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Background . The  MC1R  gene implicated in melanogenesis and skin pigmentation is highly polymorphic. Several alleles are associated with red hair and fair skin phenotypes and contribute to melanoma risk.  Objective . This work aims to assess the effect of different classes of  MC1R  variants, notably rare variants, on melanoma risk.  Methods .  MC1R  coding region was sequenced in 1131 melanoma patients and 869 healthy controls.  MC1R  variants were classified as RHC ( R ) and non-RHC ( r ). Rare variants (frequency < 1%) were subdivided into two subgroups, predicted to be damaging ( D ) or not ( nD ).  Results . Both  R  and  r  alleles were associated with melanoma (OR = 2.66 [2.20–3.23] and 1.51 [1.32–1.73]) and had similar population attributable risks (15.8% and 16.6%). We also identified 69 rare variants, of which 25 were novel.  D  variants were strongly associated with melanoma (OR = 2.38 [1.38–4.15]) and clustered in the same  MC1R  domains as  R  alleles (intracellular 2, transmembrane 2 and 7).  Conclusion . This work confirms the role of  R  and  r  alleles in melanoma risk in the French population and proposes a novel class of rare  D  variants as important melanoma risk factors. These findings may improve the definition of high-risk subjects that could be targeted for melanoma prevention and screening.

A Large French Case-Control Study Emphasizes the Role of RareMc1RVariants in Melanoma Risk