Two novel AXIN2 variants in isolated tooth agenesis and the AXIN2-associated tooth agenesis pattern

Variants in the AXIN2 gene are associated with colorectal cancer, oligodontia-colorectal cancer syndrome, and isolated tooth agenesis. To date, only 19 AXIN2 variants have been linked to tooth agenesis. This study aimed to identify novel AXIN2 variants in individuals with isolated tooth agenesis, evaluate their pathogenicity, and summarize possible patterns of AXIN2-associated tooth agenesis through a systematic literature review.

Whole-exome sequencing (WES) was performed to detect AXIN2 variants in individuals with isolated tooth agenesis. AXIN2 cDNA clone sequencing and mRNA expression analysis were performed using peripheral blood mononuclear cells (PBMCs) from carriers. Pathogenicity of the identified variants was evaluated through bioinformatic analyses, structural modeling, and in vitro functional assays. A systematic literature review was further performed to characterize the AXIN2-associated tooth agenesis pattern.

Two novel heterozygous AXIN2 variants were identified: a missense variant (c.2078C > T; p.Thr693Met) and a splicing variant (c.1060-3T > C; p.Arg354Leufs*2). Bioinformatic analyses classified the c.2078C > T variants as likely pathogenic and the c.1060-3T > C as pathogenic. Structural predictions indicated that the p.Thr693Met variant may impair RNA base pairing and disrupt protein structure, while the p.Arg354Leufs*2 variant led to a truncated protein due to premature termination. Functional assays demonstrated that p.Thr693Met aberrantly activated Wnt/β-catenin signaling in vitro, and p.Arg354Leufs*2 resulted in approximately 50% reduction of AXIN2 transcript levels in patients' PBMCs. Analysis of tooth agenesis patterns revealed that the mandibular (67.9%) and maxillary (64.1%) second premolars were the most frequently missing teeth.

This study expands the mutational spectrum of AXIN2-associated isolated tooth agenesis and provides in vitro functional evidence supporting the pathogenicity of the identified variants. These findings offer important insights for genetic diagnosis and counseling in affected families.