Introduction and Aim: Cleft lip and palate (CLP) is complex craniofacial deformity in which both the environmental and genetic factors play a role. Congenital hypodontia is the absence of permanent teeth. As congenitally missing maxillary lateral incisors (CMML) and CLP both occur at the suture between premaxilla and maxillary posterior segments, this finding has directed us to investigate if both anomalies could be affected by the same genetic factors. Therefore, the aim of our study is to investigate if there is a common genetic pattern between the occurrence of CLP and congenitally CMMLs. Subjects and Methods: Muscle Segment Homeobox-1 (MSX1) is one of the common candidate genes of hypodontia and CLP. In this study, the role of MSX1 for CLP and CMML was evaluated. The CLP and CMML groups were consisted of 51 and 48 participants, respectively. 3cc blood samples with EDTA were collected and genomic deoxyribonucleic acids were isolated. To screen for putative mutations, two exons of MSX1 gene as well as their exon–intron boundaries were amplified by the PCR and analyzed with Sanger sequencing method. Results: In both groups, the same SNP (c. *6C>T, rs 8670) which is localized in 3'untranslated region of MSX1 gene was detected. Minor allele frequency, heterozygosity, and Chi-square test for Hardy–Weinberg equilibrium at c. *6C>T variation were computed. The expected wild-type, heterozygous, and homozygous allele frequencies of c. *6C>T variation were % 65.61, % 30.78, and % 3.61, respectively. However, the frequencies were %47.9, %45.8, and %6.3 in CMML group and %80.4, %11.8, and % 7.8 in CLP group. These frequencies were diverted from normal for both groups, and the differences between the groups were statistically significant P < 000.1 (Chi-square test). Conclusion: The existence of common polymorphisms and diversions from the normal population in the 3'untranslated region of the MSX1 gene is supporting the hypothesis of a possible relationship between CLP and CMML incisors.
