rs117480223 (SEMA6D): Pigmentary Traits Variant

Key takeaways

• This variant maps to SEMA6D (Semaphorin 6D) and was identified in a GWAS of 13 pigmentary traits in approximately 20,000 South European adults.
• The study found 37 risk loci for pigmentary traits; some of these were identified as novel candidates not previously recorded in the GWAS Catalog.
• Specific effect size and trait association data for this locus are not detailed in the available study text.
• Evidence comes from a single study with no PubMed identifier; replication in independent cohorts has not been described.

What the research says A GWAS and polygenic risk score (PRS) study analyzed 13 pigmentary traits - including skin color, hair color, eye color, freckle presence, and sun sensitivity - in approximately 20,000 adults from the GCAT cohort in Catalonia, Spain, identifying 37 risk loci associated with 10 of the 13 traits. rs117480223, located in the SEMA6D (Semaphorin 6D) gene region, is among the loci reported in this work, though the available study text does not specify the associated pigmentary trait or report an effect size for this variant. The study identified 16 genes significantly associated with at least two pigmentary traits, including well-established pigmentation genes (MC1R, HERC2, OCA2, TYR, TYRP1, SLC45A2) alongside novel candidate genes not previously recorded in the GWAS Catalog, such as C1QTNF3, LINC02876, and C1QTNF3-AMACR.

Reported associations

• Pigmentary traits: this locus was identified among 37 risk loci for pigmentary traits in a South European GWAS of approximately 20,000 participants; the specific trait and effect size for this locus are not reported in the available study text.

Evidence quality The single available study enrolled approximately 20,000 participants from the GCAT population-based cohort in Catalonia, Spain, representing one of the larger South European GWAS analyses for pigmentary traits conducted to date. No PubMed identifier is available for this study, and the specific statistical parameters (p-value, odds ratio, or beta coefficient) for this variant are not present in the provided text. Replication of this locus in independent cohorts is not described in the available excerpt, so evidence should be considered preliminary. As broader study context, PRS analyses linked fair phototype with non-melanoma skin cancer (OR = 0.93), melanoma (OR = 0.95), and basal cell carcinoma (OR = 0.97), and darker phototype with vitiligo (OR = 1.02) and cataracts (OR = 1.04); these figures apply to phototype categories across all identified loci combined, not to this specific variant.

Lifestyle considerations No lifestyle considerations on file for this variant.