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43 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
1001 OMIA:001271-9796 horse Miniature Horse (Horse) Dwarfism, ACAN-related ACAN D4 deletion, small (<=20) Naturally occurring variant yes EquCab3.0 1 g.95257480_95257500del c.7633_7653del p.(F2545_D2551del) 220110: corrected genomic position from g.95257458_95257500del to 95257480_95257500 and updated cDNA and published protein coordinates (p.(F2017_D2023del)) based on the following transcripts: ENSECAT00000040213.1:c.7633_7653del ENSECAP00000032890.1:p.Phe2545_Cys2551del rs1095048839 2018 30058072
788 OMIA:001271-9796 horse Miniature Horse (Horse) Shetland Pony (Horse) Dwarfism, ACAN-related ACAN D3* missense Naturally occurring variant yes EquCab3.0 1 g.95282140C>G c.1513G>C p.(A505P) ENSECAT00000040213.1:c.1513G>C ENSECAP00000032890.1:p.Ala505Pro This variant was named D3* by Eberth et al. (2018) rs1095048823 rs1095048823 2017 27942904 Variant coordinates obtained from Eberth et al. (2018) and EVA_ID link
1000 OMIA:001271-9796 horse Miniature Horse (Horse) Dwarfism, ACAN-related ACAN D2 missense Naturally occurring variant yes EquCab3.0 1 g.95284530C>T p.(V424M) rs3091781465 2018 30058072
999 OMIA:001271-9796 horse Miniature Horse (Horse) Dwarfism, ACAN-related ACAN D1 deletion, small (<=20) Naturally occurring variant yes EquCab3.0 1 g.95291271del c.245del p.(K82Rfs*54) 220110: changed g.95291270del to g.95291271del based on HGVS 3'rule. ENSECAT00000040213.1:c.245del ENSECAP00000032890.1:p.Lys82ArgfsTer54 rs1095048841 rs1095048841 2018 30058072
436 OMIA:000991-9796 horse Quarter Horse (Horse) Androgen insensitivity syndrome (AIS) AR regulatory Naturally occurring variant yes EquCab3.0 X g.52728703A>G c.1A>G NM_001163891.1; NP_001157363.1; mutation in start codon 2012 22095250 The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022
1143 OMIA:000991-9796 horse Tennessee Walking Horse (Horse) Androgen insensitivity syndrome (AIS) AR deletion, small (<=20) Naturally occurring variant yes EquCab3.0 X g.52728885del c.183del p.(R63Gfs) NM_001163891.1; NP_001157363.1; published as c.183delT and p.(Ser61fs); c. and p. information in the table has been updated to HGVS nomenclature 2020 31936796 The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022
783 OMIA:000991-9796 horse Androgen insensitivity syndrome AR deletion, gross (>20) Naturally occurring variant yes EquCab3.0 X g.52808634_52808658del c.1630_1654del NM_001163891.1; NP_001157363.1; the deletion is predicted to create a frameshift: "resulting in altered amino acid composition from p.543Lys and a premature stop codon 44 amino acid residues downstream in exon 3" 2017 28192783
786 OMIA:000991-9796 horse Thoroughbred (Horse) Androgen insensitivity syndrome AR missense Naturally occurring variant yes EquCab3.0 X g.52872393G>C c.2042G>C p.(W681S) NM_001163891.1; NP_001157363.1 2016 27073903 The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022; p. coordinates obtained from Villagomez et al. (2019)
1144 OMIA:000991-9796 horse Thoroughbred (Horse) Androgen insensitivity syndrome (AIS) AR missense Naturally occurring variant yes EquCab3.0 X g.52878093C>T c.2132C>T p.(A711V) NM_001163891.1; NP_001157363.1 2020 31936796
348 OMIA:000487-9796 horse Belgian Draft (Horse) Friesian (Horse) Hydrocephalus B3GALNT2 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 1 g.76887901C>T c.1423C>T p.(Q475*) XM_001491545; XP_001491595; Ducro et al. (2015): "The nomenclature for the mutation is c.1423C>T [GenBank:XM_001491545] corresponding to p.Gln475* [GenBank:XP_001491595]". As at 25 April 2019, Ensembl's Variant Effect Predictor (VEP) gives the EquCab3 c. and p. coordinates as having not changed from the EquCab2 coordinates reported by Ducro et al. (2015). The Ensembl ref is ENSECAT00000049072 rs3429464524 rs3429464524 2015 26452345 c. and p. variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. EquCab3 g. coordinate provided by Meredith O’Connell, working under the supervision of Professor Ernie Bailey, 24 April 2019
421 OMIA:002068-9796 horse Friesian (Horse) Dwarfism, Friesian B4GALT7 splicing Naturally occurring variant yes EquCab3.0 14 g.3772591C>T c.50G>A p.(R17K) rs3447120064 2016 27793082 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. FN thanks Elizabeth Huffman, who updated the g. coordinates to EquCab3, working under the supervision of Professor Ernie Bailey; 23 April 2020.
