SLC45A2 — a second major pigment gene
What this means
SLC45A2 (also called MATP) is a transporter in the melanosome membrane that affects how efficiently melanin is produced. The L374F amino-acid change (rs16891982) is the second-largest single contributor to skin pigmentation differences between European and other populations, after SLC24A5. The "lighter" allele frequency drops sharply from northern Europe (near 99%) to sub-Saharan Africa (near 0%), and like SLC24A5 it shows strong signals of recent positive selection in lighter-skinned populations.
SLC45A2 is the second-biggest single gene behind skin colour differences between people, after SLC24A5. The "lighter" version of this DNA change makes the pigment-producing machinery less efficient, which lightens skin, hair, and eyes. It's almost universal in northern Europe and almost absent in sub-Saharan Africa — a striking pattern that tells you it spread fast in lighter-skinned populations relatively recently in human evolution.
Caveats
- One of many genes shaping pigmentation; it explains a meaningful fraction but not most of the variance.
- Near-fixed in northern Europe — within-Europe predictive value is low.
- Most predictive in admixed populations or as part of multi-SNP scores.
- Pigmentation is also strongly modified by environment (sun, age, hormones).