Cited by 240melanin and skin pigmentationGenetic Associations and EpidemiologyForensic and Genetic Research

A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation

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Duffy, David L., Montgomery, Grant W., Chen, Wei, Zhao, Zhen Zhen, Le, Lien, James, Michael R., Hayward, Nicholas K., Martin, Nicholas G. +1 more·2007·The American Journal of Human Genetics

Abstract

We have previously shown that a quantitative-trait locus linked to the OCA2 region of 15q accounts for 74% of variation in human eye color. We conducted additional genotyping to clarify the role of the OCA2 locus in the inheritance of eye color and other pigmentary traits associated with skin-cancer risk in white populations. Fifty-eight synonymous and nonsynonymous exonic single-nucleotide polymorphisms (SNPs) and tagging SNPs were typed in a collection of 3,839 adolescent twins, their siblings, and their parents. The highest association for blue/nonblue eye color was found with three OCA2 SNPs: rs7495174 T/C, rs6497268 G/T, and rs11855019 T/C (P values of 1.02x10(-61), 1.57x10(-96), and 4.45x10(-54), respectively) in intron 1. These three SNPs are in one major haplotype block, with TGT representing 78.4% of alleles. The TGT/TGT diplotype found in 62.2% of samples was the major genotype seen to modify eye color, with a frequency of 0.905 in blue or green compared with only 0.095 in brown eye color. This genotype was also at highest frequency in subjects with light brown hair and was more frequent in fair and medium skin types, consistent with the TGT haplotype acting as a recessive modifier of lighter pigmentary phenotypes. Homozygotes for rs11855019 C/C were predominantly without freckles and had lower mole counts. The minor population impact of the nonsynonymous coding-region polymorphisms Arg305Trp and Arg419Gln associated with nonblue eyes and the tight linkage of the major TGT haplotype within the intron 1 of OCA2 with blue eye color and lighter hair and skin tones suggest that differences within the 5' proximal regulatory control region of the OCA2 gene alter expression or messenger RNA-transcript levels and may be responsible for these associations.

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Crossref · 10.1086/510885

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  • Normal polymorphism of OCA2 is predominantly associated with eye color, although effects on skin and hair color have also been reported.

    “Normal polymorphism of OCA2 appears to be predominantly associated with eye color, although effects on skin and hair color have also been reported”
  • Duffy et al. (2007) previously identified a three-SNP haplotype system (rs4778138, rs4778241, and rs7495174) associated with blue eyes.

    “Duffy et al. (2007) previously identified a three-SNP haplotype system (rs4778138, rs4778241, and rs7495174) associated with blue eyes; for the purpose of this paper, we will refer to this system as BEH1, blue-eye associated haplotype #1.”

    From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Duffy et al. 2007

  • Several sites in and around OCA2 have been reported to be the functional variant or tightly linked to the functional variant leading to blue eyes, including a three-SNP haplotype (rs4778138, rs4778241, rs7495174) and four individual SNPs, rs1129038, rs12913832, rs916977, and rs1667394.

    “Several sites in and around OCA2 have been reported to be the functional variant or to be tightly linked to the functional variant leading to blue eyes. These sites include a three-SNP haplotype (rs4778138, rs4778241, rs7495174) and four individual SNPs, rs1129038, rs12913832, rs916977, and rs1667394 (Duffy et al. 2007; Sturm et al. 2008; Kayser et al. 2008; Sulem et al. 2007; Mengel-From et al. 2”

    From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Duffy et al. 2007

  • OCA2 has been implicated in iris, skin, and hair pigmentation in humans.

    “In humans, it has been implicated in iris, skin, and hair pigmentation (Duffy et al. 2007; Sturm et al. 2008; Kayser et al. 2008; Sulem et al. 2007).”

    From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Duffy et al. 2007

  • The TG allele of BEH2 has a much more restricted global distribution compared to the ACA allele of BEH1 and the CA allele of BEH3, the other two haplotypes published as associated with blue eyes.

    “We have shown that the TG allele of BEH2 has a much more restricted global distribution compared to the ACA allele of BEH1 and the CA allele of BEH3, the other two haplotypes published as associated with blue eyes”

    From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Duffy et al. 2007

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Research works printed but not linked: 1

  1. McGregor B, Pfitzner J, Zhu G, Grace M, Eldridge A, Pearson J, Mayne C, Aitken JF, Green AC, Martin NG (1999) Genetic and environmental contributions to size, color, shape, and other characteristics of melanocytic naevi in a sample of ad- olescent twins. Genet Epidemiol 16:40-53

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Authors
Duffy, D. L., Montgomery, G. W., Chen, W., Zhao, Z. Z., Le, L., James, M. R., Hayward, N. K., Martin, N. G., & Sturm, R. A.
Affiliations
  • QIMR Berghofer Medical Research Institute (AU)
  • The University of Queensland (AU)
Corresponding author
Sturm, Richard A.
Venue
The American Journal of Human Genetics
Publisher
Elsevier BV
Published
2007-02
Volume
80
Issue
2
Pages
241-252
ISSN
0002-9297 (ISSN-L)
OpenAlex
W2014370194
Cited by
240
References
64
Citations by year
2026: 2 · 2025: 7 · 2024: 14 · 2023: 8 · 2022: 8 · 2021: 15 · 2020: 12 · 2019: 8 · 2018: 8 · 2017: 5 · 2016: 8 · 2015: 10 · 2014: 10 · 2013: 15 · 2012: 15
FWCI
11.17
Type
journal article
Language
en
Open access
Locations
  • The American Journal of Human Genetics (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Medical Research Council
  • Australian Research Council (241944, 389875)
  • National Health and Medical Research Council (301173, 241944, 389875)
  • National Cancer Institute (R01CA088363, CA88363)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Keywords
OCA2, eye color, single nucleotide polymorphisms, haplotypes, intron 1, skin pigmentation, hair color, freckles, skin cancer risk, quantitative trait loci
MeSH terms
Adolescent, Child, Chromosomes, Human, Pair 15, Eye Color, Female, Genotype, Hair Color, Haplotypes, Humans, Introns, Male, Melanosis, Nevus, Pigmented, Skin Pigmentation, Twins, Polymorphism, Single Nucleotide, Membrane Transport Proteins

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