161 OMIA:000698-9796 horse New Forest Pony (Horse) Myotonia CLCN1 missense Naturally occurring variant yes EquCab3.0 4 g.96518592A>C c.1775A>C p.(D592A) c.1775A>C, Genbank acc. XM_001915636); p.D592A, Genbank acc. XP_001915671 (Wijnberg et al., 2014) rs5334475185 2012 22197188 (FN thanks Izabela De Assis Rocha, who provided genomic location in EquCab3.0 and the Genbank acc IDs, working under the supervision of Professor Ernie Bailey; 15 April 2020) Revised genomic location kindly provided by Cord Drögemüller; 21 May 2021
167 OMIA:000735-9796 horse Belgian Draft (Horse) Connemara Pony (Horse) Haflinger (Horse) Rocky Mountain, United States of America (Bighorn sheep) Ocular squamous cell carcinoma DDB2 missense Naturally occurring variant yes EquCab3.0 12 g.11726667C>T c.1013C>T p.(T338M) The EquCab2 coordinates, obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool, are g.11608667, c.1013C>T and p.T338M rs1139682898 rs1139682898 2017 28425625 The EquCab3 g. coordinates were provided by by Meredith O’Connell, working under the guidance of Professor Ernie Bailey, 5 March 2019
160 OMIA:000629-9796 horse American Paint (Horse) Miniature Horse (Horse) Quarter Horse (Horse) Thoroughbred (Horse) Megacolon EDNRB frame overo delins, small (<=20) Naturally occurring variant yes EquCab3.0 17 g.50503041_50503042delinsCT c.353_354delinsAG p.(I118K) NM_001081837.2; NP_001075306.2 1998 9530628
322 OMIA:000420-9796 horse American Paint (Horse) Quarter Horse (Horse) Glycogen storage disease IV GBE1 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 26 g.8667651C>A c.102C>A p.(Y34*) NM_001081940.2; NP_001075409.1 rs3437568674 rs3437568674 2004 15366377 The genomic position in EquCab3.0 was provided by Elizabeth Clark, working under the guidance of Professor Ernie Bailey in April 2022
1552 OMIA:002692-9796 horse American Saddle Horse (Horse) American Trotter (Horse) Miniature Horse (Horse) Missouri Fox Trotting Horse, United States of America (Horse) Morgan (Horse) Quarter Horse (Horse) Racking Horse (Horse) Rocky Mountain, United States of America (Horse) Spotted Saddle Horse (Horse) Tennessee Walking Horse (Horse) Night blindness, congenital stationary, GRM6-related GRM6 missense Naturally occurring variant yes EquCab3 14 g.2655618C>T c.533C>T p.(T178M) XM_001916934.4; XP_001916969.3; variant initially reported in Tennessee Walking horse and later reported in other breeds [PMID:37815029] rs1138010744 rs1138010744 2021 32654228
163 OMIA:001158-9796 horse American Paint (Horse) Appaloosa (Horse) Quarter Horse (Horse) Polysaccharide storage myopathy/Exertional rhabdomyolysis GYS1 missense Naturally occurring variant yes EquCab3.0 10 g.19203501C>T c.926G>A p.(R309H) ENSECAT00000023453.3:c.926G>A ENSECAP00000019426.2:p.Arg309His rs1150416011 rs1150416011 2008 18358695 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
691 OMIA:000081-9796 horse Arab (Horse) Atlanto occipital fusion HOXD3 deletion, gross (>20) Naturally occurring variant yes 18 "a 2.7-kb deletion located 4.4 kb downstream of the end of HOXD4 and 8.2 kb upstream of the start of HOXD3." 2017 28111759
337 OMIA:001899-9796 horse Quarter Horse (Horse) Incontinentia pigmenti IKBKG nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 X g.126898409C>T c.202C>T p.(R68*) rs3433281055 2013 24324710 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
164 OMIA:001000-9796 horse Quarter Horse (Horse) Thoroughbred (Horse) Thrombasthenia ITGA2B missense Naturally occurring variant yes EquCab3.0 11 g.19245752G>C c.215G>C p.(R72P) NM_001081793.1; NP_001075262.1; originally published as p.(R41P) and listed by Leite et al. (2019) as c.122G>C; coordinates in this table have been updated to a recent reference genome and / or transcript 2006 16407493
