Predicting pathogenicity for novel hearing loss mutations based on genetic and protein structure approaches

Paula I Buonfiglio,Liliana Francipane,Carlos D Bruque,Bibiana Paoli,Ana Belén Elgoyhen,Ernesto Goldschmidt,Sebastián Menazzi,Vanesa Lotersztein,Florencia Giliberto,Viviana Dalamón,Leonela Luce

doi:10.1038/s41598-021-04081-2

Abstract

Hearing loss is a heterogeneous disorder. Identification of causative mutations is demanding due to genetic heterogeneity. In this study, we investigated the genetic cause of sensorineural hearing loss in patients with severe/profound deafness. After the exclusion of GJB2-GJB6 mutations, we performed whole exome sequencing in 32 unrelated Argentinean families. Mutations were detected in 16 known deafness genes in 20 patients: ACTG1, ADGRV1 (GPR98), CDH23, COL4A3, COL4A5, DFNA5 (GSDDE), EYA4, LARS2, LOXHD1, MITF, MYO6, MYO7A, TECTA, TMPRSS3, USH2A and WSF1. Notably, 11 variants affecting 9 different non-GJB2 genes resulted novel: c.12829C > T, p.(Arg4277*) in ADGRV1; c.337del, p.(Asp109*) and c.3352del, p.(Gly1118Alafs*7) in CDH23; c.3500G > A, p.(Gly1167Glu) in COL4A3; c.1183C > T, p.(Pro395Ser) and c.1759C > T, p.(Pro587Ser) in COL4A5; c.580 + 2 T > C in EYA4; c.1481dup, p.(Leu495Profs*31) in LARS2; c.1939 T > C, p.(Phe647Leu), in MYO6; c.733C > T, p.(Gln245*) in MYO7A and c.242C > G, p.(Ser81*) in TMPRSS3 genes. To predict the effect of these variants, novel protein modeling and protein stability analysis were employed. These results highlight the value of whole exome sequencing to identify candidate variants, as well as bioinformatic strategies to infer their pathogenicity.

Highlights

Deafness affects approximately 1 out of 500–1000 newborns and is mainly of genetic origin
This study presents a custom-designed multistep methodology to evaluate the impact of genetic variants found in patients with hearing loss (HL) on protein function
Thirty-two patients with different forms of hearing loss were studied by Whole-exome sequencing (WES), followed by data filtering based on 183 genes reported for this pathology

Summary

Introduction

Deafness affects approximately 1 out of 500–1000 newborns and is mainly of genetic origin. Despite the wide genetic heterogeneity of Nonsyndromic autosomal recessive hearing loss, a few mutations in the GJB2 and GJB6 genes (encoding connexin-26 and 30, respectively) account for nearly 50% of the cases in the Mediterranean p opulation[4,5,6,7,8]. After the exclusion of GJB2 and GJB6 in patients, new genes and new genetic variants in reported genes have been described using WES in the research and clinical molecular diagnosis of syndromic and nonsyndromic forms of hearing impairment. This study presents a custom-designed multistep methodology to evaluate the impact of genetic variants found in patients with HL on protein function This highlights the importance of developing combined molecular protein structure studies together with database analysis to evaluate and characterize the impact of reported and novel gene variants

Methods

Results

Conclusion