Novel Mutations in CLPP, LARS2, CDH23, and COL4A5 Identified in Familial Cases of Prelingual Hearing Loss

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

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.

TMPRSS3 Gene Variants With Implications for Auditory Treatment and Counseling

Objective: To identify and report novel variants in the TMPRSS3 gene and their clinical manifestations related to hearing loss as well as intervention outcomes. This information will be helpful for genetic counseling and treatment planning for these patients.

Methods: Literature review of previously reported TMPRSS3 variants was conducted. Reported variants and associated clinical information was compiled. Additionally, cohort data from 18 patients, and their families, with a positive result for TMPRSS3-associated hearing loss were analyzed. Genetic testing included sequencing and copy number variation (CNV) analysis of TMPRSS3 and the Laboratory for Molecular Medicine’s OtoGenome-v1, -v2, or -v3 panels. Clinical data regarding patient hearing rehabilitation was interpreted along with their genetic testing results and in the context of previously reported cochlear implant outcomes in individuals with TMPRSS3 variants.

Results: There have been 87 previously reported TMPRSS3 variants associated with non-syndromic hearing loss in more than 20 ancestral groups worldwide. Here we report occurrences of known variants as well as one novel variant: deletion of Exons 1–5 and 13 identified from our cohort of 18 patients. The hearing impairment in many of these families was consistent with that of previously reported patients with TMPRSS3 variants (i.e., typical down-sloping audiogram). Four patients from our cohort underwent cochlear implantation.

Conclusion: Bi-allelic variants of TMPRSS3 are associated with down-sloping hearing loss regardless of ancestry. The outcome following cochlear implantation in patients with variants of TMPRSS3 is excellent. Therefore, cochlear implantation is strongly recommended for hearing rehabilitation in these patients.

Molecular genetic landscape of hereditary hearing loss in Pakistan

Approximately 14.5 million Pakistani individuals have a hearing loss and half of these cases may be due to genetic causes. Though significant progress has been made in uncovering genetic variants for recessively inherited nonsyndromic deafness, Pendred syndrome, and Usher syndromes, the same is not true for dominantly inherited hearing loss, most syndromic cases and deafness with complex inheritance patterns. Variants of 57 genes have been reported to cause nonsyndromic recessive deafness in Pakistan, though most are rare. Variants of just five genes GJB2, HGF, MYO7A, SLC26A4, and TMC1 together explain 57% of profound deafness while those of GJB2, MYO15A, OTOF, SLC26A4, TMC1, and TMPRSS3 account for 47% of moderate to severe hearing loss. In contrast, although variants of at least 39 genes have been implicated in different deafness syndromes, their prevalence in the population and the spectrum of mutations have not been explored. Furthermore, research on genetics of deafness has mostly focused on individuals from the Punjab province and needs to be extended to other regions of Pakistan. Identifying the genes and their variants causing deafness in all ethnic groups is important as it will pinpoint rare as well as recurrent mutations. This information may ultimately help in offering genetic counseling and future treatments.