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91 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1001 | OMIA:001271-9796 | horse | Miniature Horse (Horse) | Dwarfism, ACAN-related | ACAN | D4 | deletion, gross (>20) | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.952574879_95257499del | XM_005602799.2:c.7633_7653del | XP_005602856.2:p.(F2545_C2551del) | Genomic positions were previosuly incorreclty listed in OMIA as g.95257458_95257500del (until 10/01/2022) and g.95257480_95257500del (until 13/06/2024). Coordinates presented now reflect the published rs1095048839. |
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 | NC_009144.3:g.95282140C>G | XM_023650286.1:c.1513G>C | XP_023506054.1:p.(A505P) | ENSECAT00000040213.1:c.1513G>C ENSECAP00000032890.1:p.Ala505Pro This variant was named D3* by Eberth et al. (2018) | rs1095048823 | 2017 | 27942904 | Variant coordinates obtained from Eberth et al. (2018) and EVA_ID link |
1000 | OMIA:001271-9796 | horse | Miniature Horse (Horse) Quarter Horse (Horse) Warmblood (Horse) | Dwarfism, ACAN-related | ACAN | D2 | missense | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.95284530C>T | XP_023506054.1:c.1270C>T | XP_023506054.1:p.(V424M) | rs3091781465 | 2018 | 30058072 | Breed information updated based on PMID: 38600096 | |
999 | OMIA:001271-9796 | horse | Miniature Horse (Horse) | Dwarfism, ACAN-related | ACAN | D1 | deletion, small (<=20) | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.95291271del | XM_023650281.1:c.245del | XP_023506054.1:p.(K82Rfs*54) | 220110: changed g.95291270del to g.95291271del based on HGVS 3'rule. ENSECAT00000040213.1:c.245del ENSECAP00000032890.1:p.Lys82ArgfsTer54 | rs1095048841 | 2018 | 30058072 | |
436 | OMIA:000991-9796 | horse | Quarter Horse (Horse) | Androgen insensitivity syndrome (AIS) | AR | regulatory | Naturally occurring variant | yes | EquCab3.0 | X | NC_009175.3:g.52728703A>G | NM_001163891.1:c.1A>G | mutation in start codon for NP_001157363.1; | 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 | NC_009175.3:g.52728885del | NM_001163891.1:c.183del | NP_001157363.1:p.(R63Gfs) | 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 | Warmblood (Horse) | Androgen insensitivity syndrome | AR | deletion, gross (>20) | Naturally occurring variant | yes | EquCab3.0 | X | NC_009175.3:g.52808634_52808658del | NM_001163891.1:c.1630_1654del | 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 | NC_009175.3:g.52872393G>C | NM_001163891.1:c.2042G>C | NP_001157363.1:p.(W681S) | 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 | NC_009175.3:g.52878093C>T | NM_001163891.1:c.2132C>T | NP_001157363.1:p.(A711V) | 2020 | 31936796 | ||||
348 | OMIA:000487-9796 | horse | Belgian Draft (Horse) Friesian (Horse) Warmblood (Horse) | Hydrocephalus | B3GALNT2 | nonsense (stop-gain) | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.76887901C>T | XM_001491545.6:c.1423C>T | XP_001491595.2: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 | 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. Breed information updated based on PMID: 38600096 | |
421 | OMIA:002068-9796 | horse | Friesian (Horse) | Dwarfism, Friesian | B4GALT7 | splicing | Naturally occurring variant | yes | EquCab3.0 | 14 | NC_009157.3:g.3772591C>T | XM_023617086.1:c.50G>A | XP_023472854.1: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 | NC_009147.3:g.96518592A>C | XM_001915636.4:c.1775A>C | XP_001915671.3: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) Welsh Pony (Horse) | Ocular squamous cell carcinoma | DDB2 | missense | Naturally occurring variant | yes | EquCab3.0 | 12 | NC_009155.3:g.11726667C>T | XM_023654000.1:c.1013C>T | XP_023509768.1: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 | 2017 | 28425625 | The EquCab3 g. coordinates were provided by by Meredith O’Connell, working under the guidance of Professor Ernie Bailey, 5 March 2019. Breed information updated based on PMID: 38600096 | |
