Hereditary Hearing Loss - GJB2, GJB6, and Gene Panel Testing

  • Diagnostic test or carrier screening for GJB2-related nonsyndromic hearing loss (NSHL)
  • May be used as first-tier genetic test for individuals with suspected autosomal recessive 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
  • Most comprehensive genetic test for nonsyndromic and syndromic hearing loss
  • Recommended test for syndromic hearing loss if symptoms are consistent with disorders included on the panel
Related Tests

Useful when a pathogenic familial variant identifiable by sequencing is known

Hearing loss can be syndromic or nonsyndromic and may be a result of genetic, physiologic, or disease factors. Depending on the cause, hearing loss may have a variable age of onset from birth to early childhood and range in severity from mild to profound. A genetic cause is found in 50% of individuals born with hearing loss. Genetic testing to determine the etiology of hearing loss can identify previously unrecognized syndromic forms of hearing loss and may be used for genetic counseling to assess the chance of recurrence. 

Disease Overview

Symptoms

Hearing loss may be:

  • Prelingual or postlingual in onset
  • Syndromic (associated with other findings) or nonsyndromic
  • Sensorineural, conductive, or mixed etiology
  • Variable in presentation based on genetic and environmental cause(s) of the hearing loss

Prevalence and/or Incidence

  • 1/500 born with hearing loss 
    • 50% of individuals with hearing loss have a genetic cause. 
  • Up to 50% of individuals with severe-to-profound autosomal recessive hearing loss have one or two pathogenic variants in the GJB2 gene. However, the prevalence varies by ethnicity. 
    • Approximately 99% of these individuals are homozygous or compound heterozygous for pathogenic variants in GJB2.
    • Approximately 1% of these individuals have one GJB2 pathogenic variant and a GJB6 deletion.
      • Large GJB6 gene deletions involving GJB2 cis-regulatory elements result in loss of GJB2 expression.

Genotype-Phenotype Correlation

  • GJB2 (connexin 26) or GJB6 (connexin 30) biallelic variants: sensorineural 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
  • MT-RNR1 m.1555A>G: stable, severe-to-profound NSHL with variable age of onset; predisposition to aminoglycoside ototoxicity

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 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) 

Analytical Sensitivity/Specificity

Variant Class Analytical Sensitivity (PPA) Estimatea (%)
and 95% Credibility Region (%)
Analytical Specificity (NPA) (%)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

Exon-levelc Deletions

97.8 (90.3-99.8) (single coding GJB2 exon)

>99.9

Exon-levelc Duplications

83.3 (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 analytical 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 

Analytical 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.

Expanded Hearing Loss Panel, Sequencing and Deletion/Duplication

Genes Tested

Gene MIM Number Disorder Inheritance

ACTG1

102560

Progressive sensorineural NSHL

AD

ADGRV1

602851

Usher syndrome type 1

AR

CCDC50

611051

Progressive sensorineural NSHL

AD

CDH23

605516

Stable NSHL

Usher syndrome type 1

AR

CEACAM16

614591

Progressive sensorineural NSHL

AD

CLDN14

605608

Stable sensorineural NSHL

AR

CLRN1

606397

Retinitis pigmentosa

Usher syndrome type 3

AR

COCH

603196

Postlingual, progressive sensorineural NSHL, with or without vestibular involvement

AD

COL11A2

120290

Sensorineural NSHL

Otospondylomegaepiphyseal dysplasia (OSMED syndrome)

AR

Sensorineural NSHL

AD

CRYM

123740

Sensorineural NSHL

AD

DIAPH1

602121

Progressive sensorineural NSHL

AD

DNMT1

126375

Cerebellar ataxia, deafness, and narcolepsy

Hereditary sensory and autonomic neuropathy, type IE

AD

DSPP

125485

Progressive sensorineural hearing loss with dentinogenesis

AD

ESPN

606351

Sensorineural NSHL with or without vestibular involvement

AR or AD

ESRRB

602167

Sensorineural NSHL

AR

EYA4

603550

Progressive sensorineural NSHL

AD

GIPC3

608792

Stable NSHL

AR

GJB2 (connexin 26)

