The SLC24A5 gene's derived threonine or Ala111Thr allele (rs1426654) has been shown to be a major factor in the light skin tone of Europeans compared to Africans, and is believed to represent as much as 25–40% of the average skin tone difference between Europeans and West Africans. It has been the subject of recent selection in Europe, and is fixed in European populations.
NCKX5 is 43 kDa protein that is partially localized to the trans-Golgi network in melanocytes. Removal of the NCKX5 protein disrupts melanogenesis in human and mouse melanocytes, causing a significant reduction in melanin pigment production. Site-directed mutagenesis corresponding to a non-synonymous single nucleotide polymorphism in SLC24A5 alters a residue in NCKX5 (A111T) that is important for NCKX5 sodium-calcium exchanger activity.
Global frequency distribution of the SLC24A5 gene's ancestral Ala111 allele (yellow) and its derived Ala111Thr allele (blue).
SLC24A5 appears to have played a key role in the evolution of light skin in humans of European ancestry. The gene's function in pigmentation was discovered in zebrafish as a result of the positional cloning of the gene responsible for the "golden" variety of this common pet store fish. Evidence in the International HapMap Project database of genetic variation in human populations showed that Europeans, represented by the "CEU" population, had two primary alleles differing by only one nucleotide, changing the 111th amino acid from alanine to threonine, abbreviated "A111T".
The derived threonine allele (Ala111Thr; also known as A111T or Thr111) represented 98.7 to 100% of the alleles in European samples, while the ancestral or alanine form was found in 93 to 100% of samples of Sub-Saharan Africans, East Asians and Indigenous Americans. The variation is a SNP polymorphism rs1426654, which had been previously shown to be second among 3011 tabulated SNPs ranked as ancestry-informative markers. This single change in SLC24A5 explains between 25 and 38% of the difference in skin melanin index between peoples of sub-Saharan African and European ancestry.
The SNP rs2470102 independently affect skin pigmentation variation among the South Asian population.
Furthermore, the European mutation is associated with the largest region of diminished genetic variation in the CEU HapMap population, suggesting the possibility that the A111T mutation may be the subject of the single largest degree of selection in human populations of European ancestry. It is theorised that selection for the derived allele is based on the need for sunlight to produce the essential nutrient vitamin D. In northerly latitudes, where there is less sun, greater requirement for body coverage due to colder climate, and frequently, diets poor in vitamin D, making lighter skin more suitable for survival. Tests for this variation have obvious application to forensic science.
The earliest known sample of the threonine allele is 13,000 years old from Satsurblia Cave in Georgia. The allele was widespread from Anatolia to Iran at the beginning of the Neolithic, and was introduced to Europe with the arrival of the first farmers from this region about 8,000 years ago.
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