TBC1D24 mutation causes autosomal-dominant nonsyndromic hearing loss

Abstract

Hereditary hearing loss is extremely heterogeneous. Over 70 genes have been identified to date, and with the advent of massively parallel sequencing, the pace of novel gene discovery has accelerated. In a family segregating progressive autosomal-dominant nonsyndromic hearing loss (NSHL), we used OtoSCOPE® to exclude mutations in known deafness genes and then performed segregation mapping and whole-exome sequencing to identify a unique variant, p.Ser178Leu, in TBC1D24 that segregates with the hearing loss phenotype. TBC1D24 encodes a GTPase-activating protein expressed in the cochlea. Ser178 is highly conserved across vertebrates and its change is predicted to be damaging. Other variants in TBC1D24 have been associated with a panoply of clinical symptoms including autosomal recessive NSHL, syndromic hearing impairment associated with onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS syndrome), and a wide range of epileptic disorders.

Keywords: OtoSCOPE®; TBC1D24; autosomal dominant; hearing impairment; hearing loss; nonsyndromic; pleiotropy.

Figure 1. Pedigree and audiometric profiles

A: The pedigree of a four-generation family segregating ADNSHL. DNA samples were available for 10 affected and 11 unaffected individuals. Males are denoted in squares and females in circles. Black shading indicates ADNSHL while no shading represents normal hearing. G, W, and * denote genotyping, WES and OtoSCOPE® testing, respectively. Individuals marked as +/− are heterozygous for the TBC1D24 p.Ser178Leu variant. Individuals marked as −/− do not carry the variant. B: Cross-sectional linear regression analysis of binaural mean air conduction threshold on age (years) for each frequency separately. The regression line (dashed) is included for each frequency. ATD, (in bold print) the regression coefficient (dB/year), is included in each panel; asterisk indicates significant progression. C: ARTA. Binaural mean air conduction threshold (dB HL) is presented for the ages 30, 40, 50, and 60 years. Hearing levels ranged from 20 to 70 dB, depending on age and frequency; the ATD was ∼0.8 dB/year at 2-4 kHz, and ∼1.6 dB/year at the other frequencies.

Figure 2. WES, segregation analysis and TBC1D24 mutation and expression

A: WES results in affected individuals showing the final variant numbers for each exome and shared variants. 46 variants were shared amongst all three individuals. B: Identification of 3 regions on chr8, chr11 and chr16. SNP index is reported on the x-axis while the inheritance model score is indicated on the y-axis. C: Representative chromatograms from wild type and mutant sequences (red arrow indicates variant position). D: Alignment of TBC1D24 orthologs shows the conservation of Ser178 (in red) across species. E: Localization of TBC1D24 mutations associated with ADNSHL, ARNSHL, epilepsy phenotypes and DOORS syndrome. The variant p.Ser178Leu (in red) is located on the TBC domain. Phenotypes including deafness are shown above the diagram; epileptic phenotypes are shown below. F: TBC1D24 expression in P2 mouse cochlea. i: Staining with actin antibody showing 3 rows of OHC and one row of IHC. ii: Staining with DAPI antibody. iii: TBC1D24 staining in the cell body of OHC and IHC. iv: Merged pictures. v, vi and vii: SG staining with F-actin, DAPI and TBC1D24 antibodies, respectively. Scale bar represents 50 μm.