Progressive hearing loss and vestibular dysfunction caused by a homozygous nonsense mutation in CLIC5

Abstract

In a consanguineous Turkish family diagnosed with autosomal recessive nonsyndromic hearing impairment (arNSHI), a homozygous region of 47.4 Mb was shared by the two affected siblings on chromosome 6p21.1-q15. This region contains 247 genes including the known deafness gene MYO6. No pathogenic variants were found in MYO6, neither with sequence analysis of the coding region and splice sites nor with mRNA analysis. Subsequent candidate gene evaluation revealed CLIC5 as an excellent candidate gene. The orthologous mouse gene is mutated in the jitterbug mutant that exhibits progressive hearing impairment and vestibular dysfunction. Mutation analysis of CLIC5 revealed a homozygous nonsense mutation c.96T>A (p.(Cys32Ter)) that segregated with the hearing loss. Further analysis of CLIC5 in 213 arNSHI patients from mostly Dutch and Spanish origin did not reveal any additional pathogenic variants. CLIC5 mutations are thus not a common cause of arNSHI in these populations. The hearing loss in the present family had an onset in early childhood and progressed from mild to severe or even profound before the second decade. Impaired hearing is accompanied by vestibular areflexia and in one of the patients with mild renal dysfunction. Although we demonstrate that CLIC5 is expressed in many other human tissues, no additional symptoms were observed in these patients. In conclusion, our results show that CLIC5 is a novel arNSHI gene involved in progressive hearing impairment, vestibular and possibly mild renal dysfunction in a family of Turkish origin.

Figure 1

(a) Pedigree of family W05-009 and segregation of the CLIC5 c.96T>A variant. (b) Longitudinal binaural mean air-conduction pure tone thresholds are shown of affected members of family W05-009. Age (years) is shown with a symbol key. The p95 line, matched for age and sex, indicates that 95% of the population has thresholds lower than these. (c) Regression analysis of longitudinal binaural mean air conduction threshold data for each frequency separately. Circles indicate individual II.2, squares indicate individual II.3. Annual threshold deterioration is shown behind the symbol key for each frequency.

Figure 2

(a) Schematic overview of the chromosomal region 6q21.1-q15 showing the homozygous regions (black bars) identified in the affected individuals of family W05-009. The homozygous region of individual II.2 delimits the region to 47.4 Mb. Mb positions and chromosome bands are according to the UCSC genome browser (GRCh37). (b) Partial sequences are shown of CLIC5 exon 2 from an affected member, a parent and an unaffected sib of family W05-009. The predicted amino-acid changes and the surrounding amino acids are indicated above the sequence. Mutated nucleotides are marked by an arrowhead. As reference sequence NM_016929.4 was employed.

Figure 3

CLIC5 expression profile in human tissues. Relative CLIC5 mRNA levels as determined by qPCR in human fetal (a) and adult (b) tissues. The relative expression values were determined by using the comparative delta Ct method. The expression levels are relative to those in liver, which showed the lowest CLIC5 expression of all the tissues that were tested.