IRF6 rs2235371 as a risk factor for non-syndromic cleft palate only among the Deutero-Malay race in Indonesia and its effect on the IRF6 mRNA expression level

Background During the early embryological development of the face, complex orofacial failure results in a non-syndromic cleft lip and palate (NS CLP). The interferon regulatory factor 6 gene (IRF6) rs2235371 is a non-synonymous polymorphism that is one of the strong candidate genes associated with NS CLP. Objectives The purpose of this study was to determine IRF6 rs2235371 as a risk factor for NS CLP and its phenotypes, including complete unilateral cleft lip and palate (CUCLP), bilateral cleft lip and palate (BCLP), cleft lip only (CL), and cleft palate only (CP), as well as to examine the effect of the polymorphism on the IRF6 mRNA expression levels among the Deutero-Malay race in Indonesia. Material and methods This study used a case-control design and enrolled 264 samples, including 158 NS CLP cases (42 NS CUCLP, 34 NS BCLP, 33 NS CL, and 49 NS CP) and 106 control subjects. DNA was extracted from venous blood, and then subjected to polymerase chain reaction (PCR) and sequencing. The odds ratio (OR) was used to determine the risk factor for NS CLP and its phenotypes. The Livak, Kruskal-Wallis and Mann-Whitney Utests were used to determine mRNA expression levels in the oral epithelium, followed by real-time quantitative PCR (RT-qPCR). Results. Among all of the NS CLP cases, in the NS CP phenotype, OR for the A mutant allele and the GA genotype was 2,492 (p = 0.017) and 2,114 (p = 0.048), respectively. The IRF6 mRNA expression level of the GA genotype was higher in the NS CP subjects as compared to the GG genotype (p = 0.031). Conclusions The IRF6 rs2235371 polymorphism is associated with the NS CP phenotype in Deutero-Malay patients from Indonesia and it affects the IRF6 mRNA expression level.