 34518374 | ||||||
| 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 | ||||||||||
| 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 | ||||||||||
| 1122 | OMIA:002213-9447 | Ring-tailed lemur | Bitter taste | TAS2R16 | missense | Naturally occurring variant | no | p.(S282L) | 2019 | 31161904 | ||||||||||
| 1277 | OMIA:001972-9793 | ass | Non-dun | TBX3 | deletion, small (<=20) | Naturally occurring variant | no | 8 | g.42742557delT | "This 1 bp deletion (chr8:g.42742556 CT>C−) is located ~18.6 kb downstream of the transcription start site of the TBX3 gene." (Wang et al., 2020) | 2020 | 33293529 | ||||||||
| 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 | |||||||||
| 1339 | OMIA:002385-7950 | Atlantic herring | Spring spawning | tshr | missense | Naturally occurring variant | no | Ch_v2.0.2 | 15 | g.8906859C>A | c.1411C>A | p.(L471M) | cDNA position based on transcript ENSCHAT00000005367.1 | 2021 | 34172814 | |||||
| 666 | OMIA:000202-9669 | domestic ferret | Coat colour, albinism | TYR | deletion, gross (>20) | Naturally occurring variant | yes | "deletion of exon 4" | 2007 | 17655555 | ||||||||||
| 723 | OMIA:000202-8090 | Japanese medaka | Coat colour, albinism | tyr | 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 | ||||||||||
| 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 | ||||||||||
| 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 | ||||||||||
| 1162 | OMIA:000202-9557 | hamadryas baboon | Siamese coat colour pattern | TYR | missense | Naturally occurring variant | no | p.(A365T) | ENSPANT00000015629.2:c.1093G>A; A0A096MRE4:p.(Ala365Thr) [Koga et al., 2020] | 2020 | 32053406 | |||||||||
| 813 | OMIA:000202-8410 | Japanese wrinkled frog | Albinism | TYR | missense | Naturally occurring variant | yes | c.1127G>A | p.(G376D) | 2018 | 28674275 | |||||||||
| 814 | OMIA:000202-8409 | dark-spotted frog | Albinism | TYR | insertion, small (<=20) | Naturally occurring variant | yes | c.1244_1245insT | 2018 | 28674275 | ||||||||||
| 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 | |||||||||
| 812 | OMIA:000202-1772025 | Rice frog | Albinism | TYR | missense | Naturally occurring variant | yes | c.169G>A | p.(G57R) | 2018 | 28674275 | |||||||||
| 260 | OMIA:000202-452646 | American mink | Himalayan | TYR | missense | Naturally occurring variant | no | c.1835C>G | p.(H420Q) | 2009 | 19308642 | |||||||||
| 1011 | OMIA:000202-9689 | lion | White lion | TYR | missense | Naturally occurring variant | no | c.260G>A | p.(R87Q) | 2013 | 24045858 | |||||||||
| 151 | OMIA:000202-9793 | ass | Coat colour, albinism | TYR | missense | Naturally occurring variant | yes | c.604C>G | p.(H202D) | 2016 | 26763160 | |||||||||
| 355 | OMIA:000202-9515 | Tufted capuchin | Coat colour, albinism | TYR | nonsense (stop-gain) | Naturally occurring variant | yes | c.64C>T | p.(R22*) | 2017 | 28476152 | |||||||||
| 816 | OMIA:000202-8409 | dark-spotted frog | Albinism | TYR | deletion, small (<=20) | Naturally occurring variant | yes | c.682_684del | p.(L228del) | 2018 | 28674275 | |||||||||
| 1004 | OMIA:000202-10141 | domestic guinea pig | Coat colour, albinism | Tyr | missense | Naturally occurring variant | no | c.710A>G | p.(D237G) | PRJEB26285 | 2018 | 29947431 | ||||||||
| 815 | OMIA:000202-8409 | dark-spotted frog | Albinism | TYR | insertion, small (<=20) | Naturally occurring variant | yes | c.768_769insT | 2018 | 28674275 | ||||||||||
| 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 | ||||||||
| 1159 | OMIA:000202-9860 | red deer | White | TYR | missense | Naturally occurring variant | no | CerEla 1.0 | 2 | c.871G>A | p.(G291R) | 2020 | 32041521 | |||||||
| 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 | |||||
| 1255 | OMIA:001249-452646 | American mink | American Palomino coat colour | TYRP1 | b^p | insertion, gross (>20) | Naturally occurring variant | no | "a large insertion of approximately eight kb. The insertion most likely disrupts different elements necessary for the splicing of intron 2 of the TYRP1 gene" (Cicera et al., 2016) | 2016 | 26886941 | |||||||||
| 753 | OMIA:002061-345164 | Saker falcon | Feather colour, light brown | TYRP1 | complex rearrangement | Naturally occurring variant | no | c.79C>T and c.79_80insT | in exon 1, resulting in "a frameshift change and a premature stop codon at position 81 of the deduced protein sequence, which in the wild-type form contains 536 amino acids. | 2017 | 27611661 | |||||||||
| 1518 | OMIA:001249-9643 | American black bear | Cinnamon coat colour | TYRP1 | missense | Naturally occurring variant | no | HiC_scaffold_24 | g.6724152G>A | p.(R153C) | 2023 | 36528024 |
| Overall Statistics | |
|---|---|
| Total number of variants | 155 |
| Variants with genomic location | 26 (16.8% ) |
| Variants in a variant database, i.e. with rs ID | 1 (0.6%) |
| Variant Type | Count | Percent |
|---|---|---|
| complex rearrangement | 6 | 3.9% |
| deletion, gross (>20) | 12 | 7.7% |
| deletion, small (<=20) | 22 | 14.2% |
| delins, gross (>20) | 1 | 0.6% |
| duplication | 1 | 0.6% |
| haplotype | 7 | 4.5% |
| insertion, gross (>20) | 6 | 3.9% |
| insertion, small (<=20) | 6 | 3.9% |
| inversion | 1 | 0.6% |
| missense | 64 | 41.3% |
| nonsense (stop-gain) | 16 | 10.3% |
| regulatory | 1 | 0.6% |
| repeat variation | 1 | 0.6% |
| splicing | 9 | 5.8% |
| start-lost | 1 | 0.6% |
| synonymous | 1 | 0.6% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1992 | 1 | 0.6% |
| 1993 | 0 | 0.0% |
| 1994 | 0 | 0.0% |
| 1995 | 1 | 0.6% |
| 1996 | 0 | 0.0% |
| 1997 | 3 | 1.9% |
| 1998 | 4 | 2.6% |
| 1999 | 2 | 1.3% |
| 2000 | 1 | 0.6% |
| 2001 | 2 | 1.3% |
| 2002 | 3 | 1.9% |
| 2003 | 0 | 0.0% |
| 2004 | 1 | 0.6% |
| 2005 | 3 | 1.9% |
| 2006 | 1 | 0.6% |
| 2007 | 2 | 1.3% |
| 2008 | 3 | 1.9% |
| 2009 | 9 | 5.8% |
| 2010 | 3 | 1.9% |
| 2011 | 1 | 0.6% |
| 2012 | 6 | 3.9% |
| 2013 | 9 | 5.8% |
| 2014 | 9 | 5.8% |
| 2015 | 10 | 6.5% |
| 2016 | 5 | 3.2% |
| 2017 | 11 | 7.1% |
| 2018 | 20 | 12.9% |
| 2019 | 9 | 5.8% |
| 2020 | 13 | 8.4% |
| 2021 | 13 | 8.4% |
| 2022 | 6 | 3.9% |
| 2023 | 4 | 2.6% |