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 | NC_009160.3:g.50503041_50503042delinsCT | NM_001081837.2:c.353_354delinsAG | NP_001075306.2: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 | NC_009169.3:g.8667651C>A | NM_001081940.2:c.102C>A | NP_001075409.1:p.(Y34*) | NM_001081940.2; NP_001075409.1 | 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 | EquCab3.0 | 14 | NC_009157.3:g.2655618C>T | XM_001916934.4:c.533C>T | XP_001916969.3:p.(T178M) | XM_001916934.4; XP_001916969.3; variant initially reported in Tennessee Walking horse and later reported in other breeds [PMID:37815029] | rs1138010744 | 2021 | 32654228 | ||
163 | OMIA:001158-9796 | horse | American Paint (Horse) Appaloosa (Horse) Belgian Draft (Horse) Quarter Horse (Horse) | Polysaccharide storage myopathy/Exertional rhabdomyolysis | GYS1 | missense | Naturally occurring variant | yes | EquCab3.0 | 10 | NC_009153.3:g.19203501C>T | NM_001126125.2:c.926G>A | NP_001119597.2:p.(R309H) | ENSECAT00000023453.3:c.926G>A ENSECAP00000019426.2:p.Arg309His | rs1150416011 | 2008 | 18358695 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. Breed information updated based on PMID: 38600096 | |
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) Warmblood (Horse) | Incontinentia pigmenti | IKBKG | nonsense (stop-gain) | Naturally occurring variant | yes | EquCab3.0 | X | NC_009175.3:g.126898409C>T | NM_001284533.1:c.184C>T | NP_001271462.1:p.(R62*) | Previously listed as as c.202C>T and p.(R68*), updated in this table to reflect NM_001284533.1 transcript | rs3433281055 | 2013 | 24324710 | Breed information updated based on PMID: 38600096 | |
164 | OMIA:001000-9796 | horse | Quarter Horse (Horse) Thoroughbred (Horse) | Thrombasthenia | ITGA2B | missense | Naturally occurring variant | yes | EquCab3.0 | 11 | NC_009154.3:g.19245752G>C | NM_001081793.1:c.215G>C | NP_001075262.1: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 | NC_009154.3:g.19247983_19247992del | g.19247983_19247992delCAGGTGAGGA | 2007 | 17338169 | g. coordinates obtained from Dahlgren et al. (2020) | ||||
1331 | OMIA:000209-9796 | horse | American Paint (Horse) American Trotter (Horse) Belgian Draft (Horse) Icelandic Horse (Horse) Quarter Horse (Horse) Thoroughbred (Horse) Welsh Pony (Horse) | White spotting | KIT | W32 | missense | Naturally occurring variant | unknown | EquCab3.0 | 3 | NC_009146.3:g.79538738C>T | NM_001163866.1:c.2878G>A | NP_001157338.1:p.(A960T) | cDNA position previously listed as c.3214G>A; p.(A1072T) based on transcript ENSECAT00000014037.3 [16/04/2024] | rs1141982296 | 2021 | 34223905 | Breed information updated based on PMID: 38600096 |
882 | OMIA:000209-9796 | horse | Süddeutsches Kaltblut, Germany (Horse) | Coat colour, dominant white | KIT | W11 | splicing | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79540429C>T | NM_001163866.1:c.2684+1G>A | rs5334475183 | 2009 | 19456317 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
939 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W26 | deletion, small (<=20) | Naturally occurring variant | unknown | EquCab3.0 | 3 | NC_009146.3:g.79540694del | NM_001163866.1:c.2536del | NP_001157338.1:p.(S846Vfs*15) | NM_001163866.1; NP_001157338.1; published as c.2536delA | rs3101685403 | 2018 | 29333746 | |
873 | OMIA:000209-9796 | horse | Oldenburg (Horse) | Coat colour, dominant white | KIT | W16 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79540741T>A | NM_001163866.1:c.2489A>T | NP_001157338.1:p.(K830I) | rs5334475213 | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
