BACKGROUND: Hearing loss adversely impacts language development, acquisition, and the social and cognitive maturation of affected children. The hearing loss etiology mainly includes genetic factors and environmental factors, of which the former account for about 50-60%. OBJECTIVE: This study aimed to investigate the genetic basis of autosomal recessive non-syndromic hearing loss (NSHL) by identifying and characterizing novel variants in the CDH23 gene. Furthermore, it seeks to determine the pathogenic potential of the noncanonical splice site variant c.2398-6G >
A. METHODS: Comprehensive clinical evaluation and whole-exome sequencing (WES) were performed on the girl. The WES analysis revealed two novel variants in the CDH23 gene, associated with nonsyndromic deafness 12 (DFNB12). To further explore the pathogenicity of these variants, functional studies involving in vivo splicing analysis were performed on the novel noncanonical splice site variant, c.2398-6G >
A, which was initially classified as a variant of uncertain significance (VUS). RESULTS: Whole-exome sequencing of the patient identified two compound heterozygous variants in CDH23: c.2398-6G >
A, a noncanonical splice site variant, and c.6068C >
A (p. Ser2023Ter), a nonsense mutation. In vitro splicing assays demonstrated that c.2398-6G >
A caused aberrant splicing, leading to a frameshift (p. Val800Alafs*6) and the production of a truncated protein, as confirmed by structural protein analysis. The study revealed novel mutations as likely pathogenic, linking both variants to autosomal recessive NSHL. CONCLUSIONS: Our analyses revealed novel compound heterozygous mutations in CDH23 associated with autosomal recessive NSHL, thereby expanding the mutational landscape of CDH23-related hearing loss and increasing knowledge about the CDH23 splice site variants.