Skin pigmentation (light vs dark)

SLC24A5 is one of the largest-effect genes for skin tone. One variant, carried by nearly all Europeans and South Asians, lightens pigmentation considerably.

What SLC24A5 does

SLC24A5 moves calcium and potassium across the membrane of melanosomes, the compartments inside pigment cells where melanin is made. This variant, A111T, reduces that activity and results in less melanin, and it is one of the largest single-gene contributors to the difference in skin pigmentation between populations.

It was found in an unusual way. A zebrafish mutant called golden, which has pale stripes, turned out to carry a defect in the fish version of the same gene, and that led directly to the human variant in 2005.

One of the most extreme frequency differences in the genome

In 1000 Genomes reference data, essentially every European-ancestry individual carries two copies of the light-associated allele, at over 99%. In East Asian samples the opposite allele is near fixation at about 99%, and in African-ancestry samples around 67% carry two copies of it, with South Asian samples intermediate.

Two things follow. The variant carries almost no information within European populations, since virtually everyone has the same genotype, and light skin in East Asia arose through different genes entirely, which is one of the clearest examples of convergent evolution in humans.

What it does and does not explain

Skin colour is polygenic, and this is one large contributor among many, alongside MC1R, OCA2, TYR, SLC45A2 and others, several of which this site reads separately. The genotype here shifts baseline pigmentation, not tanning ability, freckling or burn risk directly.

Sun protection advice follows from how your skin actually behaves, not from a genotype: how quickly you burn, whether you freckle, and your history of sun exposure and sunburn, which is what dermatologists use.

A note on how this kind of result reads

Pigmentation genetics sits close to a long history of misuse, and it is worth being precise about what a variant like this is. It affects a specific biochemical step in melanin production. It carries no information about anything other than pigmentation, and the frequency differences between populations reflect migration and ultraviolet exposure rather than anything else.

What each rs1426654 genotype means

rs1426654 has three possible genotypes: AA, AG and GG.

Lighter skin tone (rs1426654 AA). You have two copies of the light-skin version of SLC24A5, one of the biggest single genes for skin tone. It's carried by nearly all people of European and South Asian descent and lightens pigmentation. Skin color comes from many genes together, so this is one major piece.

Intermediate skin tone (rs1426654 AG). You carry one light-skin and one ancestral copy of SLC24A5, placing you in an intermediate range as far as this pigment gene goes. Overall skin tone depends on many genes, so this is just one input.

Darker skin tone (rs1426654 GG). You have two ancestral copies of SLC24A5, associated with deeper skin pigmentation. This is one of several major pigment genes, and your overall tone reflects all of them together.

Evidence & sources

Across global populations, about 87% of people carry two copies of this variant, and about 7% carry none.

This variant appears in 5 published genetic studies: PubMed 29195075 · PubMed 30664655 · PubMed 30895295 · PubMed 31315583 · PubMed 34570997.

Common questions

Does this variant predict my skin tone? Only partially, and only in some populations. Within European-ancestry groups nearly everyone carries the same genotype here, so it distinguishes almost nobody, and skin colour depends on many other pigment genes as well.

Does light skin come from the same gene everywhere? No. This variant is the major light-skin allele in European and South Asian populations, while lighter pigmentation in East Asia arose through different genes. It is a well-documented case of the same trait evolving twice by different routes.

Related

Endurance / aerobic capacity (PPARGC1A) · Eye color (blue, green/hazel, brown) · Hair thickness / shovel-shaped incisors · Height · Male-pattern baldness tendency · Muscle fiber type (power vs endurance) · Red hair / fair skin (MC1R gene)