Association of with Non-Syndromic Cleft Lip with or without Cleft Palate in a Japanese Population.

Non-syndromic cleft lip with or without palate (NSCL/P) is a common, multifactorial congenital anomaly. As genetic associations can be population-specific, this study aimed to investigate single-nucleotide polymorphisms (SNPs) in the , , and genes for association with NSCL/P in a Japanese cohort. A case-control study was conducted with 310 Japanese patients with NSCL/P and 308 ethnically matched healthy controls from Aichi Gakuin Dental Hospital. We genotyped SNPs rs7078160 (), rs13041247 (), and rs3809857 () using TaqMan assays. Associations were assessed using chi-squared tests, with results stratified by sex and corrected for multiple comparisons using the Bonferroni method. The rs7078160 A allele was significantly associated with an increased risk for NSCL/P (OR = 1.67, < 0.00001). The association was particularly strong in females (OR = 1.93, < 0.00001) but not significant in males after correction. The rs13041247 variant showed a nominal protective association with the NSCLO subtype that was not significant after Bonferroni correction. No significant association was found for . A notable gene-gene interaction was observed, where carrying risk alleles for both and significantly increased overall NSCL/P risk (OR = 2.65, = 0.00008). rs7078160 is a significant risk factor for NSCL/P in the Japanese population, with a pronounced female-specific effect. A synergistic interaction between and elevates disease risk, whereas was not implicated in this cohort. These findings underscore the population-specific genetic architecture of NSCL/P.