Loci associated with skin pigmentation identified in African populations

Science. 2017 Nov 17;358(6365):eaan8433. doi: 10.1126/science.aan8433. Epub 2017 Oct 12.


Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2, and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in South Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Africa, Eastern
  • African Continental Ancestry Group / genetics*
  • Animals
  • Antiporters / genetics
  • DNA-Binding Proteins / genetics
  • Ethnic Groups / genetics
  • Evolution, Molecular*
  • Gene Flow*
  • Genetic Loci*
  • Genome, Human
  • Genome-Wide Association Study
  • Humans
  • Melanins / biosynthesis
  • Melanins / genetics*
  • Melanins / metabolism
  • Melanocytes / metabolism
  • Membrane Proteins / genetics
  • Mice
  • Polymorphism, Single Nucleotide
  • Radiation Exposure
  • Skin Pigmentation / genetics*
  • Suppression, Genetic
  • Ultraviolet Rays


  • Antiporters
  • DDB1 protein, human
  • DNA-Binding Proteins
  • MFSD12 protein, human
  • Melanins
  • Membrane Proteins
  • SLC24A5 protein, human
  • TMEM138 protein, human
  • eumelanin