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These results suggest that IRF6 rs2235375 SNP play a major role in the pathogenesis and risk of developing non-syndromic cleft lip with or without palate.

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Objective: This present study is aimed to investigate the association between interferon regulatory factor 6 (IRF6), single nucleotide polymorphisms (SNPs), and nonsyndromic cleft lip without without cleft palate (NSCLP) in the South Indian population. Subject and Methods: For this study, 190 unrelated NSCLP patients and 189 controls without clefts were genotyped with rs2235371 (V2741) and rs642961 SNPs using PCR-RFLP. The associations between NSCLP groups and IRF6 gene polymorphisms, as well as haplotypes, were analyzed using chi-squared test and 95% confidence interval (95%CI) of the odds ratios were calculated with the control groups as reference. Results: For controls, the minor allele frequencies of both variants, V2741 and rs642961, were 7.1% and 21.1%, respectively. Genotype data for both variants in control and cleft groups follow the Hardy Weinberg Equilibrium. Between cases with NSCLP and controls, the two SNPs showed no differences in frequencies of the genotypes or alleles. The pairwise linkage disequilibrium (LD) values (D’=1 and r2=0.027) between V2741 and rs642961 revealed that these two SNPs are not in strong LD. Haplotype G-T showed a significantly reduced risk for oral clefts (p<0.001) and haplotype A-T increased the risk for oral clefts (p=0.043). Gene-gene interaction showed that the higher risk group contains more GG-CC combination of cases that the controls, but this model was not significantly associated with cleft status (p=0.136) Conclusion: In conclusion, while IRF6 is strongly associated in other populations, this study demonstrated that variants in IRF6 may play a role in NSCLP in a South Indian population, but other genes are expected to play a role in this population as well.