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Comprehensive candidate gene study highlights UGT1A and BNC2 as new genes determining continuous skin color variation in Europeans
Abstract
Natural variation in human skin pigmentation is primarily due to genetic causes rooted in recent evolutionary history. Genetic variants associated with human skin pigmentation confer risk of skin cancer and may provide useful information in forensic investigations. Almost all previous gene-mapping studies of human skin pigmentation were based on categorical skin color information known to oversimplify the continuous nature of human skin coloration. We digitally quantified skin color into hue and saturation dimensions for 5,860 Dutch Europeans based on high-resolution skin photographs. We then tested an extensive list of 14,185 single nucleotide polymorphisms in 281 candidate genes potentially involved in human skin pigmentation for association with quantitative skin color phenotypes. Confirmatory association was revealed for several known skin color genes including HERC2, MC1R, IRF4, TYR, OCA2, and ASIP. We identified two new skin color genes: genetic variants in UGT1A were significantly associated with hue and variants in BNC2 were significantly associated with saturation. Overall, digital quantification of human skin color allowed detecting new skin color genes. The variants identified in this study may also contribute to the risk of skin cancer. Our findings are also important for predicting skin color in forensic investigations.
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“a high-frequency introgressed haplotype that influences skin pigmentation levels in Europeans (Fig. S15)59,60”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [59]
In the citing paper
“However, it shows little evidence of having been a direct target of selection ( Jacobs et al., 2013 ).”
From The genetic architecture of human skin pigmentation: evolution and adaptation across global populations (2026) · cites this paper as Jacobs et al., 2013
In the citing paper
“UGT1A , in contrast, appears to influence pigmentation primarily through metabolic pathways rather than the canonical pathway of melanogenesis.”
From The genetic architecture of human skin pigmentation: evolution and adaptation across global populations (2026) · cites this paper as Jacobs et al., 2013
In the citing paper
“The rs6742078 variant of this gene is strongly associated with quantitative measures of skin hue in Europeans, marking it as a genuine but noncanonical pigmentation locus.”
From The genetic architecture of human skin pigmentation: evolution and adaptation across global populations (2026) · cites this paper as Jacobs et al., 2013
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“04 1 .00 -0.038 0.012 1.1E-03 1.00 OCA2 rs7495174 15 26017833 G A 0.06 -0 .425 0.131 1.1E-03 1.00 0 .007 0.002 3.8E-03 1.00 0.114 0.021 1.1E207 0.01 HERC2 rs12913832 15 26039213 A G 0.17 0.126 0.069 0.07 1.00 0.009 0.001 3.1E211 \0.01 0.256 0.011 1.5E2109 \0.01 SLC24A5 rs17426596 15 48424083 C T 2.6E-04 1.785 1.609 0.…”
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Additional file 4 of Epigenetics insights from perceived facial aging
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Additional file 1 of Epigenetics insights from perceived facial aging
Vladimir, K., Perišić, M. M., Štorga, M., Mostashari, A., & Khanin, R. (2024) · Figshare · doi:10.6084/m9.figshare.26635365
Additional file 5 of Epigenetics insights from perceived facial aging
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Metadata
- Authors
- Jacobs, L. C., Wollstein, A., Lao, O., Hofman, A., Klaver, C. C., Uitterlinden, A. G., Nijsten, T., Kayser, M., & Liu, F.
- Affiliations
- Erasmus MC (NL)
- Leiden University Medical Center (NL)
- Corresponding author
- Liu, Fan
- ORCID
- Venue
- Human Genetics
- Published
- 2012-10-11
- Volume
- 132
- Issue
- 2
- Pages
- 147-158
- ISSN
- 0018-7348 (ISSN-L)
- 0340-6717
- 1432-1203
- OpenAlex
- W2080521432
- Cited by
- 99
- References
- 59
- Citations by year
- 2026: 4 · 2025: 6 · 2024: 5 · 2023: 4 · 2022: 7 · 2021: 5 · 2020: 11 · 2019: 6 · 2018: 8 · 2017: 7 · 2016: 7 · 2015: 11 · 2014: 14 · 2013: 4
- FWCI
- 4.39
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Human Genetics (publishedVersion)
- PubMed (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- 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
- skin pigmentation, UGT1A, BNC2, single nucleotide polymorphisms, skin cancer risk, HERC2, MC1R, IRF4, TYR, OCA2, ASIP
- MeSH terms
- UGT1A1 Enzyme, Aged, DNA-Binding Proteins, Female, Humans, Male, Phenotype, Skin Pigmentation, Glucuronosyltransferase, Polymorphism, Single Nucleotide, White People, Genetic Association Studies
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