Functional reassessment of extended splice region variants in MYO7A with hearing loss and Usher syndrome

MYO7A is a causal gene, underlying Usher syndrome type 1B (USH1B) and both autosomal recessive (DFNB2) and dominant (DFNA11) non-syndromic hearing loss. Despite the large number of reported MYO7A variants (over 2,200), variants located in an extended splice region remain difficult to interpret and are often classified as variants of uncertain significance (VUS). We investigated the clinical impact of MYO7A extended splice region variants, located within ±50 bp of exon-intron boundaries, by analyzing a nationwide Chinese cohort of 10,664 undiagnosed individuals with hearing loss. Twelve such variants (in 11 probands, two variants were in cis) were identified for functional analysis. Using minigene splicing assays coupled with in silico splicing predictions, we evaluated each variant's effect on pre-mRNA processing and applied ACMG/AMP guidelines for classification. Six of the tested variants completely disrupted normal splicing, and eight variants in total were reclassified from VUS to pathogenic or likely pathogenic based on aberrant transcript outcomes. Notably, several variants generated multiple distinct abnormal transcripts, and two-thirds of these variants fell within the myosin motor domain (others in the FERM2 domain). Splicing predictions from in silico algorithms were largely concordant with the experimental results, further supporting their utility in variant interpretation. This functional evidence enabled definitive molecular diagnoses in previously unresolved cases spanning DFNA11, DFNB2, and USH1B phenotypes. In summary, our study demonstrated that integrating experimental splicing assays with predictive tools can definitively determine the pathogenicity of extended splice region variants in MYO7A, thereby improving the diagnostic accuracy of genetic testing for both non-syndromic and syndromic hearing loss. This approach could be applied to other genes to enhance genetic diagnosis.