Major allelic variants in IRF6 and the association with Non-Syndromic orofacial Clefts: Insights from a Kerala-Based Case-Control study

Abstract

Orofacial clefts, are among the most common congenital defects. Previous research has consistently shown that particular IRF6 gene polymorphisms are related to nonsyndromic cleft lip with or without cleft palate (NSCL/P), which has been verified across many populations. This study aimed to investigate the role of specific IRF6 polymorphisms in nonsyndromic orofacial clefts (NSOFC) within the Kerala population. A total of 100 NSOFC cases and matched controls were genotyped for five IRF6 single nucleotide polymorphisms (SNPs): rs2235371, rs7552506, rs2235373, rs2235375, and rs2013162 using Next-Generation Sequencing. Statistical analyses (VassarStats, SNPstat, and MedCalc) and haplotype construction (Haploview) were performed to assess allelic, genotypic, and haplotype associations. Results showed that the major alleles (primarily “G” in four SNPs and “C” in rs2013162) were significantly more frequent in healthy controls, suggesting a protective effect. Conversely, minor alleles were overrepresented in NSOFC cases, indicating an elevated risk. Four SNPs (rs2235371, rs7552506, rs2235373, rs2235375) demonstrated robust protective effects under multiple inheritance models, while rs2013162 exhibited a less pronounced influence, displaying a notable protective effect only in the nonsyndromic cleft lip with palate (NSCLP) subgroup. Haplotype analysis identified G-C-G as consistently protective, whereas C-A-C and C-A-G conferred a higher risk for NSOFC. Overall, these findings underscore the importance of IRF6 variants in NSOFC etiology and suggest that considering both individual SNPs and haplotypes can enhance understanding of orofacial cleft susceptibility. Further large-scale studies are recommended to validate these associations.