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Objective: To investigate the association between the risk of tooth agenesis and single-nucleotide polymorphisms (SNPs) of MSX1 and PAX9 genes in nonsyndromic cleft patients. Materials and Methods: The subjects were 126 Korean nonsyndromic cleft patients. Tooth agenesis type (TAT) was classified as none (0); cleft area (1); cleft area + other area (2); and other area (3) based on agenesis of the maxillary lateral incisor (MXLI) and another tooth within or outside the cleft area. TAT was further grouped into two subcategories (0 and 1) and four subcategories (0, 1, 2, and 3). Three SNPs of MSX1 and 10 SNPs of PAX9 were investigated using Fisher's exact test and logistic regression analysis. Results: Although the association between genotype distribution of PAX9-rs7142363 and TAT was significant (P &amp;lt; .05 in four subcategories), genotypic odds ratios (GORs) of SNPs in each TAT were not meaningful. However, for MSX1-rs12532 and PAX9-rs2073247, associations between genotypic distribution and TAT were significant (P &amp;lt; .01 in four subcategories and P &amp;lt; .05 in two subcategories; P &amp;lt; .01 in two subcategories, respectively). In cleft area, GORs of MXLI agenesis in genotypes GA of MSX1-rs12532 and CT of PAX9-rs2073247 were increased by 3.14-fold and 4.15-fold compared with genotype GG of MSX1-rs12532 and CC of PAX9-rs2073247, respectively (P &amp;lt;. 01; P &amp;lt; .05). In cleft area + other area, the GOR of agenesis of MXLI and another tooth in genotype AA of MSX1-rs12532 was increased by fivefold compared with genotype GG (P &amp;lt; .05). Conclusion: Genetic disturbances of MSX1 and PAX9 genes are associated with tooth agenesis within and outside the cleft area.

Associations between the risk of tooth agenesis and single-nucleotide polymorphisms of MSX1 and PAX9 genes in nonsyndromic cleft patients