Paired box gene 3 (PAX3) plays an important role in craniofacial development. Mutations in this gene are associated with Waardenburg syndrome, which is a condition characterized by facial anomalies such as widely spaced inner corners of the eyes. PAX3 gene polymorphisms are associated with the relative position of the nasal root (nasion), even among healthy individuals. Facial morphology has primarily been examined using three-dimensional (3D) facial scans of soft tissues, whereas studies focusing on hard tissues remain limited. Therefore, the present study aimed to analyze 3D craniofacial morphology in hard tissues using computed tomography imaging and investigate the influence of PAX3 polymorphisms on the 3D morphology of the nasal root. The analysis was conducted on three populations: 201 healthy Japanese, 74 healthy Korean, and 142 healthy Egyptian individuals. DNA was extracted from saliva samples, and the genotypes of two PAX3 single-nucleotide polymorphisms (SNPs; rs9288572 and rs7559271) were analyzed. A multiple regression analysis of the association between these SNPs and measurements related to nasal root morphology revealed a significant association between rs7559271 and the protrusion angle of the nasion. These findings suggest that PAX3 gene polymorphisms influence the morphological development of the nasal root within the normal range of hard tissues.

Parathyroid hormone 1 receptor (PTH1R) regulates chondrocyte differentiation and mandibular condylar cartilage development, but its contribution to adult mandibular morphology remains unclear. We investigated associations of two PTH1R single-nucleotide polymorphisms (SNPs), rs724448 and rs2242116, with three-dimensional mandibular morphology in 448 orthodontic patients recruited in Japan (199), Korea (79), and Egypt (170). Salivary DNA was genotyped, and computed tomography images were analyzed using geometric morphometrics and conventional measurements. Multivariate Procrustes analysis evaluated overall mandibular shape. Cohort-specific regressions examined natural-log-transformed centroid size (ln(centroid size)), principal component scores, and conventional measurements, adjusting for sex and age and additionally for imaging modality in Japan. Estimates were combined using inverse-variance fixed-effect meta-analysis. Neither variant showed a significant whole-shape association after correction for two SNP tests. Secondary analyses yielded negative estimates for ln(centroid size) and nominal associations with selected anteroposterior dimensions and cohort-specific principal component scores. None remained significant after either Bonferroni or Benjamini–Hochberg false-discovery-rate correction across 408 tests. These findings provide no statistically robust evidence linking either variant to adult mandibular morphology. Nominal findings require independent replication.