OMIA:001344-9796 : Coat colour, cream dilution in Equus caballus

In other species: dog

Categories: Pigmentation phene

Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 606574 (trait) , 227240 (trait) , 606202 (gene)

Links to MONDO diseases: No links.

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal

Considered a defect: no

Key variant known: yes

Year key variant first reported: 2003

Species-specific name: Palomino

Species-specific description: In 2003, Mariat et al. showed that this classic coat-colour locus encodes membrane-associated transporter protein (MATP), now renamed SLC45A2, and that the dilution allele in horses is due to a missense mutation [FN 16 Oct 2003]

Inheritance: Holl et al. (2019): "Cream dilution is inherited in an incomplete dominant manner, diluting only red in the heterozygous state but both red and black pigments when two alleles are present. The pearl dilution is recessive and dilutes only the red and black pigment in the homozygous state or when paired with a cream allele. Horses that inherit one copy of pearl (C^prl) and one copy of the dominant cream allele (C^Cr) display a dilution phenotype similar to that of homozygous cream, suggesting that pearl is the result of a different variation in the same gene responsible for cream".

Mapping: Mariat et al. (2003) showed that the candidate gene MATP is completely linked (theta = 0) to the equine cream locus.

Molecular basis: Building on the strong evidence from mapping (see Mapping section above), Mariat et al. (2003) identified a missense G457A transition in the equine MATP gene (now called SLC45A2), giving rise to a D153N amino acid substitution in cream horses.

Sevane et al. (2019) reported a "missense variation in exon 4 [SLC45A2:c.985G>A; SLC45A2:p.(Ala329Thr)] as the causative mutation for the pearl coat colour". These authors also explained "the cremello, perlino and smoky cream like phenotypes associated with the compound C^Cr and C^prl heterozygous genotype (known as cream pearl in the Purebred Spanish horse breed)"

Having sequenced a "'false double dilute'" horse (one that is "phenotypically homozygous cream but tested as possessing only a single C^Cr allele") and a non-dilute offspring, Holl et al. (2019) reported that both horses were "heterozygous for a novel missense variant ECA21:SLC45A2:c.568G>A (p.Gly190Arg), the proposed C^sun variant (for the name of the horse). This variant produces a recessive dilution similar to pearl and indicates that multiple alleles of SLC45A2 result in dilution phenotypes in the domestic horse."

Bisbee et al. (2020) identified an SLC45A2 variant in exon 1 (c.305G>A; p.(Arg102Gln); ENSECAT00000026240.1 in the Ensembl EquCab2.0 assembly) as the likely causal variant for an autosomal recessive coat colour of "a Gypsy breed mare that appeared phenotypically cremello (light creamy white) but tested negative for any known dilution or spotting alleles, including sabino, W20, tobiano, PATN1 and SW1‐4". They named this variant snowdrop (C^sno).

Breed: Traditional Gypsy Cob, United Kingdom of Great Britain and Northern Ireland (Horse) (VBO_0011496).

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
SLC45A2 solute carrier family 45, member 2 Equus caballus 21 NC_009164.3 (31683230..31717264) SLC45A2 Homologene, Ensembl , NCBI gene


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 Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Inferred EVA rsID Year Published PubMed ID(s) Acknowledgements
1140 Traditional Gypsy Cob, United Kingdom of Great Britain and Northern Ireland (Horse) Coat colour, snowdrop SLC45A2 C^sno missense Naturally occurring variant EquCab3.0 21 g.31688649G>A c.305G>A p.(R102Q) Bisbee et al. (2020): transcript ENSECAT00000026240.1 in the Ensembl EquCab2.0 assembly 2020 31961951
153 Coat colour, cream dilution SLC45A2 C^Cr missense Naturally occurring variant EquCab3.0 21 g.31690653G>A c.457G>A p.(D153N) rs1140980396 2003 12605854 EquCab3 coordinates obtained from Table S2 of Holl et al. (2019)
1074 Standardbred x Tennessee Walking Horse cross (Horse) Coat colour, sunshine SLC45A2 C^sun missense Naturally occurring variant EquCab3.0 21 g.31705726G>A c.568G>A p.(G190R) Holl et al. (2019): "The exon sequence containing this variant was deposited in Genbank under accession no. MF688761." rs394940514 2019 31006892
1069 American Paint (Horse) Lusitanian (Horse) Purebred Spanish (Horse) Quarter Horse (Horse) Coat colour, pearl SLC45A2 C^prl missense Naturally occurring variant EquCab3.0 21 g.31709690G>A c.985G>A p.(A329T) rs3101690631 2019 30968968 EquCab3 g. coordinate kindly provided by Natalia Sevane


Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.

