A Single SNP in an Evolutionary Conserved Region within Intron 86 of the HERC2 Gene Determines Human Blue-Brown Eye Color
Open accessAbstract
We have previously demonstrated that haplotypes of three single nucleotide polymorphisms (SNPs) within the first intron of the OCA2 gene are extremely strongly associated with variation in human eye color. In the present work, we describe additional fine association mapping of eye color SNPs in the intergenic region upstream of OCA2 and within the neighboring HERC2 (hect domain and RLD2) gene. We screened an additional 92 SNPs in 300-3000 European individuals and found that a single SNP in intron 86 of HERC2, rs12913832, predicted eye color significantly better (ordinal logistic regression R(2) = 0.68, association LOD = 444) than our previous best OCA2 haplotype. Comparison of sequence alignments of multiple species showed that this SNP lies in the center of a short highly conserved sequence and that the blue-eye-associated allele (frequency 78%) breaks up this conserved sequence, part of which forms a consensus binding site for the helicase-like transcription factor (HLTF). We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a penetrance modifier of this new HERC2 SNP for eye color, and somewhat independently, of melanoma risk. We conclude that the conserved region around rs12913832 represents a regulatory region controlling constitutive expression of OCA2 and that the C allele at rs12913832 leads to decreased expression of OCA2, particularly within iris melanocytes, which we postulate to be the ultimate cause of blue eye color.
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The SNP responsible for pigmentation variation in OCA2 is not located within the protein-coding region but within a putative regulatory region located within an upstream gene (rs12913832).
“Unlike for the MATP and NCKX5 proteins however, the SNP responsible for pigmentation variation is not located within the protein-coding region of the OCA2 gene, but rather within a putative regulatory region located within an upstream gene (rs12913832, Sturm et al., 2008).”
From Analysis of Cultured Human Melanocytes Based on Polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P Loci (2009) · cites this paper as Sturm et al., 2008
The observed lower OCA2 mRNA in C/C cells is consistent with the predicted function of the conserved region surrounding rs12913832 as a locus control region for OCA2.
“This is consistent with the predicted function for the conserved region surrounding the rs12913832 SNP acting as a locus control region for OCA2 (Sturm et al., 2008).”
From Analysis of Cultured Human Melanocytes Based on Polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P Loci (2009) · cites this paper as Sturm et al., 2008
The eye color locus was later refined to a small region 50 kb upstream of OCA2 in an intron of the HERC2 gene.
“This eye color locus was later refined to a small region 50 kb upstream of OCA2 in an intron of the HERC2 gene [7], [8], [10].”
From Genetic Architecture of Skin and Eye Color in an African-European Admixed Population (2013) · cites this paper as [10]
Sturm et al. (2008) concluded that the derived allele of rs1800407 increased the penetrance of the blue eye phenotype associated with the derived allele of rs12913832.
“Sturm et al. (2008) concluded that the derived allele of rs1800407 increased the penetrance of the blue eye phenotype associated with the derived allele of rs12913832.”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Sturm et al. 2008
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 Sturm et al. 2008
The association between the T allele of rs1800407 and the TG allele at BEH2 may explain the increased blue-eye penetrance seen by Sturm et al. (2008) as a type of ascertainment effect.
“This association may explain the increased blue-eye penetrance seen by Sturm et al. (2008) as a type of ascertainment effect.”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Sturm et al. 2008
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 Sturm et al. 2008
The T allele of rs1800407 has also been associated with blue-eye penetrance.
“The T allele of rs1800407 has also been associated with blue-eye penetrance (Sturm et al. 2008).”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Sturm et al. 2008
Sturm et al. (2008) reported that rs12913832 is associated with blue eyes.
“Sturm et al. (2008) reported that rs12913832 is associated with blue eyes.”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Sturm et al. 2008
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 Sturm et al. 2008
The derived allele (G) at rs12913832 is recessive and is associated with blue eye color.
“The derived allele (G) at rs12913832 is recessive and is associated with blue eye color.”
From Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations (2012) · cites this paper as [34]
rs1667394 is also in LD with rs12913832 (D' = 1, r2 = 0.65), which was not genotyped in the study but is thought to be the likely causative variant for blue versus brown eye color by genetic and functional analyses.
“rs1667394 is also in LD with rs12913832 (D’ = 1, r2 = 0.65), which was not genotyped in our study but is thought to be the likely causative variant for blue versus brown eye color by genetic and functional analyses [33], [34].”
From Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations (2012) · cites this paper as [34]
The correlation among the three pigmentary phenotypes may result from the existence of shared or linked genetic determinants of multiple pigmentation phenotypes, such as rs12913832 in HERC2.
“This correlation may result from the existence of shared or linked genetic determinants of multiple pigmentation phenotypes, such as rs12913832 in HERC2, which was shown to be very strongly associated with eye color but more weakly associated with hair color [9], [34].”
From Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations (2012) · cites this paper as [34]
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- Authors
- Sturm, R. A., Duffy, D. L., Zhao, Z. Z., Leite, F. P. N., Stark, M. S., Hayward, N. K., Martin, N. G., & Montgomery, G. W.
- Affiliations
- The University of Queensland (AU)
- QIMR Berghofer Medical Research Institute (AU)
- Corresponding author
- Montgomery, Grant W.
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2008-02
- Volume
- 82
- Issue
- 2
- Pages
- 424-431
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC2427173
- OpenAlex
- W2160460000
- Cited by
- 378
- References
- 54
- Citations by year
- 2026: 11 · 2025: 9 · 2024: 20 · 2023: 12 · 2022: 20 · 2021: 26 · 2020: 16 · 2019: 19 · 2018: 24 · 2017: 15 · 2016: 18 · 2015: 21 · 2014: 23 · 2013: 29 · 2012: 26
- FWCI
- 12.97
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- 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 › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- eye color, HERC2, OCA2, single nucleotide polymorphisms, blue eyes, conserved sequences, HLTF, transcriptional regulation, melanogenesis, melanoma risk, fine mapping
- MeSH terms
- Adolescent, Base Sequence, Chromosome Mapping, DNA-Binding Proteins, Eye Color, Gene Expression Regulation, Gene Frequency, Genotype, Humans, Introns, Lod Score, Molecular Sequence Data, Transcription Factors, Twins, Sequence Alignment, Conserved Sequence, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Guanine Nucleotide Exchange Factors, Membrane Transport Proteins, Ubiquitin-Protein Ligases
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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