Compensatory interplay between clarin-1 and 1 clarin-2 deafness-associated proteins govern phenotypic variability in hearing

Usher syndrome type III (USH3), caused by mutations in CLRN1 encoding clarin-1, presents with progressive hearing loss, vestibular dysfunction, and retinitis pigmentosa, with striking phenotypic variability even among patients sharing identical mutations. Clarin-1's paralog, clarin-2 (encoded by CLRN2), is similarly implicated in hearing loss, suggesting potential functional interplay between these proteins. To investigate this relationship, we conducted RNA-sequencing of cochlear tissues from Clrn1-/-, Clrn2-/-, and Clrn1-/-Clrn2-/- double-knockout mice, revealing that clarin-1 and clarin-2 cooperatively regulate essential auditory processes, including mechanoelectrical transduction, ionic homeostasis, and synaptic organization. The double knockout mice exhibited synergistic disruption of these pathways, resulting in more severe hearing deficits than either single knockout, demonstrating that these proteins functionally compensate for one another. These findings suggest that CLRN2 variants may influence hearing outcomes in USH3 patients, supporting the integration of CLRN2 analysis into genetic diagnostics. By demonstrating that clarin-1 and clarin-2 share overlapping functional roles in the inner ear, this study redefines USH3 as a network-dependent disorder, offering new insights for therapeutic development. The RNA-seq dataset provides a comprehensive resource for exploring gene interactions in auditory function and advancing precision medicine approaches for hearing loss.