SLC45A2 rs1393350: What Your Genotype Means
The rs1393350 variant is a single nucleotide polymorphism located within or near the SLC45A2 gene region. It is widely studied as a genetic marker associated with normal human variation in skin, hair, and eye pigmentation.
What each genotype means
Associated with pigmentation variation
This genotype is associated with variations in human skin, hair, and eye pigmentation. Research suggests this variant may influence melanin synthesis, though its specific contribution to an individual's appearance is part of a complex interaction with many other genetic and environmental factors.
This genotype is less common than the G/G genotype in many global populations, with frequency varying significantly by ancestry.
Associated with pigmentation variation
Carrying one copy of each allele is associated with normal variation in human pigmentation traits. As with other genotypes at this locus, this result should be viewed as one small piece of a larger genetic puzzle that influences skin, hair, and eye color.
This heterozygous genotype is observed at varying frequencies across different ancestral groups.
Associated with pigmentation variation
This is the most common genotype observed in many populations for this variant. It is associated with the standard range of human pigmentation, though it does not determine specific physical traits on its own due to the polygenic nature of skin, hair, and eye color.
This is the most frequently occurring genotype in many populations, often referred to as the common or major allele combination.
Understanding the Variant
A single nucleotide polymorphism, or SNP, is a variation at a single position in a DNA sequence among individuals. The variant rs1393350 represents a specific location in the human genome where different individuals may carry different nucleotides. Researchers track these variations to understand how they correlate with observable physical traits, known as phenotypes. In the case of rs1393350, the focus is on its role as a marker for pigmentation. Because this SNP is located in a region associated with the SLC45A2 gene, it is frequently included in genome-wide association studies (GWAS) that aim to map the genetic architecture of human physical appearance. It is important to note that while this SNP is statistically associated with pigmentation, it is one of many genetic and environmental factors that contribute to the final expression of skin, hair, and eye color.
The Role of SLC45A2
The SLC45A2 gene, also known as MATP, encodes a protein that functions as a membrane transporter. This protein is primarily expressed in melanocytes, the specialized cells responsible for producing melanin, the pigment that gives color to our skin, hair, and eyes. By regulating the environment within melanosomes—the organelles where melanin is synthesized—the SLC45A2 protein plays a critical role in determining the type and amount of pigment produced. Mutations in this gene are known to cause oculocutaneous albinism type 4, a condition characterized by significantly reduced melanin production. Beyond these rare clinical mutations, common variations in the SLC45A2 gene are well-documented contributors to the natural spectrum of human pigmentation. Research suggests that these variations influence how efficiently the transporter functions, thereby impacting the overall pigmentation profile of an individual.
Research and Evidence
The evidence linking rs1393350 to pigmentation traits is considered moderate and is primarily derived from association studies in populations of European ancestry. Research has observed that the A allele of this SNP is associated with an increased likelihood of specific traits, such as lighter hair color, blue eye color, and variations in skin sensitivity to the sun. These findings are based on statistical correlations rather than direct causation, meaning the SNP serves as a proxy or marker for the underlying biological mechanisms. While the association is robust in certain cohorts, the strength and direction of these effects can vary significantly across different global populations. As with many complex traits, pigmentation is polygenic, meaning it is influenced by the cumulative effect of many different genetic variants across the entire genome, not just a single SNP.
Population Frequency
The frequency of the rs1393350 alleles varies significantly across different global ancestries. Genetic markers associated with pigmentation often show high levels of differentiation between populations due to historical evolutionary pressures related to ultraviolet radiation exposure in different geographic regions. In some populations, the A allele may be common, while in others, it may be rare or absent. Because of this, the predictive value of this SNP for pigmentation traits is highly dependent on an individual's ancestral background. Researchers use these differences to study human migration and adaptation, but it also means that findings from one population cannot be automatically generalized to another. Understanding these frequency differences is essential for interpreting the results of genetic studies accurately and avoiding oversimplified conclusions about the relationship between specific genotypes and physical traits.
Interpreting Your Information
Information about your genotype for rs1393350 provides insight into your genetic predisposition for certain pigmentation traits, but it is not a definitive diagnostic tool. Because pigmentation is a complex trait influenced by many genes and environmental factors, a single SNP cannot predict your exact hair, skin, or eye color. You cannot use this information to make medical decisions, such as determining your risk for skin conditions or sun-related health issues. If you have concerns about skin health, sun sensitivity, or any other medical condition, it is essential to consult with a qualified healthcare professional or dermatologist. They can provide personalized advice based on your clinical history and physical examination, which are far more informative than genetic data alone. Treat this information as an educational look into the genetic factors that contribute to human diversity rather than a medical assessment.
How common is this variant?
The frequency of the rs1393350 alleles shows significant variation across global populations, reflecting diverse evolutionary histories and ancestral backgrounds.
Frequently asked questions
Can this SNP predict my exact eye color?
No, this SNP cannot predict your exact eye color. Pigmentation is a complex trait influenced by many different genes and environmental factors, and this variant is only one small piece of that puzzle.
Is rs1393350 linked to skin cancer risk?
While this SNP is associated with sun sensitivity, it is not a diagnostic marker for skin cancer. You should always consult a dermatologist for professional skin health assessments and sun protection advice.
Why do results vary between different populations?
Genetic variants often have different frequencies and effects in different populations due to historical evolutionary pressures. A marker that is highly informative in one ancestry may have a different significance in another.
Should I change my sun protection habits based on this result?
No. Regardless of your genetic results, you should follow standard medical guidelines for sun protection, such as using sunscreen and wearing protective clothing, as recommended by health authorities.
Sources & further reading
Educational information only, last refreshed 10/1/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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This synonymous variant is in high linkage disequilibrium with functional alleles that influence human skin, hair, and eye pigmentation.
This missense variant (p.Phe374Leu) is a major determinant of human skin, hair, and eye pigmentation, showing strong evidence of selection in European populations.
Synonymous marker in the SLC45A2 locus associated with skin reflectance, tanning response, and freckling phenotypes.
This missense variant (p.Phe374Leu) is a key ancestry-informative marker and a classic signature of recent positive selection, strongly associated with skin pigmentation and melanoma risk.
This variant (p.Phe374Leu) is strongly associated with lighter skin, hair, and eye pigmentation, as well as an increased sensitivity to UV-induced skin damage.
The p.Phe374Leu variant in SLC45A2 is a major determinant of human pigmentation variation, influencing skin, hair, and eye color across global populations.