Compound heterozygous mutations of SLC26A4 in 4 Chinese families with enlarged vestibular aqueduct

A systematic review of the monogenic causes of Non-Syndromic Hearing Loss (NSHL) and discussion of Current Diagnosis and Treatment options

Hearing impairment is one of the most widespread inheritable sensory disorder affecting at least 1 in every 1000 born. About two-third of hereditary hearing loss (HHL) disorders are non-syndromic. To provide comprehensive update of monogenic causes of non-syndromic hearing loss (NSHL), literature search has been carried out with appropriate keywords in the following databases-PubMed, Google Scholar, Cochrane library, and Science Direct. Out of 2214 papers, 271 papers were shortlisted after applying inclusion and exclusion criterion. Data extracted from selected papers include information about gene name, identified pathogenic variants, ethnicity of the patient, age of onset, gender, title, authors' name, and year of publication. Overall, pathogenic variants in 98 different genes have been associated with NSHL. These genes have important role to play during early embryonic development in ear structure formation and hearing development. Here, we also review briefly the recent information about diagnosis and treatment approaches. Understanding pathogenic genetic variants are helpful in the management of affected and may offer targeted therapies in future.

Increased diagnosis of enlarged vestibular aqueduct by multiplex PCR enrichment and next-generation sequencing of the SLC26A4 gene

Background

The enlarged vestibular aqueduct (EVA) is the commonest malformation of inner ear accompanied by sensorineural hearing loss in children. Three genes SLC26A4, FOXI1, and KCNJ10 have been associated with EVA, among them SLC26A4 being the most common. Yet, hotspot mutation screening can only diagnose a small number of patients.

Methods

Thus, in this study, we designed a new molecular diagnosis panel for EVA based on multiplex PCR enrichment and next‐generation sequencing of the exon and flanking regions of SLC26A4. A total of 112 hearing loss families with EVA were enrolled and the pathogenicity of the rare variants detected was interpreted according to the American College of Medical Genetics and Genomics (ACMG) guidelines.

Results

Our results showed that 107/112 (95.54%) families carried SLC26A4 biallelic mutations, 4/112 (3.57%) carried monoallelic variants, and 1/112 (0.89%) had none variant, resulting in a diagnostic rate of 95.54%. A total of 49 different variants were detected in those patients and we classified 30 rare variants as pathogenic/likely pathogenic, of which 13 were not included in the Clinvar database.

Conclusion

Our diagnostic panel has an increased diagnostic yield with less cost, and the curated list of pathogenic variants in the SLC26A4 gene can be directly used to aid the genetic counseling to patients.

Identification of SLC26A4 mutations p.L582LfsX4, p.I188T and p.E704K in a Chinese family with large vestibular aqueduct syndrome (LVAS)

Large vestibular aqueduct syndrome (LVAS) is a type of hearing loss characterized by an autosomal recessive inheritance. LVAS has been shown to be associated with mutations in SLC26A4 gene. In the present study, we report the clinical, genetic and molecular characterization of a Chinese family with LVAS. By using the targeted sequence capture and next-generation sequencing, we identified heterozygous mutations of SLC26A4 p.I188T (c.563T > C), p.L582LfsX4 (c.1746 delG) and p.E704K (c.2110G > A) in the affected individual of this family, of which SLC26A4 p.E704K is a novel mutation associated with LVAS. By tracing the transmission and functional prediction of these mutations in the pedigree, the heterozygous mutations of p.I188T, p.L582LfsX4 and p.E704K in SLC26A4 gene were responsible for the LVAS of the affected individual. This is the first case of LVAS caused by these mutations.

A study of deafness-related genetic mutations as a basis for strategies to prevent hereditary hearing loss in Hebei, China

Hearing loss is the most common sensory disorder, and at least 50% of cases are due to a genetic etiology. Two-thirds of individuals with congenital deafness are nonsyndromic. Among the nonsyndromic forms, the large majority are monogenic autosomal recessive traits. The current work summarizes mutations in the GJB2, SLC26A4, 12SrRNA, and GJB3 and their prevalence in 318 students with autosomal recessive nonsyndromic hearing loss at schools for the deaf or special needs schools in 9 cities in Hebei Province, China. Deafness gene mutations were identified in 137 students via a gene chip, time-of-flight mass spectrometry, fluorescence quantitative PCR, and gene sequencing. Mutations were detected at a rate of 43.08%. A homozygous mutation of the GJB2 gene was found in 16 students (5.03%), a heterozygous mutation of that gene was found in 38 (11.95%), a homozygous mutation of the SLC26A4 gene was found in 22 (6.92%), a heterozygous mutation of that gene was found in 59 (18.55%), and a heterozygous mutation of the mitochondrial 12SrRNA gene was found in 2 (0.63%). In addition, there were 15 families in which a student's parents had normal hearing. Compound heterozygous mutations of the GJB2 gene were found in 3 families (20%) and mutations of the SLC26A4 gene were found in 9 (60%). Thus, this study has provided a molecular diagnostic basis for the causes of deafness, and this study has also provided a scientific basis for the early prevention of and intervention in deafness.