883 | OMIA:000209-9796 | horse | Miniature Horse (Horse) Quarter Horse (Horse) Shetland Pony (Horse) | Coat colour, dominant white | KIT | W13 | splicing | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79544066C>G | NM_001163866.1:c.2472+5G>C | NM_001163866.1 | rs3102773259 | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
889 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W14 | deletion, gross (>20) | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79544098_79544151del | NM_001163866.1:c.2392_2445del | NP_001157338.1:p.(H798_N815del) | NM_001163866.1; NP_001157338.1 | 2011 | 21554354 | genomic coordinates updated from g.79544151_79544204del to g.79544098_79544151del in EquCab3.0 [17/09/2023] | |
891 | OMIA:000209-9796 | horse | Icelandic Horse (Horse) | White spotting | KIT | W21 | deletion, small (<=20) | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79544174del | NM_001163866.1:c.2369delC | NP_001157338.1:p.(A790Efs*20) | rs5334475210 | 2015 | 26059442 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
885 | OMIA:000209-9796 | horse | Appaloosa (Horse) Haflinger (Horse) Lipizzan horse (Horse) Noric (Horse) Quarter Horse (Horse) | Coat colour, dominant white | KIT | sabino 1 (SB1) | splicing | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79544206A>T | "SNP AX-103727726 (ECA3:77735520; SB1, SNP KI16+1037A)" (Druml et al., 2018) | rs5334475211 | 2005 | 16284805 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
893 | OMIA:000209-9796 | horse | Trottatore Italiano, Italy (Horse) | Coat colour, dominant white | KIT | W24 | splicing | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79545245C>T | NM_001163866.1:c.2349+1G>A | rs3443588955 | 2017 | 28856698 | |||
1462 | OMIA:000209-9796 | horse | American Trotter (Horse) | Dominant white spotting | KIT | W33 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79545248T>A | NM_001163866.1:c.2347A>T | NP_001157338.1:p.(N783Y) | NC_009146.3; previously listed as ENSECAT00000014037.3: c.2783A>T / p.(N895Y) [16/04/2024] | 2022 | 35641888 | ||
881 | OMIA:000209-9796 | horse | Icelandic Horse (Horse) | Coat colour, dominant white | KIT | W8 | splicing | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79545374C>T | NM_001163866.1:c.2222-1G>A | NM_001163866.1 | rs3434854925 | 2009 | 19456317 | ||
886 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W5 | deletion, small (<=20) | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79545900del | NM_001163866.1:c.2193delG | NP_001157338.1:p.(T732Qfs*9) | rs5334475194 | 2009 | 19456317 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
878 | OMIA:000209-9796 | horse | Freiberger (Horse) | Coat colour, dominant white | KIT | W1 | nonsense (stop-gain) | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79545942G>C | NM_001163866.1:c.2151C>G | NP_001157338.1:p.(Y717*) | rs5334475201 | 2007 | 17997609 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
877 | OMIA:000209-9796 | horse | American Paint (Horse) American Trotter (Horse) Appaloosa (Horse) Arab (Horse) Belgian Draft (Horse) Clydesdale (Horse) Freiberger (Horse) German Riding Pony (Horse) Morgan (Horse) Noric (Horse) Oldenburg (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Thoroughbred (Horse) Tori hobune, Estonia (Horse) Traditional Gypsy Cob, United Kingdom of Great Britain and Northern Ireland (Horse) Warmblood (Horse) Welsh Pony (Horse) | Coat colour, dominant white | KIT | W20 | missense | Naturally occurring variant | unknown | EquCab3.0 | 3 | NC_009146.3:g.79548220T>C | NM_001163866.1:c.2045G>A | NP_001157338.1:p.(R682H) | ENSECAT00000014037.3:c.2381A>G ENSECAP00000011188.2:p.His794Arg; reference genome corresponds to g.79548220T and the transcript NM_001163866.1 represents g.79548220C | rs1143160924 | 2013 | 23659293 | Variant coordinates initially gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124. Breed information updated based on PMID: 38600096 |
