Single nucleotide polymorphisms in theMATP gene are associated with normal human pigmentation variation
Open accessAbstract
Human physical pigmentation is determined by the type and amount of melanin and the process of pigmentation production probably involves more than 100 genes. A failure to synthesize melanin results in oculocutaneous albinism (OCA). A recently identified form of OCA results from mutations in the Membrane Associated Transporter Protein (MATP) gene. The role of MATP in human pigmentation is not clear. We investigated the role of two nonpathogenic nonsynonymous single nucleotide polymorphisms (SNPs) in the MATP gene to determine if they are associated with normal human skin, hair, and eye color variation. A total of 608 individuals from four different population groups (456 Caucasians, 31 Asians, 70 African-Americans, and 51 Australian Aborigines) were genotyped for c.814G>A (p.Glu272Lys) and c.1122C>G (p.Phe374Leu). Results indicate that the allele frequencies of both polymorphisms are significantly different between population groups. The two alleles, 374Leu and 272Lys, are significantly associated with dark hair, skin, and eye color in Caucasians. The odds ratios (ORs) of the LeuLeu genotype for black hair and olive skin are 25.63 and 28.65, respectively, and for the LysLys genotype are 43.23 and 8.27, respectively. The OR for eye color is lower at 3.48 for the LeuLeu and 6.57 for LysLys genotypes. This is the first report of this highly significant association of MATP polymorphisms with normal human pigmentation variation.
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SNPs within the MATP coding region specifying E272K and L374F, and polymorphisms within the promoter, are associated with normal variation in human skin coloration.
“Later, SNPs within the MATP coding region of the SLC45A2 gene specifying amino acids at position E272K (rs26722) and L374F (rs16891982), and also polymorphisms within the promoter, were shown to be associated with normal variation in human skin coloration”
From Analysis of Cultured Human Melanocytes Based on Polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P Loci (2009) · cites this paper as Graf et al., 2005
The MATP allele encoding 374L is found at a higher frequency in non-Caucasian populations than the 374F allele and is associated with darker pigmentation of the skin, hair, and eyes in populations of European ancestry.
“The MATP allele encoding 374L was found at a higher frequency in non-Caucasian populations than the 374F allele, and also to be associated with darker pigmentation of the skin, hair, and eyes in populations of European ancestry”
From Analysis of Cultured Human Melanocytes Based on Polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P Loci (2009) · cites this paper as Graf et al., 2005
These results are in contrast to those previously reported, where both the MATP-374 and MATP-272 polymorphisms were associated with hair, skin, and eye color variation in a Caucasian-derived Australian sample.
“These results are in contrast to those previously reported (Graf et al., 2005), where both the MATP-374 and MATP-272 polymorphisms were associated with hair, skin, and eye color variation in an Caucasian-derived Australian sample.”
From Analysis of Cultured Human Melanocytes Based on Polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P Loci (2009) · cites this paper as Graf et al., 2005
rs16891982 in SLC45A2 (98% frequency in CEU for the derived allele) may contribute to skin pigmentation differences in Europe as suggested in a candidate gene study for subjective skin color.
“This variant (98% frequency in CEU for the derived allele) may contribute to skin pigmentation differences in Europe as suggested in a candidate gene study for subjective skin color [39].”
From Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations (2012) · cites this paper as [39]
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References 27 · Cited by 221
- Authors
- Graf, J., Hodgson, R., & van Daal, A.
- Affiliations
- Queensland University of Technology (AU)
- Venue
- Human Mutation
- Publisher
- Hindawi Limited
- Published
- 2005
- Volume
- 25
- Issue
- 3
- Pages
- 278-284
- ISSN
- 1059-7794 (ISSN-L)
- 1098-1004
- OpenAlex
- W2130504205
- Cited by
- 221
- References
- 27
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 7 · 2023: 7 · 2022: 2 · 2021: 6 · 2020: 9 · 2019: 5 · 2018: 7 · 2017: 9 · 2016: 7 · 2015: 11 · 2014: 18 · 2013: 18 · 2012: 10
- FWCI
- 6.37
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Mutation (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Queensland Health
- 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
- single nucleotide polymorphisms, human pigmentation, skin color, hair color, eye color, oculocutaneous albinism, non-synonymous mutations, allele frequency variation, melanin, genotype-phenotype correlation
- MeSH terms
- Alleles, Antigens, Neoplasm, Australia, Black or African American, Eye Color, Gene Frequency, Hair Color, Humans, Membrane Proteins, Pigmentation, Polymorphism, Restriction Fragment Length, Skin Pigmentation, Virginia, Odds Ratio, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Membrane Transport Proteins, White People, Asian People, Racial Groups
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