Comprehensive interpretation of single-nucleotide substitutions in GJB2 reveals the genetic and phenotypic landscape of GJB2-related hearing loss

Abstract

Genetic variants in the GJB2 gene are the most frequent causes of congenital and childhood hearing loss worldwide. In addition to nonsyndromic hearing loss, GJB2 pathogenic variants are also correlated with syndromic phenotypes, showing high genetic and phenotypic heterogeneity. To comprehensively delineate the genetic and phenotypic landscape of GJB2 variants, we interpreted and manually curated all the 2043 possible single-nucleotide substitution (SNS) coding variants in this gene following the hearing loss-specific ACMG/AMP guidelines. As a result, 61 (3.0%), 188 (9.2%), 1487 (72.8%), 301 (14.7%) and 6 (0.3%) variants were classified as pathogenic, likely pathogenic, variant of uncertain significance, likely benign and benign, respectively. Interestingly, 54% (84/156) of pathogenic/likely pathogenic missense variants were not recorded in ClinVar. Further analysis showed that the second transmembrane domain (TM2) and the 310 helix are highly enriched for pathogenic missense variants. The N-terminal tail and the extracellular loop (E1) showed a high density of variants that are associated with syndromic or dominant nonsyndromic hearing loss. On the other hand, the intracellular loops (CL and CT) were extremely tolerant to variation. Based on this new information, we propose refinements of the guidelines for variant interpretation in GJB2. In summary, our study interpreted all possible SNS variants in the coding region of the GJB2 gene, characterized novel clinically significant (N = 249) and benign or likely benign (N = 307) in this gene, and revealed significant genotype-phenotype correlations at this common hearing loss locus.The interpretation of GJB2 SNS variants in the coding region provides a prototype for genes with similarly high genetic and phenotypic heterogeneity.

Molecular Mechanisms and Clinical Phenotypes of GJB2 Missense Variants

“…The GJB2 gene is the most prevalent gene responsible for HL worldwide. Although less common than truncating variants, missense variants are the most abundant variant type of the GJB2 gene [ 99 ]. Cx26 contains 226 amino acid residues, and each residue can be mutated to one of the other 19 amino acids; therefore, there are 4294 possible missense variants.…”

“…Of these 4294 variants, 1334 can be achieved by a single base pair variant in a codon (simple missense variants), while 2960 can only be achieved by variant in more than two bases in a codon (complex variants) ( Figure 4 ). We have compiled a comprehensive dataset of GJB2 missense variants based on public databases, including HGMD, Clinvar, and the Deafness Variation Database, and literature articles [ 99 ]. We have classified these 1334 simple missense variants into five tiers ( Supplemental Table S1 ), and approximately 84.2% of missense variants are VUS ( Figure 4 ).…”

Genotypic and Allelic Frequencies of GJB2 Variants and Features of Hearing Phenotypes in the Chinese Population of the Dongfeng-Tongji Cohort

“…Currently, c.109G>A is considered a pathogenic mutation with incomplete penetrance [13], and the homozygous mutation is associated with various hearing phenotypes [10,17]. Similarly, the other GJB2 variants show diverse phenotypes, ranging from mild to profound [8,18], which largely depend on the genotype [8,10,19]. Patients with biallelic "truncating" mutations that completely block protein expression generally have severe to profound hearing loss, whereas patients with at least one "non-truncating" mutant allele have a lower hearing threshold due to impaired but not inactivated protein function [8,10,19].…”

Genetic screening of 15 hearing loss variants in 77,647 neonates with clinical follow‐up

“…There are 2043 SNV variations of the coding region of GJB2 . Truncated mutations such as c.235delC and c.35delG cause more severe clinical symptoms than non‐truncated mutations (Xiang et al., 2023). In our present study, 4 infants carried either homozygous or compound heterozygous variants in GJB2 .…”