875 | OMIA:000209-9796 | horse | Japanese Draft, Japan (Horse) | Coat colour, dominant white | KIT | W17b | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79548244A>G | NM_001163866.1:c.2021T>C | NP_001157338.1:p.(L674P) | rs5334475224 | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
1261 | OMIA:000209-9796 | horse | Berber, Germany (Horse) | Extensive coat white patterning | KIT | W30 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79548244A>T | NM_001163866.1:c.2021T>A | NP_001157338.1:p.(L674H) | published as g.79548244, c.2020T>A; p.L674H (Martin et al., 2020) - changed to NM_001163866.1:c.2021T>A [16/042024] | rs5334475224 | 2020 | 33111383 | |
874 | OMIA:000209-9796 | horse | Japanese Draft, Japan (Horse) | Coat colour, dominant white | KIT | w17a | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79548265T>A | NM_001163866.1:c.2000A>T | NP_001157338.1:p.(E667D) | previously listed as c.2001A>T [16/04/2024] | rs5334475222 | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 |
890 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | White spotting | KIT | W22 | deletion, gross (>20) | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79548925_79550822del | 1898bp deletion | 2017 | 28444912 | ||||
868 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W2 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79549540C>T | NM_001163866.1:c.1960G>A | NP_001157338.1:p.(G654R) | rs5334475198 | 2007 | 17997609 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
869 | OMIA:000209-9796 | horse | Camarillo White Horse, United States of America (Horse) | Coat colour, dominant white | KIT | W4 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79549781G>A | NM_001163866.1:c.1805C>T | NP_001157338.1:p.(A602V) | Previously incorrectly listed as g.79549780G>A [16/04/2024] | 2007 | 17997609 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
871 | OMIA:000209-9796 | horse | Holsteiner (Horse) | Coat colour, dominant white | KIT | W9 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79549797C>T | NM_001163866.1:c.1789G>A | NP_001157338.1:p.(G597R) | rs5334475209 | 2009 | 19456317 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
872 | OMIA:000209-9796 | horse | Arab (Horse) | Coat colour, dominant white | KIT | W15 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79550351A>G | NM_001163866.1:c.1597T>C | NP_001157338.1:p.(C533R) | rs5334475202 | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
940 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W27 | missense | Naturally occurring variant | unknown | EquCab3.0 | 3 | NC_009146.3:g.79551937A>C | NM_001163866.1:c.1473T>G | NP_001157338.1:p.(C491W) | NM_001163866.1; NP_001157338.1 | rs3110307743 | 2018 | 29333746 | |
884 | OMIA:000209-9796 | horse | CH-Warmblut, Switzerland (Horse) | Coat colour, dominant white | KIT | W18 | splicing | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79553751C>T | NM_001163866.1:c.1346+1G>A | rs5334475221 | 2013 | 23659293 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
876 | OMIA:000209-9796 | horse | Arab (Horse) | Coat colour, dominant white | KIT | W19 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79553776T>C | NM_001163866.1:c.1322A>G | NP_001157338.1:p.(Y441C) | rs5334475217 | 2013 | 23659293 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
