A Novel Pathogenic Haplotype in CDH23 Causing DFNB12: The Combined Effect of Two Individually Benign Variants

Background: account for a significant proportion of familial autosomal recessive non-syndromic hearing loss (DFNB12), a common subtype of hereditary hearing loss worldwide. Aims: To elucidate the molecular basis and pathogenic mechanism of DFNB12 in an affected girl from a nine-member pedigree. Study Design: Family-based genetic study with pedigree analysis. Methods: Clinical whole-exome sequencing combined with pedigree analysis was used to identify disease-causing mutations. The potential functional consequences of these mutations were investigated using structural bioinformatic approaches, including homology modeling, molecular dynamics simulations, and other relevant tools. Results: The proband carried compound heterozygous variants: a known pathogenic maternal variant (c.6049G > A) and a paternal haplotype comprising two linked variants (c.3262G > A and c.6911G > A), each individually classified as benign. Pedigree segregation analysis demonstrated that the paternal haplotype acts as a single pathogenic allele. Conclusion: Two individually benign variants can combine to form a novel pathogenic haplotype (c.3262A–c.6911A). This mechanism may be under-recognized in routine variant interpretation pipelines. Our findings underscore the importance of evaluating the combined effects of linked benign variants to ensure accurate genetic counseling.