A Novel Missense WFS1 Variant: Expanding the Mutational Spectrum Associated with Nonsyndromic Low-Frequency Sensorineural Hearing Loss

Abstract

Background: Nonsyndromic low-frequency sensorineural hearing loss (LFSNHL) is an uncommon form of hearing loss (HL) that typically affects frequencies at 2000 Hz and below. Heterozygous variants in the WFS1 gene at the DFNA6/14/38 locus are considered a common cause of LFSNHL. To date, 34 different pathogenic genetic variants have been reported to cause LFSNHL with seven of these variants identified in the Chinese population. However, limited reports are available on the association between WFS1 gene and LFSNHL. Here, we report a five-generation Chinese family with an autosomal dominant inheritance pattern of postlingual and progressive LFSNHL.

Methods: Routine clinical and audiological examinations were performed on 16 affected and 7 healthy members in this family. The targeted next-generation sequencing of 127 known deafness genes was performed to identify variants in affected individuals. Sanger sequencing were further employed to confirm the pathogenic variant identified.

Results: A novel heterozygous pathogenic genetic variant c.2530G > T (p.Ala844Ser) was identified in the WFS1 gene in all patients of this family. The mutated Ala residue is evolutionarily conserved and cosegregated with HL. The variant was predicted to be deleterious by MutationTaster, PolyPhen-2, LRT, and Fathmm software. Conservation analysis and 3D protein structure model indicated that the variant caused a structural change in the protein.

Conclusions: Our present study identifies a novel heterozygous WFS1 variant associated with LFSNHL in a Chinese family.

Figure 1

Pedigree of the 5-generation Chinese Han family and their audiological phenotypes. (a) Pedigree of the family affected with nonsyndromic hearing loss showing an autosomal dominant hereditary pattern. Males are denoted by squares, females by circles, and deceased by a diagonal line through the symbol. Proband: arrow; white symbol: normal hearing; black symbol: hearing impairment. (b) The pure-tone audiograms of some representative members in this family. Frequency in hertz (Hz) is plotted on the x-axis and the auditory threshold in decibels (dB HL) on the y-axis.

Figure 2

Age (increment of 5 years) of onset of hearing loss in the members of the 5-generation Chinese family.

Figure 3

Sequence chromatograms, conservation analysis of WFS1 (a) Chromatograms showing the c.2530G > T variant in the 5-generation Chinese family with LFSNHL. Partial sequence chromatograms of WFS1 gene from the affected individual IV-12, the normal-hearing individual IV-14 of the family, and a control. The red arrow indicates the location of the nucleotide changes at position 2530. (b) Protein alignment shows highly conserved nature of the p.Ala844 residue (indicated by a red arrow) in patients in our study and other 8 sequences from Homo sapiens, Pan troglodytes, Bos taurus, Canis familiaris, Rattus norvegicus, Mus musculus, Gallus gallus, and Danio rerio.

Figure 4

The 3D protein structural modeling comparison of wild-type (WT) and mutant WFS1. (a) Molecular modeling of WT WFS1. The black dotted box indicates the position of amino acid residue 844 of WT WFS1. (b) Molecular modeling of mutant WFS1. Hydrogen bonds linking Ser844 with Glu824, Ser844 with Cys847, and Ser844 with Leu848 (yellow dotted lines) are shown.

Figure 5

Subcellular localization of wild-type (WT) and mutated WFS1. Immunofluorescence staining was performed after transient transfection in HEK-293 cells and HEI-OC1 cells. Images display DAPI in blue, endoplasmic reticulum-specific marker Calnexin in green, Flag-tagged protein in red, and merged pictures. In both HEK-293 cells and HEI-OC1 cells, the variant protein was located in the cytoplasmic endoplasmic reticulum as in the WT. Scale bars =30 μm.

Figure 6

Variants of WFS1. (a) The position of WFS1 c.2530G > T (p.Ala844Ser) highlighted with a red arrow. The gray region indicates the noncoding region; the blue arrows indicate the total number of variants reported in exons for WFS1-associated LFSNHL. (b) Overview of the reported WFS1-associated LFSNHL variants and their locations in the protein structure. The red dots indicate reported variants; the green dots indicate novel variant found in this study.