1476 | OMIA:000209-9796 | horse | American Paint (Horse) American Trotter (Horse) Appaloosa (Horse) Arab (Horse) Mangalarga (Horse) Morgan (Horse) Mustang (Horse) Quarter Horse (Horse) Rocky Mountain, United States of America (Bighorn sheep) Warmblood (Horse) | Increased white spotting | KIT | W34 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79566881T>C | NM_001163866.1:c.1171A>G | NP_001157338.1:p.(T391A) | Previously listed as ENSECAT00000014037.3:c.1495A>G; ENSECAP00000011188.2:p.(T499A) [16/04/2024] | rs1140732842 | 2022 | 35953947 | Breed information updated based on PMID: 38600096 |
887 | OMIA:000209-9796 | horse | Quarter Horse (Horse) | Coat colour, dominant white | KIT | W10 | deletion, small (<=20) | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79566923_79566926del | NM_001163866.1:c.1126_1129del | NP_001157338.1:p.(E376Ffs*3) | NM_001163866.1; NP_001157338.1; published as c.1126_1129delGAAC | 2009 | 19456317 | Genomic coordinates updated in this table from g.79566926_79566929del in EquCab3.0 after feedback from Micaela Vierra identified that these coordinates were incorrect [27/09/2023]. | |
870 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W6 | missense | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79573754C>T | NM_001163866.1:c.856G>A | NP_001157338.1:p.(G286R) | rs5334475167 | 2009 | 19456317 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
892 | OMIA:000209-9796 | horse | Arab (Horse) | White spotting | KIT | W23 | splicing | Naturally occurring variant | unknown | EquCab3.0 | 3 | NC_009146.3:g.79578484C>G | NM_001163866.1:c.756+1G>C | rs1095048836 | 2017 | 28378922 | |||
879 | OMIA:000209-9796 | horse | Arab (Horse) | Coat colour, dominant white | KIT | W3 | nonsense (stop-gain) | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79578535T>A | NM_001163866.1:c.706A>T | NP_001157338.1:p.(K236*) | rs5334475200 | 2007 | 17997609 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
938 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W25 | missense | Naturally occurring variant | unknown | EquCab3.0 | 3 | NC_009146.3:g.79578573A>G | NM_001163866.1:c.668T>C | NP_001157338.1:p.(L223P) | NM_001163866.1; NP_001157338.1 | rs3103992630 | 2018 | 29333746 | |
888 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W12 | deletion, small (<=20) | Naturally occurring variant | unknown | EquCab3.0 | 3 | NC_009146.3:g.79579774_79579778del | NM_001163866.1:c.559_563del | NP_001157338.1:p.(S187Rfs*10) | NM_001163866.1; NP_001157338.1; published as c.559_563delTCTGC | rs5334475188 | 2010 | Reference not in PubMed; see OMIA 000209-9796 for reference details | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 |
1091 | OMIA:000209-9796 | horse | German Riding Pony (Horse) | White spotting | KIT | W28 | deletion, gross (>20) | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79579925_79581197del | 2019 | 31463981 | |||||
880 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W7 | splicing | Naturally occurring variant | no | EquCab3.0 | 3 | NC_009146.3:g.79580000C>G | NM_001163866.1:c.338-1G>C | rs5334475216 | 2009 | 19456317 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
1330 | OMIA:000209-9796 | horse | Quarter Horse (Horse) | White spotting | KIT | W31 | insertion, small (<=20) | Naturally occurring variant | unknown | EquCab3.0 | 3 | NC_009146.3:g.79618532_79618533insA | NM_001163866.1:c.30_31insT | NP_001157338.1:p.(L11Sfs*115) | 2021 | 34223905 | |||
658 | OMIA:001677-9796 | horse | American Saddle Horse (Horse) | Epidermolysis bullosa, junctionalis, LAMA3-related | LAMA3 | deletion, gross (>20) | Naturally occurring variant | yes | EquCab3.0 | 8 | NC_009151.3:g.48678342_48684920del | "6589-bp deletion spanning exons 24-27 . . . in the LAMA3 gene in American Saddlebred foals" | 2009 | 19016681 | Coordinates in EquCab3.0 kindly provided by Haley Rutstein, working under the guidance of Professor Ernie Bailey. | ||||
