Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment

Abstract

DNA samples from five members of a multiplex non-consanguineous Cameroonian family, segregating prelingual and progressive autosomal recessive non-syndromic sensorineural hearing impairment, underwent whole exome sequencing. We identified novel bi-allelic compound heterozygous pathogenic variants in CLIC5. The variants identified, i.e., the missense [NM_016929.5:c.224T>C; p.(L75P)] and the splicing (NM_016929.5:c.63+1G>A), were validated using Sanger sequencing in all seven available family members and co-segregated with hearing impairment (HI) in the three hearing impaired family members. The three affected individuals were compound heterozygous for both variants, and all unaffected individuals were heterozygous for one of the two variants. Both variants were absent from the genome aggregation database (gnomAD), the Single Nucleotide Polymorphism Database (dbSNP), and the UK10K and Greater Middle East (GME) databases, as well as from 122 apparently healthy controls from Cameroon. We also did not identify these pathogenic variants in 118 unrelated sporadic cases of non-syndromic hearing impairment (NSHI) from Cameroon. In silico analysis showed that the missense variant CLIC5-p.(L75P) substitutes a highly conserved amino acid residue (leucine), and is expected to alter the stability, the structure, and the function of the CLIC5 protein, while the splicing variant CLIC5-(c.63+1G>A) is predicted to disrupt a consensus donor splice site and alter the splicing of the pre-mRNA. This study is the second report, worldwide, to describe CLIC5 involvement in human hearing impairment, and thus confirms CLIC5 as a novel non-syndromic hearing impairment gene that should be included in targeted diagnostic gene panels.

Etiologies of Childhood Hearing Impairment in Schools for the Deaf in Mali

“…In fact, most of the familial cases reported in this study were seen in the Soninke ethnic group, which has a high tendency for consanguineous marriage. In Mali, as in numerous understudied African populations, it is probable that numerous variants of known and potentially novel genes remain to be discovered (37)(38)(39). Among cases with a suspected genetic origin, we identified two families with WS, the most common SHI reported in some countries (8).…”

Mutation of the EPHA2 Tyrosine-Kinase Domain Dysregulates Cell Pattern Formation and Cytoskeletal Gene Expression in the Lens

“…The most downregulated gene in Epha2-indel722 mutant lenses (<−1000-fold), and to a lesser extent in Epha2-null lenses (<−2-fold), was that for chloride intracellular channel 5 (CLIC5). Mutations in the human CLIC5 gene have been linked with progressive autosomal recessive, non-syndromic sensorineural hearing impairment with or without vestibular dysfunction and CLIC5 was found to be abundantly expressed in the fetal inner ear [71,72]. Similarly, in jitterbug (jbg) mice a spontaneous deletion mutation in Clic5 underlies hearing loss with vestibular and renal dysfunction and CLIC5 was localized to the base of hair cell stereocilia where it complexes with radixin, taperin, and myosin VI to stabilize cell membrane-actin cytoskeleton attachments [73].…”

A monoallelic variant in EYA1 is associated with Branchio‐Otic syndrome in a Malian family

“…We initially sent DNA samples of individuals II.5 and II.6 (Figure 1a ) for exome sequencing at Omega Bioservices (Norcross, GA, USA). The library preparation was performed with an Illumina Nextera Rapid Capture Exome Kit® (Illumina, San Diego, CA, USA) following the manufacturer's instructions, and the resulting libraries were hybridized with a 37‐Mb probe pool to enrich exome sequences (Wonkam‐Tingang et al, 2020 ). Sequencing was performed on an Illumina HiSeq 2500 sequencer using the pair‐end 150 bp run format.…”

“…Candidate variants were considered when: (1) they occurred in known HI genes (and genes expressed in the inner ear); (2) they had a predicted effect on protein function or pre‐mRNA splicing (nonsense, missense, start‐loss, frameshift, splicing, start‐loss, etc. ); and (3) they co‐segregated with the phenotype within the family (Wonkam‐Tingang et al, 2020 ).…”