Genotyping data and novel haplotype diversity of STR markers in the SLC26A4 gene region in five ethnic groups of the Iranian population

BACKGROUND AND AIMS

SLC26A4 gene mutations are the second currently identifiable genetic cause of autosomal recessive nonsyndromic hearing loss after GJB2 mutations. Because of the extensive size of the SLC26A4 gene and the variety of mutations, indirect diagnosis using linkage analysis has been suggested. Therefore, in this investigation three potential short tandem repeat (STR) markers related to this region including D7S2420, D7S496, and D7S2459 were selected for further analysis.

METHODS

The characteristics and haplotype frequency of the markers were examined for the first time in five ethnic groups of the Iranian population including Fars, Azari, Turkmen, Gilaki, and Arab using the polymerase chain reaction followed by fluorescent capillary electrophoresis. RESULTS were analyzed by GeneMarker HID Human STR Identity, GenePop, Microsatellite tools, PowerMarker 3.25, and Arlequin 3.5 software.

RESULTS

Analysis of the allelic frequency revealed the presence of 11, 10, and 8 alleles for D7S2420, D7S496, and D7S2459 markers, respectively, in the Iranian population. The detailed analysis of each ethnic group was reported. Calculated polymorphism information content values were above 0.7 in the Iranian population. Pairwise linkage disequilibrium (LD) revealed a significant LD in pairing markers of D7S2420-D7S496 and in D7S496-D7S2459. Estimation of the haplotype frequency showed the presence of 20, 13, 15, 15, and 20 informative haplotypes in Fars, Azari, Turkmen, Gilaki, and Arabian ethnics, respectively.

CONCLUSION

Together, the investigated markers could be suggested as powerful tools for linkage analysis of SLC26A4 gene mutations in the Iranian population.

Genetic mutations in nonsyndromic deafness patients of Chinese minority and Han ethnicities in Yunnan, China

BACKGROUND

Each year in China, 30,000 babies are born with congenital hearing impairment. However, the molecular etiology of hearing impairment in the Yunnan Province population where more than 52 minorities live has not been thoroughly investigated. To provide appropriate genetic testing and counseling to these families, we investigated the molecular etiology of nonsyndromic deafness in this population.

METHODS

Unrelated students with hearing loss (n = 235) who attended Kunming Huaxia secondary specialized school in Yunnan enrolled in this study. Three prominent deafness-related genes, GJB2, SLC26A4 and mtDNA 12S rRNA, were analyzed. High-resolution temporal bone computed tomography (CT) scan examinations were performed in 100 cases, including 16 cases with SLC26A4 gene variants, and 37 minorities and 47 Han cases without any SLC26A4 gene mutation.

RESULTS

The GJB2 mutation was detected in 16.67% (7/42) of minority patients and 17.62% (34/193) of Chinese Han patients (P > 0.05). 235delC was the hotspot mutation in nonsyndromic hearing loss (NSHL) patients, whereas 35delG was not found. The 431_450del19 mutation was detected for the first time in Han NSHL patients, which resulted in a premature stop codon and changed the protein. The SLC26A4 mutation was found in 9.52% (4/42) of minority patients and 9.84% (19/193) of Han Chinese patients (P > 0.05). The frequencies of mtDNA 12S rRNA mutation in minority and Han Chinese patients were 11.90% (5/42) and 7.77% (15/193; P > 0.05), respectively. Sixteen (16/23, 69.57%) patients with SLC26A4 mutations received temporal bone CT scan, and 14 patients were diagnosed with enlarged vestibular aqueducts (EVAs); the other 2 patients had normal inner ear development. The ratio of EVA in the minorities was 14.63% (6/41).

CONCLUSIONS

In this study, a total of 35.74% deaf patients showed evidence of genetic involvement, based on either genetic screening or family history; 17.45%, 9.79%, and 8.51% of the patients were determined to have inherited hearing impairment caused by GJB2, SLC26A4, and mtDNA 1555A > G mutations. There was no significant difference in deafness associated gene mutational spectrum and frequency between the Yunnan minority and Han patients.