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69 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 Year Published PubMed ID(s) Acknowledgements
1060 OMIA:001271-9915 indicine cattle (zebu) Miniature Zebu, United Kingdom of Great Britain and Northern Ireland (Cattle) Bulldog calf ACAN insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 21 g.20428539_20428540insC c.5688_5689insC p.(V1897fs*9) cDNA position based on transcript NM_173981.2 2018 30305023
1076 OMIA:001645-10036 golden hamster Black tremor Atrn insertion, gross (>20) Naturally occurring variant yes Kuramoto et al. (2002): "an approximately 10-kb DNA fragment, which had 557-bp direct repeats in both ends and was flanked by the identical 6-bp target duplication sequences, [that] was inserted into exon 24" 2002 11773967
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
1490 OMIA:002573-151761 yellow-crowned parrot Lewy body-like disease CADPS2 missense Naturally occurring variant yes c.1675G>C p.(V559L) 2022 36086934
490 OMIA:000685-9915 indicine cattle (zebu) Brahman (Cattle) Myasthenic syndrome, congenital, CHRNE-related CHRNE 470del20 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.26485848_26485867del c.470_489del Kraner et al. (2002): "a loss of 20 bp within the coding sequence of exon 5 (Fig. 2), between nucleotide 469 and 490 (nucleotide numbering referring to the cDNA sequence published under accession number X02597". These authors (and subsequent authors) call this variant "470del20". The current (2020) HGVS nomenclature is c.470_489del 200922: g. information move here (g.27119615) until standardised 2002 12481987 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
399 OMIA:000698-89462 water buffalo Murrah (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
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
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
148 OMIA:000361-9783 Asiatic elephant Factor VII deficiency F7 missense Naturally occurring variant yes c.202A>G p.(R68G) 2017 28118558
559 OMIA:000439-10036 golden hamster Hair, long Fgf5 deletion, small (<=20) Naturally occurring variant no c.546delG p.(R184GfsX6) 2015 26481120
517 OMIA:000578-9544 Rhesus monkey Krabbe disease GALC deletion, small (<=20) Naturally occurring variant yes c.387delAC 1997 9192853
190 OMIA:001473-9915 indicine cattle (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
1584 OMIA:001243-9601 Sumatran orangutan Alkaptonuria HGD missense Naturally occurring variant yes Susiae_PABv2/ponAbe3 3 g.17314095G>A c.1081G>A p.(G361R) 2023 37354891
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
1622 OMIA:002763-9541 crab-eating macaque Severe combined immunodeficiency disease IL2RG nonsense (stop-gain) Base-editing yes Macaca_fascicularis_5.0 X g.68110639G>A c.391C>T p.(Q131*) XM_005593892.2; XP_005593949.1 2023 37661226
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
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
1556 OMIA:000499-9544 Rhesus monkey Hypercholesterolaemia LDLR nonsense (stop-gain) Naturally occurring variant yes 19 p.(W284*) G>A in exon 6 in position 914 of the human cDNA resulting in p.(W284*) 1990 2326270
1557 OMIA:000499-9544 Rhesus monkey Hypercholesterolaemia LDLR missense Naturally occurring variant yes 19 c.245G>A p.(C82Y) 2023 37186395
1672 OMIA:002796-9541 crab-eating macaque Cardiomyopathy, dilated, LMNA-related LMNA splicing Base-editing yes MFA1912RKSv2 1 NC_052255.1:g.93546791T>C XM_045371898.1:c.357-2A>G 2024 38559624
518 OMIA:000185-452646 American mink Chediak-Higashi syndrome LYST deletion, small (<=20) Naturally occurring variant yes c.9468delC 2013 22762706
249 OMIA:000625-10141 domestic guinea pig Mannosidosis, alpha Man2b1 missense Naturally occurring variant yes c.679C>T p.(R227W) 2002 11959458
1287 OMIA:002309-9646 giant panda Cataract MIP missense Naturally occurring variant yes c.686G>A p.(S229N) 2021 33530927
385 OMIA:001401-10036 golden hamster Waardenburg syndrome, type 2A MITF splicing Naturally occurring variant yes A T>A base substitution in intron 6 of MITF leads to the skipping of exon 7 and a premature termination. 2003 12871913
505 OMIA:000755-93934 Japanese quail Osteopetrosis MITF deletion, small (<=20) Naturally occurring variant yes same MITF variant as for silver, as reported in 1998 2001 11169846
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
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
316 OMIA:000545-93934 Japanese quail Hypotrophic axonopathy NEFL nonsense (stop-gain) Naturally occurring variant yes c.352C>T p.(Q114*) 1993 8468353