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 | NC_009148.3:g.17498175dup | NM_001081768.1:c.1372dup | NP_001075237.1: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] | ||
1023 | OMIA:000214-9796 | horse | American Paint (Horse) | White spotting, blue eyes and deafness | MITF | SW5 | deletion, gross (>20) | Naturally occurring variant | yes | EquCab3.0 | 16 | NC_009159.3:g.21503211_21566617del | "~63-kb deletion spanning exons 6-9 of the MITF gene" | 2019 | 30644113 | ||||
1180 | OMIA:000214-9796 | horse | American Paint (Horse) | Splashed white | MITF | SW6 | deletion, gross (>20) | Naturally occurring variant | no | EquCab3.0 | 16 | NC_009159.3:g.21551060_21559770del | NC_009159.3:g.21551060-21559770del (Magdesian et al., 2020) | 2020 | 32242630 | ||||
1626 | OMIA:000214-9796 | horse | Thoroughbred (Horse) | Splashed white | MITF | SW8 | deletion, gross (>20) | Naturally occurring variant | yes | EquCab3.0 | 16 | NC_009159.3:g.21555811_21558139delinsAAAT | 2023 | 37697831 | |||||
166 | OMIA:000214-9796 | horse | American Trotter (Horse) | White | MITF | MITF^244Glu | missense | Naturally occurring variant | no | EquCab3.0 | 16 | NC_009159.3:g.21556522C>T | NM_001163874.1:c.1031G>A | NP_001157346.1:p.(G344E) | Published as XM_005600318.1:c.731G>A; XP_005600375.1:p.Gly244Glu) - updated in this table to reflect recent transcript ID | rs3435075789 | 2017 | 27592871 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 |
1606 | OMIA:000214-9796 | horse | Purebred Spanish (Horse) | Splashed white | MITF | SW9 | missense | Naturally occurring variant | yes | EquCab3.0 | 16 | NC_009159.3:g.21559940T>A | NM_001163874.1:c.961A>T | NP_001157346.1:p.(N321Y) | NM_001163874.1; NP_001157346.1; published as c.993A>T, variant associated with increased depigmentation | 2023 | 37406837 | ||
1488 | OMIA:000214-9796 | horse | American Paint (Horse) Quarter Horse (Horse) | Splashed white | MITF | SW7 | deletion, small (<=20) | Naturally occurring variant | yes | EquCab3.0 | 16 | NC_009159.3:g.21559953_21559955del | NM_001163874.1:c.949_951del | NP_001157346.1:p.R317del | NM_001163874.1; NP_001157346.1; published as c.949_951delTCT | 2022 | 35672910 | ||
156 | OMIA:000214-9796 | horse | Freiberger (Horse) | Macchiato | MITF | macchiato | missense | Naturally occurring variant | no | EquCab3.0 | 16 | NC_009159.3:g.21564980T>C | NM_001163874.1:c.629A>G | NP_001157346.1:p.(N310S) | rs5334475186 | 2012 | 22511888 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
793 | OMIA:000214-9796 | horse | Quarter Horse (Horse) | Splashed white | MITF | SW3 | deletion, small (<=20) | Naturally occurring variant | no | EquCab3.0 | 16 | NC_009159.3:g.21567245_21567249del | NM_001163874.1:c.837_841del | NP_001157346.1:p.(C280Sfs*20) | NM_001163874.1; NP_001157346.1; published as c.837_841delGTGTC | 2012 | 22511888 | ||
792 | OMIA:000214-9796 | horse | American Miniature Horse (Horse) American Paint (Horse) Appaloosa (Horse) Icelandic Horse (Horse) Morgan (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Tori hobune, Estonia (Horse) Trakehner (Horse) | Splashed white | MITF | SW1 | delins, small (<=20) | Naturally occurring variant | no | EquCab3.0 | 16 | NC_009159.3:g.21579201delinsATAATAACCTA | g.20117302Tdelins11 | rs5334475212 | 2012 | 22511888 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
