A novel mutation in the OTOF gene in a Chinese family with auditory neuropathy

Abstract

Gene therapy for monogenic auditory neuropathy (AN) has successfully improved hearing function in target gene-deficient mice. Accurate genetic diagnosis can not only clarify the etiology but also accurately locate the lesion site, providing a basis for gene therapy and guiding patient intervention and management strategies. In this study, we collected data from a family with a pair of sisters with prelingual deafness. According to their auditory tests, subject Ⅱ-1 was diagnosed with profound sensorineural hearing loss (SNHL), Ⅱ-2 was diagnosed with AN, Ⅰ-1 was diagnosed with high-frequency SNHL, and Ⅰ-2 had normal hearing. Using whole-exome sequencing (WES), one nonsense mutation, c.4030C>T (p.R1344X), and one missense mutation, c.5000C>A (p.A1667D), in the OTOF (NM_001287489.1) gene were identified in the two siblings. Their parents were heterozygous carriers of c.5000C>A (father) and c.4030C>T (mother). We hypothesized that c.5000C>A is a novel pathogenic mutation. Thus, subject Ⅱ-1 should also be diagnosed with AN caused by OTOF mutations. These findings not only expand the OTOF gene mutation spectrum for AN but also indicate that WES is an effective approach for accurately diagnosing AN.

Keywords: OTOF gene; auditory neuropathy; whole-exome sequencing.

Figure 1.

Pedigree and sequence analysis of OTOF mutations in the family. (A) Pedigree map of this family. (B) In this family, the compound heterozygous mutations c.4030C>T and c.5000C>A were observed in both affected siblings (Ⅱ-1 and Ⅱ-2); the c.5000C>A mutation was inherited from the father (Ⅰ-1), and the c.4030C>T mutation was inherited from the mother (Ⅰ-2).

Figure 2.

Variant screening process. 1. At least one mutation with a frequency higher than 1% was selected from four frequency databases: 1000g_all, ESP6500, gnomAD_ALL and gnomAD_EAS. 2. Variations in the coding region or splicing region (upper and lower 10 bp) were retained. 3. Synonymous SNP mutations not located in highly conserved regions that were not predicted by software to affect splicing and frameless InDel mutations of small fragments (< 10 bp) in the repeat region were removed. 4. Mutations were retained if they met one of the following conditions: a) predicted to be harmful or b) predicted to affect splicing. 5. Dominant inheritance: the sites with heterozygous mutations (mutation sites in sex chromosomes) in the patient's autosome and no mutations in healthy people in the family were selected as candidate sites; recessive inheritance: genes with at least two heterozygous mutation sites in patients were selected; the distribution of mutation sites on this gene in patients cannot be the same as that observed in any healthy person or a subset of the mutation sites in any healthy person. 6. Pathogenic and likely pathogenic mutations according to the ACMG guidelines were selected. 7. Steps 5 and 6 were combined to obtain candidate mutations. 8. The mutations that cosegregated with the phenotype in the pedigree were analyzed.

Figure 3.

Oblique sagittal MRI of Patient Ⅱ-2. (A) The distal slice shows the facial (F), superior vestibular (SV), inferior vestibular (IV) and cochlear (C) nerves of the right ear. (B) The distal slice shows the F, SV, IV, and C nerves of the left ear.

Figure 4.

Audiologic tests of subjects Ⅱ-1 and Ⅱ-2. (A) DPOAE, distortion product otoacoustic emission; (B) ASSR, auditory steady-state response; (C) ABR, auditory brainstem response; (D) CM, cochlear microphonic potential.

Figure 5.

Conservation analysis of the p.A1667 mutation site of otoferlin. The p.A1667 site is conserved in multiple species.