1602 OMIA:002130-9544 Rhesus monkey Coat colour, oculocutaneous albinism OCA2 missense Naturally occurring variant yes c.2363C>T p.(S788L) 2020 32259106
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
1507 OMIA:000944-447135 Bank vole Susceptibility to atypical scrapie PRNP missense Naturally occurring variant yes p.(M109I) 2022 35731839
1621 OMIA:002763-9541 crab-eating macaque Severe combined immunodeficiency disease RAG1 nonsense (stop-gain) Base-editing yes Macaca_fascicularis_5.0 14 g.30840789G>T c.181C>T p.(Q61*) XM_005578172.2; XP_005578229.1 2023 37661226
1427 OMIA:002531-74940 Chinook salmon XY female sdY missense Naturally occurring variant yes p.(I183N) 2022 35100376
651 OMIA:000162-10036 golden hamster Cardiomyopathy, dilated SGCD deletion, gross (>20) Naturally occurring variant yes genomic deletion was found to be located at 6.1 kb 5' upstream of the second exon of δ-SG gene, and its 5' upstream region of more than 27.4 kb, including the authentic first exon of δ-SG gene, was deleted 1997 9391120
652 OMIA:002211-10036 golden hamster Cardiomyopathy, hypertrophic SGCD deletion, gross (>20) Naturally occurring variant yes a large deletion in the delta-SG gene 1997 9097966
386 OMIA:000370-93934 Japanese quail Feather colour, albinism, sex-linked, imperfect SLC45A2 splicing Naturally occurring variant yes a splice-site mutation in the SLC45A2 gene: "a G → T transversion at the splice acceptor site just preceding exon 4" 2007 17151254
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
259 OMIA:000370-93934 Japanese quail Feather colour, cinnamon SLC45A2 missense Naturally occurring variant no c.287C>A p.(A72D) 2007 17151254
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
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
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
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
1620 OMIA:000240-8839 Mallard Crest cushion TAS2R40 regulatory Naturally occurring variant unknown 1 published as variant in the 5′UTR of TAS2R40 (123272114_c. G78A) 2023 37652165
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
666 OMIA:000202-9669 domestic ferret Coat colour, albinism TYR deletion, gross (>20) Naturally occurring variant yes "deletion of exon 4" 2007 17655555
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
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
723 OMIA:000202-8090 Japanese medaka Skin colour, albinism tyr i1 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
1555 OMIA:000202-8090 Japanese medaka Skin colour, albino (weak) tyr i(b) insertion, gross (>20) Naturally occurring variant yes a 4.7-kb insertion in the 5' untranslated region (Tol2) 2004 15016305
1554 OMIA:000202-8090 Japanese medaka Skin colour, albino (quasi-albino) tyr i4 insertion, gross (>20) Naturally occurring variant yes a 4.7-kb insertion in exon 5 (Tol2-tyr) 1996 8779712
1599 OMIA:000202-9544 Rhesus monkey Coat colour, golden TYR missense Naturally occurring variant no 14 p.(H256Q) 2023 37522525
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
260 OMIA:000202-452646 American mink Himalayan TYR missense Naturally occurring variant no c.1835C>G p.(H420Q) 2009 19308642
1600 OMIA:000202-9544 Rhesus monkey Coat colour, oculocutaneous albinism TYR nonsense (stop-gain) Naturally occurring variant yes 14 c.552C>A p.(S184*) 2000 10751629
355 OMIA:000202-9515 Tufted capuchin Coat colour, albinism TYR nonsense (stop-gain) Naturally occurring variant yes c.64C>T p.(R22*) 2017 28476152
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
1601 OMIA:000202-9544 Rhesus monkey Coat colour, oculocutaneous albinism TYR missense Naturally occurring variant yes 14 c.934C>A p.(L312I) 2020 32259106
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
Overall Statistics
Total number of variants 69
Variants with genomic location 15 (21.7% )
Variants in a variant database, i.e. with rs ID 0 (0.0%)
Variant Type Count Percent
complex rearrangement 2 2.9%
deletion, gross (>20) 6 8.7%
deletion, small (<=20) 12 17.4%
insertion, gross (>20) 5 7.2%
insertion, small (<=20) 3 4.3%
missense 21 30.4%
nonsense (stop-gain) 11 15.9%
regulatory 1 1.4%
repeat variation 1 1.4%
splicing 7 10.1%
Year First Reported Count Percent
1990 1 1.4%
1991 0 0.0%
1992 1 1.4%
1993 1 1.4%
1994 0 0.0%
1995 1 1.4%
1996 1 1.4%
1997 3 4.3%
1998 0 0.0%
1999 0 0.0%
2000 1 1.4%
2001 3 4.3%
2002 5 7.2%
2003 1 1.4%
2004 1 1.4%
2005 2 2.9%
2006 0 0.0%
2007 3 4.3%
2008 3 4.3%
2009 2 2.9%
2010 0 0.0%
2011 0 0.0%
2012 2 2.9%
2013 3 4.3%
2014 1 1.4%
2015 1 1.4%
2016 0 0.0%
2017 4 5.8%
2018 6 8.7%
2019 4 5.8%
2020 4 5.8%
2021 1 1.4%
2022 6 8.7%
2023 7 10.1%
2024 1 1.4%