512 OMIA:001000-9796 horse Peruvian Paso (Horse) Quarter Horse (Horse) Thrombasthenia ITGA2B deletion, small (<=20) Naturally occurring variant yes EquCab3.0 11 g.19247983_19247992del g.19247983_19247992delCAGGTGAGGA 2007 17338169 g. coordinates obtained from Dahlgren et al. (2020)
658 OMIA:001677-9796 horse American Saddle Horse (Horse) Epidermolysis bullosa, junctionalis, LAMA3-related LAMA3 deletion, gross (>20) Naturally occurring variant yes 8 "6589-bp deletion spanning exons 24-27 . . . in the LAMA3 gene in American Saddlebred foals" 2009 19016681
599 OMIA:001678-9796 horse Belgian Draft (Horse) Breton, France (Horse) Cavallo Agricolo Italiano da Tiro Pesante Rapido, Italy (Horse) Comtois (Horse) Epidermolysis bullosa, junctionalis, LAMC2-related LAMC2 insertion, small (<=20) Naturally occurring variant yes EquCab3.0 5 g.17498175dup c.1372dup p.(R458Pfs) NM_001081768.1; NP_001075237.1; published as c.1368insC; coordinates in the table have been updated to HGVS nomenclature (3'-rule) and recent reference genome and / or transcript inforamtion 1,372 Protein position: 458 2002 12230513 The genomic position in EquCab3.0 was provided by Margaret Higgins, working under the guidance of Professor Ernie Bailey [April 2022]
437 OMIA:000175-9796 horse Arab (Horse) Bashkir Curly (Horse) Trakehner (Horse) Welsh Pony (Horse) Cerebellar abiotrophy MUTYH not known Naturally occurring variant yes EquCab3.0 2 g.13122415C>T c.541-13539C>T ENSECAT00000009202.3:c.541-13539C>T ENSECAT00000024892.2:c.284G>A ENSECAP00000020698.1:p.Arg95His A SNP "located in exon 4 of TOE1 and approximately 1200 base pairs upstream of MUTYH, adjacent to a possible binding site for the transcription factor GATA2" (Brault et al., 2011). EquCab3.1 coordinate provided by Meredith O’Connell, working under the supervision of Professor E. Bailey. rs397160943 rs397160943 2011 21126570
973 OMIA:002141-9796 horse Quarter Horse (Horse) Immune-mediated myositis MYH1 missense Naturally occurring variant yes EquCab3.0 11 g.53345548T>C p.(E321G) The location of this likely causal variant was given as chr11:52,993,878T>C by Finno et al. (2018) in relation to the EquCab2.0 assembly. Applying NCBI's remap gives the EquCab3.0 coordinate as chr11:53,345,548 rs3435577028 2018 29510741
510 OMIA:001501-9796 horse Arab (Horse) Lavender foal syndrome MYO5A deletion, small (<=20) Naturally occurring variant yes EquCab3.0 1 g.139290592del c.4249del p.(R1417Afs*13) XM_023617258.1; XP_023473026.1; published as g.138235715delC; coordinates in the table have been updated to a recent reference genome 2010 20419149 The genomic position in EquCab3.0 was provided by Gracie Zinsmeister, working under the guidance of Professor Ernie Bailey in April 2022
1605 OMIA:001688-9796 horse Purebred Spanish (Horse) Splashed white PAX3 SW10 nonsense (stop-gain) Naturally occurring variant unknown EquCab3.0 6 g.11196181G>A c.583C>T p.(R195*) XM_005610643.3; XP_005610700.1; association with increased depigmentation, published as c.927C>T 2023 37406837
791 OMIA:001688-9796 horse Lipizzan horse (Horse) Noric (Horse) Quarter Horse (Horse) Splashed white PAX3 SW2 missense Naturally occurring variant no EquCab3.0 6 g.11199026C>T c.209G>A p.(C70Y) rs5334475189 2012 22511888 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
978 OMIA:001688-9796 horse Appaloosa (Horse) Splashed white PAX3 SW4 missense Naturally occurring variant no EquCab3.0 6 g.11199140G>C c.95C>G p.(P32R) rs5334475206 2013 23659293
