Characterization of single nucleotide variants of OPN3 gene in melanocytic nevi and melanoma

Abstract: In this study, we examined SNVs (single nucleotide variants) of OPN3 gene in MM (malignant melanoma) and MN (melanocytic nevi). A total of 20 variants of SNPs were detected. Of these variants, five nonsynonymous mutations of OPN3 gene were identified, including c.T152C, c.T401C, c.G547A, c.G768A, c.G992A. Three prediction tools of MutationTaster2, PolyPhen-2 and PROVEAN, which predict possible impact of an amino acid substitution, suggested that the mutations could be deleterious. Nine synonymous variants occurred in 3’UTR (Untranslated Regions), while two observed in 5’UTR. In all cases, four intronic variants were identified. In addition, we identified nine 3’UTR SNPs in OPN3 gene, one of them [OPN3(NM_014322:c.*83C>T)] is predicted to disrupt a conserved miRNA (has-miR-376c-3p) target site, located in the position 86-93 of OPN3 3’UTR. Our findings suggested that there was a strong possibility that OPN3 single nucleotide variant may play a role in the pathogenesis of melanocytic tumors via prediction of functional phenotype.