Association of TFAP2A gene polymorphism with susceptibility to non-syndromic cleft lip with or without palate risk in south Indian population

The aetiology of non-syndromic cleft lip with or without cleft palate (NSCL/P) is complex involving multiple interacting genes and environmental factors. The primary objective of the present study was to investigate the role of TFAP2A gene single nucleotide polymorphisms (SNPs) in the pathogenesis of NSCL/P. In this study, 173 unrelated NSCL/P patients and 176 controls without clefts were genotyped with TFAP2A rs1675414 (Exon 1), rs3798691 (Intron 1), and rs303050 (Intron 4) variants by allele-specific amplification using the KASPar SNP genotyping system. The method of multifactor dimensionality reduction (MDR) was used to analyze gene-gene interactions. TFAP2A polymorphisms are not found to be associated with non-syndromic cleft lip with or without cleft palate (NSCL/P) at either the genotype or allele levels. No linkage disequilibrium (LD) was found between TFAP2A variants. MDR analysis did not show a significant effect of the TFAP2A gene polymorphisms on susceptibility to NSCL/P (p > 0.05). These results suggest that the analyzed variations in TFAP2A gene might not be associated with NSCL/P pathogenesis in south Indian population.