165 OMIA:001982-9796 horse Thoroughbred (Horse) Warmblood breeds Fragile Foal Syndrome PLOD1 missense Naturally occurring variant yes EquCab3.0 2 g.39927817C>T c.2032G>A p.(G678R) rs1136065234 rs1136065234 2015 25637337 rsID and Variant coordinates obtained from Zhang et al. (2020): "g.39927817C>T (rs1136065234; NC_009145.3, Equ-Cab3.0)" c. and p. coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
903 OMIA:001438-9796 OMIA:000733-9796 horse American Miniature Horse (Horse) Ardennes (Horse) Comtois (Horse) Iceland Pony (Horse) Missouri Fox Trotter, Germany (Horse) Morgan (Horse) Rocky Mountain, United States of America (Bighorn sheep) Coat colour, silver AND Multiple congenital ocular anomalies PMEL missense Naturally occurring variant no EquCab3.0 6 g.74569773G>A c.1849C>T p.(R617C) NM_001163889.1; NP_001157361.1; previously listed in OMIA as g.73665304 and published a C (wild type) to T (Silver) transition, p.Arg618Cys, as well as p.(R625C); coordinates in this table have been updated to a recent reference genome and / or transcript rs3448111155 rs3448111155 2006 17029645 The genomic position in EquCab3.0 was provided by Mary Katherine Easterwood, working under the guidance of Professor Ernie Bailey in April 2022
157 OMIA:000327-9796 horse Quarter Horse (Horse) Ehlers-Danlos syndrome PPIB missense Naturally occurring variant yes EquCab3.0 1 g.129307092G>A c.115G>A p.(G39R) rs396329681 rs396329681 2007 17498917 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
511 OMIA:000220-9796 horse Arab (Horse) Severe combined immunodeficiency disease, autosomal PRKDC deletion, small (<=20) Naturally occurring variant yes EquCab3.0 9 g.36395752_36395759del c.9478_9482del p.(N3160fs*3) A 5bp deletion giving rise to a frameshift in PRKDC The following details (from which the coordinate fields were populated) were provided by Meredith O’Connell, Tanya German, Isabella Pisani and Karalie Andrews, under the supervision of Professor Ernie Bailey. 20 Feb 2019 NC_009152.3 g.36395752-36395976del; NM_001163858 c.9478_9482del; NP_001157330 p.N3160fs*3 rs5334475184 1997 9103416
1369 OMIA:002458-9796 horse Thoroughbred (Horse) Hypoparathyroidism RAPGEF5 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 4 g.54108297G>T c.2624C>A p.(S875*) 2020 32986719
159 OMIA:000621-9796 horse Quarter Horse (Horse) Malignant hyperthermia RYR1 missense Naturally occurring variant yes EquCab3.0 10 g.9678680C>G c.7363C>G p.(R2455G) XM_023649662.1; XP_023505430.1; published as c.7360C>G and p.(R2454G); coordinates in the table have been updated to a recent reference genome and / or transcript 2004 15318347 The genomic position in EquCab3.0 was provided by Hailey Anderson, working under the guidance of Professor Ernie Bailey in April 2022
162 OMIA:000785-9796 horse Quarter Horse (Horse) HYPP SCN4A H missense Naturally occurring variant yes EquCab3.0 11 g.15474228C>G c.4248C>G p.(F1416L) NM_001081761.1; NP_001075230.1; ECA11 (NC_009154.3) g.15474228C>G; NM_001081761.1: c.4248C>G; NP_001075230.1: F1416L; Sift Score 0.01. The above information (from which the coordinate fields were populated) was provided by Tatyana German and Meredith O’Connell, working under the supervision of Professor Ernie Bailey. rs1148998534 rs1148998534 1992 1338908
965 OMIA:001897-9796 horse Connemara Pony (Horse) Hoof wall separation syndrome SERPINB11 insertion, small (<=20) Naturally occurring variant yes EquCab3.0 8 g.83600643_83600644insC c.504_505insC p.(T169Hfs*3) rs3447216148 2015 25875171 FN thanks Daniel J. Schmidt, working under the supervision of Professor Ernie Bailey, for updating the coordinates to EquCab3.0.