806 | OMIA:000214-9796 | horse | American Trotter (Horse) Arab (Horse) Belgian Draft (Horse) Cavall Menorquí, Spain (Horse) Clydesdale (Horse) Freiberger (Horse) Icelandic Horse (Horse) Morgan (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Thoroughbred (Horse) Warmblood (Horse) Welsh Pony (Horse) | White splashing | MITF | regulatory | Naturally occurring variant | no | EquCab3.0 | 16 | NC_009159.3:g.21608936C>T | Published as g.20147039C>T (EquCab2.0); may not be causal as the variant was identified to be a common variant across multiple breeds in a later study: PMID: 38600096 | 2017 | 28084638 | Breed information updated based on PMID: 38600096 | ||||
437 | OMIA:000175-9796 | horse | Arab (Horse) Bashkir Curly (Horse) Quarter Horse (Horse) Trakehner (Horse) Welsh Pony (Horse) | Cerebellar abiotrophy | MUTYH | not known | Naturally occurring variant | yes | EquCab3.0 | 2 | NC_009145.3:g.13122415C>T | ENSECAT00000009202.3: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. Additional breeds added based on supplementary table 6 of Durward-Akhurst et al. (2024, PMID: 38600096). | rs397160943 | 2011 | 21126570 | |||
973 | OMIA:002141-9796 | horse | Belgian Draft (Horse) Quarter Horse (Horse) Welsh Pony (Horse) | Immune-mediated myositis | MYH1 | missense | Naturally occurring variant | yes | EquCab3.0 | 11 | NC_009154.3:g.53345548T>C | NM_001081759.1:c.959A>G | NM_001081759.1:p.(E320G) | 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 and p.(E320G) | rs3435577028 | 2018 | 29510741 | Breed information updated based on PMID: 38600096 | |
510 | OMIA:001501-9796 | horse | Arab (Horse) | Lavender foal syndrome | MYO5A | deletion, small (<=20) | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.139290592del | XM_023617258.1:c.4249del | XP_023473026.1: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 | NC_009149.3:g.11196181G>A | XM_005610643.3:c.583C>T | XP_005610700.1: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 | NC_009149.3:g.11199026C>T | XM_001495160.4:c.209G>A | XP_001495210.1: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 | NC_009149.3:g.11199140G>C | XM_001495160.4:c.95C>G | XP_001495210.1:p.(P32R) | rs5334475206 | 2013 | 23659293 | ||
165 | OMIA:001982-9796 | horse | Thoroughbred (Horse) Warmblood (Horse) | Fragile Foal Syndrome | PLOD1 | missense | Naturally occurring variant | yes | EquCab3.0 | 2 | NC_009145.3:g.39927817C>T | XM_001491331.6:c.2032G>A | XP_001491381.1:p.(G678R) | 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) Icelandic Horse (Horse) Missouri Fox Trotter, Germany (Horse) Morgan (Horse) Rocky Mountain, United States of America (Bighorn sheep) Shetland Pony (Horse) | Coat colour, silver AND Multiple congenital ocular anomalies | PMEL | missense | Naturally occurring variant | no | EquCab3.0 | 6 | NC_009149.3:g.74569773G>A | NM_001163889.1:c.1849C>T | NP_001157361.1: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 | 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. Breed information updated based on PMID: 38600096 | |
157 | OMIA:000327-9796 | horse | Quarter Horse (Horse) | Ehlers-Danlos syndrome | PPIB | missense | Naturally occurring variant | yes | EquCab3.0 | 1 | NC_009144.3:g.129307092G>A | NM_001099761.1:c.115G>A | NP_001093231.1:p.(G39R) | 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 | NC_009152.3:g.36395752_36395756del | NM_001163858.1:c.9478_9482del | NP_001157330.1: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. The g. coordinates were previously listed incorrectly in this table as g.36395752_36395759del [03/06/2024] |
1997 | 9103416 | |||
1369 | OMIA:002458-9796 | horse | Thoroughbred (Horse) | Hypoparathyroidism | RAPGEF5 | nonsense (stop-gain) | Naturally occurring variant | yes | EquCab3.0 | 4 | NC_009147.3:g.54108297G>T | XM_023639352.1:c.2624C>A | XP_023495120.1:p.(S875*) | 2020 | 32986719 | ||||
