Genetic Susceptibility to Non-Syndromic Cleft Lip and Palate and Enamel Hypomineralization: Evidence from Variants and Gene-Gene Interactions in Calcium Homeostasis Genes

Objective To investigate associations between single nucleotide polymorphisms (SNPs) in calcium homeostasis-related genes and combined phenotypes defined by non-syndromic cleft lip with or without palate involvement (NSCL ± P) and enamel hypomineralization (MIH and/or HSPM), including SNP-SNP interactions. Materials and Methods In this cross-sectional study with a comparison group, 230 children aged 6–14 years (125 with NSCL ± P; 105 controls) were clinically assessed for MIH/HSPM by calibrated examiners. Variants in VDR, CYP24A1, PTH , and CALCR were genotyped by real-time PCR. Participants were classified into four combined phenotype groups according to NSCL ± P and hypomineralization status. Genotype distributions were evaluated under codominant, dominant, and recessive models, followed by multinomial logistic regression. SNP-SNP interactions were analyzed using model-based multifactor dimensionality reduction. Results MIH/HSPM was more frequent in participants with NSCL ± P than in controls (44.8% vs. 37.1%), although not significantly (p = 0.240). PTH rs694 was the only SNP associated with the combined phenotype groups. Under the recessive model, the CC genotype was associated with lower odds of NSCL ± P with MIH/HSPM compared with controls without MIH/HSPM (OR = 0.29; 95% CI: 0.10–0.84; p = 0.023). A significant interaction between PTH rs6256 and CALCR rs1801197 was also identified for the concomitant presence of NSCL ± P and MIH/HSPM (p_perm = 0.007). Conclusion Calcium homeostasis-related genetic variation may contribute to the concomitant occurrence of NSCL ± P and MIH/HSPM, particularly through PTH -related pathways. Clinical relevance: Identifying genetic factors shared by NSCL ± P and MIH/HSPM may improve understanding of susceptibility to enamel defects in children with clefts and support more individualized preventive dental care.