2020 Bisbee, D., Carpenter, M.L., Hoefs-Martin, K., Brooks, S.A., Lafayette, C. :
Identification of a novel missense variant in SLC45A2 associated with dilute snowdrop phenotype in Gypsy horses. Anim Genet 51:342-43, 2020. Pubmed reference: 31961951 . DOI: 10.1111/age.12913.
Nguyen, T.B., Paul, R.C., Okuda, Y., LE, T.N.A., Pham, P.T.K., Kaissar, K.J., Kazhmurat, A., Bibigul, S., Bakhtin, M., Kazymbet, P., Maratbek, S.Z., Meldebekov, A., Nishibori, M., Ibi, T., Tsuji, T., Kunieda, T. :
Genetic characterization of Kushum horses in Kazakhstan based on haplotypes of mtDNA and Y chromosome, and genes associated with important traits of the horses. J Equine Sci 31:35-43, 2020. Pubmed reference: 33061782 . DOI: 10.1294/jes.31.35.
2019 Holl, H.M., Pflug, K.M., Yates, K.M., Hoefs-Martin, K., Shepard, C., Cook, D.G., Lafayette, C., Brooks, S.A., Holl, H.M., Pflug, K.M., Yates, K.M., Hoefs-Martin, K., Shepard, C., Cook, D.G., Lafayette, C., Brooks, S.A., Holl, H.M., Pflug, K.M., Yates, K.M., Hoefs-Martin, K., Shepard, C., Cook, D.G., Lafayette, C., Brooks, S.A. :
A candidate gene approach identifies variants in SLC45A2 that explain dilute phenotypes, pearl and sunshine, in compound heterozygote horses. Anim Genet 50:271-274, 2019. Pubmed reference: 31006892 . DOI: 10.1111/age.12790.
Sevane, N., Sanz, C.R., Dunner, S., Sevane, N., Sanz, C.R., Dunner, S. :
Explicit evidence for a missense mutation in exon 4 of SLC45A2 gene causing the pearl coat dilution in horses. Anim Genet 50:275-278, 2019. Pubmed reference: 30968968 . DOI: 10.1111/age.12784.
2016 Martin, L., Damaso, N., Mills, D., Martin, L., Damaso, N., Mills, D. :
Detection of single nucleotide polymorphisms (SNP) in equine coat color genes using SNaPshotTM multiplex kit or pluronic F-108 tri-block copolymer and capillary electrophoresis. Electrophoresis 37:2862-2866, 2016. Pubmed reference: 27542347 . DOI: 10.1002/elps.201600245.
Reissmann, M., Musa, L., Zakizadeh, S., Ludwig, A. :
Distribution of coat-color-associated alleles in the domestic horse population and Przewalski's horse. J Appl Genet 57:519-525, 2016. Pubmed reference: 27194311 . DOI: 10.1007/s13353-016-0352-7.
2012 Svensson, E.M., Telldahl, Y., Sjöling, E., Sundkvist, A., Hulth, H., Sjøvold, T., Götherström, A. :
Coat colour and sex identification in horses from Iron Age Sweden. Ann Anat 194:82-7, 2012. Pubmed reference: 22154005 . DOI: 10.1016/j.aanat.2011.11.001.
2010 Bellone, RR. :
Pleiotropic effects of pigmentation genes in horses. Anim Genet 41 Suppl 2:100-10, 2010. Pubmed reference: 21070283 . DOI: 10.1111/j.1365-2052.2010.02116.x.
Li, B., He, XL., Zhao, YP., Wang, XJ., Manglai, D., Zhang, YR. :
[Molecular basis and applicability in equine color genetics]. Yi Chuan 32:1133-40, 2010. Pubmed reference: 21513164 .
2009 Kakoi, H., Tozaki, T., Nagata, S., Gawahara, H., Kijima-Suda, I. :
Development of a method for simultaneously genotyping multiple horse coat colour loci and genetic investigation of basic colour variation in Thoroughbred and Misaki horses in Japan. J Anim Breed Genet 126:425-31, 2009. Pubmed reference: 19912416 . DOI: 10.1111/j.1439-0388.2009.00841.x.
Lewin, H.A. :
Genetics. It's a bull's market. Science 324:478-9, 2009. Pubmed reference: 19390037 . DOI: 10.1126/science.1173880.
Rieder, S. :
Molecular tests for coat colours in horses. J Anim Breed Genet 126:415-24, 2009. Pubmed reference: 19912415 . DOI: 10.1111/j.1439-0388.2009.00832.x.
2008 Royo, L.J., Fernández, I., Azor, P.J., Alvarez, I., Pérez-Pardal, L., Goyache, F. :
Technical note: a novel method for routine genotyping of horse coat color gene polymorphisms. J Anim Sci 86:1291-5, 2008. Pubmed reference: 18310485 . DOI: 10.2527/jas.2007-0498.
2003 Mariat, D., Taourit, S., Guerin, G. :
A mutation in the MATP gene causes the cream coat colour in the horse Genetics Selection Evolution 35:119-33, 2003. Pubmed reference: 12605854 . DOI: 10.1051/gse:2002039.
2001 Locke, M.M., Ruth, L.S., Millon, L.V., Penedo, M.C.T., Murray, J.D., Bowling, A.T. :
The cream dilution gene, responsible for the palomino and buckskin coat colours, maps to horse chromosome 21 Animal Genetics 32:340-343, 2001. Pubmed reference: 11736803 .
1974 Adalsteinsson, S. :
Inheritance of the palomino color in Icelandic horses. J Hered 65:15-20, 1974. Pubmed reference: 4847742 .
1961 Castle, W.E., Singleton, W.R. :
The palomino horse. Genetics 46:1143-50, 1961. Pubmed reference: 13877241 .
1951 Castle, W.E., King, F.L. :
New evidence on the genetics of the Palomino horse Journal of Heredity 42:60-64, 1951. Pubmed reference: 14832452 .
1948 Castle, W.E. :
The Abc of Color Inheritance in Horses. Genetics 33:22-35, 1948. Pubmed reference: 17247268 .
1946 Castle, W.E. :
Genetics of the Palomino horse; confirmation of the Salisbury-Britton hypothesis. J Hered 37:35-38, 1946. Pubmed reference: 21025138 .

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