159 | OMIA:000621-9796 | horse | Quarter Horse (Horse) | Malignant hyperthermia | RYR1 | missense | Naturally occurring variant | yes | EquCab3.0 | 10 | NC_009153.3:g.9678680C>G | XM_023649662.1:c.7363C>G | XP_023505430.1: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 | NC_009154.3:g.15474228C>G | NM_001081761.1:c.4248C>G | NP_001075230.1: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 | 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 | NC_009151.3:g.83600643_83600644insC | XM_001491598.3:c.504_505insC | XP_001491648.1: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 | NC_009169.3:g.31894278C>T | NM_001247992.1:c.1352C>T | NP_001234921.1: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 | ||
1040 | OMIA:002175-9796 | horse | Bashkir Curly (Horse) Missouri Fox Trotter, Germany (Horse) | Curly coat with/without hypotrichosis | SP6 | missense | Naturally occurring variant | yes | EquCab3.0 | 11 | NC_009154.3:g.24096309C>T | XM_023652659.1:c.1090G>A | XP_023508427.1:p.(G364S) | Thomer et al. (2018): "SP6; NC_009154.2:g.24022045C>T, ss3021042887" with respect to EquCab2. Updated coordinates in this entry obtained from EVA rs1095048852; 14 Mar 2019. Protein coordinates in this table previously inocrrectly shown as p.(D346N); corrected 13/06/2024. | rs1095048852 | 2018 | 29686323 | ||
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 | NC_009150.3:g.39710628G>T | 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) | ||
438 | OMIA:001356-9796 | horse | Coat colour, grey/gray (slow greying) | STX17 | G2 | repeat variation | Naturally occurring variant | no | EquCab3 | 25 | NC_009168.3:g.6625295_6629872dup | two tandom copies of a 4.6kb intronic region in STX17, which increase the expression of both STX17 and a neighbouring gene NR4A3 | 2008 | 18641652 | |||||
1732 | OMIA:001356-9796 | horse | Coat colour, grey/gray (fast greying) | STX17 | G3 | repeat variation | Naturally occurring variant | yes | EquCAb3 | 25 | NC_009168.3:g.6625295_6629872[3] | three tandom copies of a 4.6kb intronic region in STX17 which increase the expression of both syntaxin-17 and a neighbouring gene NR4A3 | 2024 | 39209879 | |||||
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 | EquCab3.0 | 1 | NC_009144.3:g.109211964_109211965insN[1378] | "a 1378 bp retroviral LTR insertion in intron 1 of TRPM1", EquCab2.0: g.108297929_108297930insN[1378] | 2013 | 24167615 | Coordinates in EquCab3.0 kindly provided by Haley Rutstein, working under the guidance of Professor Ernie Bailey. |
Overall Statistics | |
---|---|
Total number of variants | 91 |
Variants with genomic location | 87 (95.6% ) |
Variants in a variant database, i.e. with rs ID | 54 (59.3%) |
Variant Type | Count | Percent |
---|---|---|
deletion, gross (>20) | 13 | 14.3% |
deletion, small (<=20) | 12 | 13.2% |
delins, small (<=20) | 2 | 2.2% |
insertion, gross (>20) | 1 | 1.1% |
insertion, small (<=20) | 3 | 3.3% |
missense | 38 | 41.8% |
nonsense (stop-gain) | 8 | 8.8% |
not known | 1 | 1.1% |
regulatory | 2 | 2.2% |
repeat variation | 2 | 2.2% |
splicing | 9 | 9.9% |
Year First Reported | Count | Percent |
---|---|---|
1992 | 1 | 1.1% |
1993 | 0 | 0.0% |
1994 | 0 | 0.0% |
1995 | 1 | 1.1% |
1996 | 0 | 0.0% |
1997 | 1 | 1.1% |
1998 | 1 | 1.1% |
1999 | 0 | 0.0% |
2000 | 0 | 0.0% |
2001 | 0 | 0.0% |
2002 | 1 | 1.1% |
2003 | 0 | 0.0% |
2004 | 2 | 2.2% |
2005 | 1 | 1.1% |
2006 | 2 | 2.2% |
2007 | 6 | 6.6% |
2008 | 2 | 2.2% |
2009 | 8 | 8.8% |
2010 | 2 | 2.2% |
2011 | 8 | 8.8% |
2012 | 6 | 6.6% |
2013 | 6 | 6.6% |
2014 | 0 | 0.0% |
2015 | 4 | 4.4% |
2016 | 4 | 4.4% |
2017 | 10 | 11.0% |
2018 | 8 | 8.8% |
2019 | 2 | 2.2% |
2020 | 5 | 5.5% |
2021 | 3 | 3.3% |
2022 | 3 | 3.3% |
2023 | 3 | 3.3% |
2024 | 1 | 1.1% |