686 OMIA:002013-9796 horse Shetland Pony (Horse) Skeletal atavism SHOX Del-1 deletion, gross (>20) Naturally occurring variant yes PAR 160−180 kb deletion in the pseudoautosomal region (PAR) of chromosome X/Y; removing the entire coding region of the short stature homeobox (SHOX) gene and parts of the cytokine receptor-like factor 2 (CRLF2) gene located downstream of SHOX 2016 27207956
1455 OMIA:002013-9796 horse Shetland Pony (Horse) Skeletal atavism SHOX Del-2 deletion, gross (>20) Naturally occurring variant yes PAR 60−80 kb deletion in the pseudoautosomal region (PAR) of chromosome X/Y; removing parts of the cytokine receptor-like factor 2 (CRLF2) gene located downstream of SHOX 2016 27207956
158 OMIA:001578-9796 horse Dales (Horse) Fell Pony (Horse) Foal immunodeficiency syndrome in the Fell and Dales Pony SLC5A3 missense Naturally occurring variant yes EquCab3.0 26 g.31894278C>T c.1352C>T p.(P451L) NM_001247992.1; NP_001234921.1; previously listed in OMIA as g.30660224G>T in EquCab2.0, c.1337G>T and published as p.(P446L); coordinates in the table have been updated to a recent reference genome and / or transcript 2011 21750681 Briana Moreno, working under the guidance of Professor Ernie Bailey, provided genomic coordinates in EquCab3.0 in April 2022
659 OMIA:001230-9796 horse American Trotter (Horse) XY sex reversal SRY deletion, gross (>20) Naturally occurring variant yes Y "at least the DNA-binding domain of the SRY gene was deleted from the Y chromosome of the XY mare" 1995 7558880
354 OMIA:002096-9796 horse Akhal-Teke (Horse) Naked foal syndrome ST14 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 7 g.39710628G>T c.388G>T p.(E130*) XM_005611718.2 (c.388G>T); XP_005611775.1 (p.(E130*)) rs5334475187 2017 28235824 (FN thanks Emily Rogers for providing the genomic location (determined using BLAT with the XM_005611718.2 sequence against Equcab 3.0) and the sequence refs for the cDNA and protein variants, working under the supervision of Professor Ernie Bailey; 24 April 2020)
725 OMIA:001341-9796 OMIA:002139-9796 horse American Miniature Horse (Horse) Appaloosa (Horse) British Spotted Pony, Spotted Pony, United Kingdom of Great Britain and Northern Ireland (Horse) English Spotted Pony, Australia (Horse) Knabstrupper (Horse) Noric (Horse) Pony Of the Americas, Germany (Horse) Thoroughbred (Horse) Stationary congenital night blindness & Leopard Complex/Appaloosa spotting TRPM1 insertion, gross (>20) Naturally occurring variant no EquCab2.0 1 g.108297929_108297930insN[1378] "a 1378 bp retroviral LTR insertion in intron 1 of TRPM1" 2013 24167615
Overall Statistics
Total number of variants 43
Variants with genomic location 38 (88.4% )
Variants in a variant database, i.e. with rs ID 13 (30.2%)
Variant Type Count Percent
deletion, gross (>20) 6 14.0%
deletion, small (<=20) 6 14.0%
delins, small (<=20) 1 2.3%
insertion, gross (>20) 1 2.3%
insertion, small (<=20) 2 4.7%
missense 18 41.9%
nonsense (stop-gain) 6 14.0%
not known 1 2.3%
regulatory 1 2.3%
splicing 1 2.3%
Year First Reported Count Percent
1992 1 2.3%
1993 0 0.0%
1994 0 0.0%
1995 1 2.3%
1996 0 0.0%
1997 1 2.3%
1998 1 2.3%
1999 0 0.0%
2000 0 0.0%
2001 0 0.0%
2002 1 2.3%
2003 0 0.0%
2004 2 4.7%
2005 0 0.0%
2006 2 4.7%
2007 2 4.7%
2008 1 2.3%
2009 1 2.3%
2010 1 2.3%
2011 2 4.7%
2012 3 7.0%
2013 3 7.0%
2014 0 0.0%
2015 3 7.0%
2016 4 9.3%
2017 5 11.6%
2018 4 9.3%
2019 0 0.0%
2020 3 7.0%
2021 1 2.3%
2022 0 0.0%
2023 1 2.3%