Hereditary Hearing Loss - GJB2 and GJB6 Testing

Last Literature Review: October 2024 Last Update:
  • Diagnostic test or carrier screening for GJB2-related nonsyndromic hearing loss (NSHL)
  • Diagnostic test for individuals with NSHL and one identified GJB2 variant
  • Carrier screening if family history of GJB6 deletion or for reproductive partner of individual with GJB6 or GJB2 pathogenic variants

In the United States, up to 3 in every 1,000 infants are born with hearing loss, with the majority of cases being hereditary. Hereditary hearing loss can be syndromic or nonsyndromic. Age of onset varies, and severity can range from mild to profound. The American College of Medical Genetics and Genomics (ACMG) recommends genetic testing to determine the etiology of confirmed hearing loss in individuals with a clinical picture compatible with a hereditary cause. An estimated 50% of autosomal recessive nonsyndromic hearing loss is caused by variants in the DFNB1 locus (GJB2 and GJB6 genes). 

Disease Overview

Prevalence and/or Incidence

  • 2-3/1,000 born with hearing loss 
    • 70% of hereditary hearing loss is nonsyndromic. 
      • 50% of autosomal recessive (AR) nonsyndromic hearing loss results from variants in the GJB2 and GJB6 genes. 
        • Approximately 1% of these individuals are compound heterozygous for a GJB2 variant and a large deletion involving GJB2 cis-regulatory elements (eg, GJB6) resulting in loss of GJB2 expression. 

Genotype-Phenotype Correlation

  • GJB2 (connexin 26) or GJB6 (connexin 30) biallelic variants: sensorineural nonsyndromic hearing loss (NSHL) that is commonly stable and bilateral with prelingual onset 
    • Truncating GJB2 variants are associated with a higher chance for severe hearing loss than nontruncating variants. 
  • GJB2 autosomal dominant sequence variants: causative of autosomal dominant deafness type 3A (DFNA3A) as well as syndromic forms of hearing loss, including keratosis and ichthyosis 

Test Interpretation

Connexin 26 (GJB2) Sequencing and Deletion/Duplication

Gene(s) Tested

GJB2 (NM_004004)

Testing Procedure

This test is performed using the following sequence of steps:

  • Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
  • Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
  • Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
  • Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.

Clinical Sensitivity

Greater than 99% for GJB2-associated hearing loss (DFNB1A) 

Analytic Sensitivity/Specificity

Variant ClassAnalytic Sensitivity (PPA) Estimatea (%)
and 95% Credibility Region (%)		Analytic Specificity (NPA) (%)
SNVs>99 (96.9-99.4)>99.9
Deletions 1-10 bpb93.8 (84.3-98.2)>99.9
Insertions 1-10 bpb94.8 (86.8-98.5)>99.9
Exon-levelc Deletions97.8 (90.3-99.8) (single coding GJB2 exon)>99.9
Exon-levelc Duplications83.3 (56.4-96.4) (single coding GJB2 exon)>99.9

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA).

bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced.

cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp.

bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants

Limitations

  • A negative result does not exclude a heritable form of hearing loss.
  • Diagnostic errors can occur due to rare sequence variations.
  • Interpretation of this test result may be impacted if the individual has had an allogeneic stem cell transplant.
  • The following will not be evaluated:
    • Variants outside the coding regions, intron-exon boundaries and selected noncoding variants of GJB2
    • Regulatory region variants and deep intronic variants
    • Breakpoints of large deletions/duplications
    • Noncoding transcripts
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by massively parallel sequencing
    • Some variants due to technical limitations in the presence of pseudogenes, repetitive, or homologous regions
    • Low-level somatic variants

Hearing Loss, Nonsyndromic, Connexin 30 (GJB6) 2 Deletions

Gene(s) Tested

GJB6

Clinical Sensitivity

Dependent on ethnicity 

Analytic Sensitivity

99%

Limitations

  • Diagnostic errors can occur due to rare sequence variations.
  • GJB6 variants other than 309kb del(GJB6-D13S1830) and 232kb del(GJB6-D13S1854) will not be identified.
  • Interpretation of this test result may be impacted if the individual has had an allogeneic stem cell transplant.

References