Two Variants of KIT Causing White Patterning in Stock-Type Horses

Over 30 polymorphisms in the KIT Proto-Oncogene ReceptorTyrosine Kinase (KIT) gene have been implicated in white spotting patterns ranging from small areas to full dermal depigmentation in the horse. We performed a candidate-gene exon sequencing approach on KIT and MITF, 2 known causatives of white spotting patterns, within 2 families of horses of unknown white spotting. Family 1 (Fam1, N = 5) consisted of a Quarter Horse stallion and 4 offspring with white spotting pattern ranging from legs, lower ventral, and head regions with jagged borders, to almost complete white.The second family (Fam2, N= 7) consisted of 6 half-sibling American Paint Horse/ Quarter Horse and their dam, demonstrating unpigmented limbs with belly spots and an extensive white patterning on the face. This approach resulted in 2 variants significantly associated with familial phenotypes, where Fam1 variant is an indel leading to a frameshift mutation, and Fam2 a non-synonymous SNP. We validated the variants within an unrelated population of horses (Fam2 variant, P = 0.00271944) as well as for protein functional impact with ExPASy, Protter, Phyre2, SMART, PROVEAN, SIFT, and 1-TASSER, confirming the reported associations. Fam1 associated variant, deemed W31, alters the protein sequence, leading to an early stop codon truncating the normal amino acid sequence from 972 to just 115 amino acids. Fam2 associated variant, deemed W32, may have a subtle impact on receptor function or could be in linkage with a non-coding or regulatory change creating the mild spotting pattern observed in this family.

Automated summary

More than 30 polymorphisms in the KIT gene are linked to white spotting patterns in horses. Through candidate-gene exon sequencing, two variants (Fam1 and Fam2) significantly associated with familial phenotypes were identified, causing a frameshift mutation and a non-synonymous SNP, respectively. Functional impact of these variants was validated using multiple tools, confirming their association with the observed white spotting patterns.