Tooth agenesis-related GLI2 and GLI3 genes may contribute to craniofacial skeletal morphology in humans

•Tooth agenesis and skeletal malocclusions may share a similar genetic background.•GLI2 and GLI3 genes are possible genetic markers for tooth agenesis.•GLI2 and GLI3 genes may contribute to the development of skeletal malocclusions.•GLI2 rs3738880 may play a role in the development of tooth agenesis and Class III.•Tooth agenesis could be a predictor of craniofacial morphology in some cases. The present cross-sectional, multi-centre, genetic study aimed to determine, whether single nucleotide polymorphisms (SNPs) in tooth agenesis (TA)-associated GLI2 and GLI3 genes contribute to the development of craniofacial skeletal morphology in humans. Orthodontic patients from an ethnically heterogeneous population were selected for the present study (n = 594). The presence or absence of TA was determined by analysis of panoramic radiography and dental records. The subjects were classified according to their skeletal malocclusion and facial growth pattern by means of digital cephalometric analysis. Genomic DNA was extracted from squamous epithelial cells of the buccal mucosa and SNPs in GLI2 (rs3738880, rs2278741) and GLI3 (rs929387, rs846266) were analysed by polymerase chain reaction using TaqMan chemistry and end-point analysis. Class II skeletal malocclusion presented a significantly lower frequency of TA (P