The landscape of gene mutations in a cohort of 3353 Han Chinese children with nonsyndromic hearing loss.

BACKGROUND: Genetic diagnosis plays a critical role in enhancing the identification and clinical management of pediatric hearing loss, ultimately improving both physiological outcomes and social-emotional development. As one of the most prevalent sensory disorders characterized by substantial genetic heterogeneity, hearing loss requires the implementation of efficient diagnostic approaches to inform targeted clinical interventions and personalized care strategies. METHODS: Here, we recruited 3353 Han Chinese children with nonsyndromic hearing loss, including 598 multiplex cases with family history. We employed SNPscan, targeted panel sequencing (TPS), and whole-exome sequencing (WES) to delineate the mutation landscape. FINDINGS: Utilizing a tiered genomic testing strategy, we performed SNPscan for all 3353 participants, TPS for 675 cases, and WES for 204 multiplex cases. We achieved an overall diagnostic yield of 48.3% (1620/3353) in this cohort. Our analysis identified 87 previously unreported variants across 24 genes, including a de novo FOXI1 mutation (c.479_481del) linked to Mondini malformation and enlarged vestibular aqueduct, validated through knock-in mouse models. Additionally, we discovered NEU4 as a candidate gene related to hearing loss, with knockout mice and cellular models demonstrating its role in auditory dysfunction via disrupted neuraminidase activity and axonal development. These findings enrich the spectrum of deafness-related genes and provide a new theoretical foundation for diagnosing hearing loss. INTERPRETATION: This study not only expands the genetic spectrum of hearing loss but also underscores the clinical utility of advanced sequencing in guiding precision therapies and early syndromic surveillance. This study offers a detailed characterization of the genetic landscape of pathogenic variants associated with hearing loss in the Han Chinese population, which will contribute to the design of a cost-effective genetic screening scheme, and also provides valuable insights that contribute to the global understanding of the genetics of hearing loss. FUNDING: This work was supported by the Key Program of National Natural Science Foundation of China, the National Key Research and Development Program of China, the National Natural Science Foundation of China and the Major Fundamental Research Program of the Natural Science Foundation of Shandong Province, China.