Rare missense variants in NECTIN1 alter local protein structure and may contribute to non-syndromic cleft lip with or without palate

Abstract

Introduction Orofacial cleft is a congenital anomaly influenced by genetic and environmental factors. NECTIN1 encodes an adhesion protein critical for the adherens junctions and has been associated with orofacial clefts. This study aimed to investigate the contribution of NECTIN1 to the etiology of NSCL/P in a population from Patagonia, Argentina, a region with a high prevalence of orofacial clefts. Methods First, an association study was conducted to evaluate the relationship between orofacial clefts and two NECTIN1 single nucleotide variants: rs3829260 (G > C) and rs7940667 (C > A). Genotyping of 132 affected families was performed. The transmission disequilibrium test was applied, and identified variants were analyzed in silico using VarSome and ClinVar. No statistically significant association was found for rs3829260 (G > C) or rs7940667 (C > A). Subsequently, all six exons of NECTIN1 were sequenced in 116 probands. Molecular modeling was then performed to evaluate the functional impact on protein structure. Results Three rare heterozygous variants were identified in five probands: two non-synonymous variants (p.(Arg199Gln) and p.(Gly44Ser)) and one synonymous variant p.(His394=). Molecular modeling suggested that p.(Arg199Gln) and p.(Gly44Ser) could locally impact the structural dynamics and glycosylation pattern. Conclusion These findings show the potential involvement of NECTIN1 in orofacial clefts and suggest that rare genetic variants may contribute to disease susceptibility.