Abstract
COCH is the most abundantly expressed gene in the cochlea. Unsurprisingly, mutations in COCH underly hearing loss in mice and humans. Two forms of hearing loss are linked to mutations in COCH, the well-established autosomal dominant nonsyndromic hearing loss, with or without vestibular dysfunction (DFNA9) via a gain-of-function/dominant-negative mechanism, and more recently autosomal recessive nonsyndromic hearing loss (DFNB110) via nonsense variants. Using a combination of targeted gene panels, exome sequencing, and functional studies, we identified four novel pathogenic variants (two nonsense variants, one missense, and one inframe deletion) in COCH as the cause of autosomal recessive hearing loss in a multi-ethnic cohort. To investigate whether the non-truncating variants exert their effect via a loss-of-function mechanism, we used minigene splicing assays. Our data showed both the missense and inframe deletion variants altered RNA splicing by creating an exon splicing silencer and abolishing an exon splicing enhancer, respectively. Both variants create frameshifts and are predicted to result in a null allele. This study confirms the involvement of loss-of-function mutations in COCH in autosomal recessive nonsyndromic hearing loss, expands the mutational landscape of DFNB110 to include coding variants that alter RNA splicing, and highlights the need to investigate the effect of coding variants on RNA splicing.
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Acknowledgements
We would like to thank the patients for their participation in this study. This study was funded by NIDCDs R01s DC002842, DC012049, and DC017955 to RJS and R56DC011803 to SR.
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KTB, AG, MH, ZMA, RJS, HA, and SR: conception and study design; KTB, MR, LTH, MH, KF, EMR, CJN, and MS performed experiments; KTB, AG, ZMA, RJS, HA, and SR analyzed data and drafted the initial manuscript. All authors have reviewed and approved the finalized manuscript.
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439_2020_2197_MOESM2_ESM.tif
Supplementary Figure 1. Minigene splicing assays. Gel electrophoresis and sequence chromatograms of wildtype, empty pET01 vector, and the c.271C>G mutation. Visualization and Sanger sequencing showed no difference in splicing between the wildtype and mutant (TIF 9982 kb)
439_2020_2197_MOESM3_ESM.tif
Supplementary Figure 2. Amino acid conservation analysis among different vertebral species through Clustal omega (TIF 19105 kb)
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Booth, K.T., Ghaffar, A., Rashid, M. et al. Novel loss-of-function mutations in COCH cause autosomal recessive nonsyndromic hearing loss. Hum Genet 139, 1565–1574 (2020). https://doi.org/10.1007/s00439-020-02197-5
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DOI: https://doi.org/10.1007/s00439-020-02197-5