121011

Stable sensorineural NSHL

AR

Progressive sensorineural NSHL

Keratitis-ichthyosis-deafness (KID) syndrome

Hystrix-like ichthyosis-deafness (HID) syndrome

Vohwinkel syndrome

Bart-Pumphrey syndrome

AD

GJB3

603324

Progressive sensorineural NSHL

Erythrokeratodermia variabilis

AD

GJB6 (connexin 30)

604418

Stable sensorineural NSHL

AR

Progressive sensorineural NSHL

Hidrotic ectodermal dysplasia type 2/Clouston syndrome

KID syndrome

AD

GPSM2

609245

Chudley-McCullough syndrome

AR

GRHL2

608576

Progressive, postlingual sensorineural hearing loss

AD

GSDME

608798

Progressive sensorineural NSHL

AD

HARS2

600783

Perrault syndrome 2

AR

HSD17B4

601860

Perrault syndrome 1

D-bifunctional protein deficiency

AR

ILDR1

609739

Stable sensorineural NSHL

AR

KCNQ4

603537

Progressive sensorineural NSHL

AD

LHFPL5

609427

Stable NSHL

AR

LOXHD1

613072

Progressive sensorineural NSHL

AR

LRTOMT

612414

Sensorineural NSHL

AR

MARVELD2

610572

Stable NSHL

AR

MASP1

600521

3MC syndrome 1

AR

MT-RNR1 (m.15555 A>G variant only) 561000 Predisposition to aminoglycoside ototoxicity and/or late onset sensorineural NSHL

MYH14

608568

Progressive sensorineural NSHL

Peripheral neuropathy, myopathy, hoarseness, and hearing loss

AD

MYH9

160775

Progressive sensorineural NSHL

Macrothrombocytopenia and granulocyte inclusions with or without nephritis or sensorineural hearing loss

AD

MYO15A

602666

Sensorineural NSHL

AR

MYO3A

606808

Progressive NSHL

AR

MYO6

600970

Progressive sensorineural NSHL

AD

NSHL

AR

MYO7A

276903

Progressive sensorineural NSHL

AD

Sensorineural NSHL

Usher syndrome type 1

AR

OTOA

607038

Stable sensorineural NSHL

AR

OTOF

603681

Stable sensorineural NSHL

Nonsyndromic auditory neuropathy (NSAN)

AR

PCDH15

605514

Stable sensorineural NSHLS

Usher syndrome type 1

AR

PDZD7

612971

Usher syndrome, type 2

Sensorineural NSHL

AR

PJVK

610219

Sensorineural NSHL

AR

POU3F4

300039

NSHL

XL

POU4F3

602460

Progressive sensorineural NSHL

AD

RDX

179410

Stable sensorineural NSHL

AR

SIX1

601205

NSHL

Branchiootic syndrome 3

AD

SLC26A4

605646

Stable or progressive NSHL with enlarged vestibular aqueduct

Pendred syndrome

AR

SLC26A5

604943

Stable sensorineural NSHL

AR

SMPX

300226

Progressive sensorineural hearing loss

XL

TECTA

602574

Sensorineural NSHL

AR or AD

TMC1

606706

Progressive sensorineural NSHL

AD

Stable sensorineural NSHL

AR

TMIE

607237

Stable sensorineural NSHL

AR

TMPRSS3

605511

Sensorineural NSHL

AR

TPRN

613354

Progressive sensorineural NSHL

AR

TRIOBP

609761

Stable sensorineural NSHL

AR

USH1C

605242

Stable sensorineural NSHL

Usher syndrome type 1

AR

USH1G

607696

Usher syndrome type 1

AR

USH2A

608400

Usher syndrome type 2

Retinitis pigmentosa

AR

WFS1

606201

Progressive sensorineural NSHL, Wolfram-like syndrome

AD

Wolfram syndrome

AR

WHRN

607928

Sensorineural NSHL

Usher syndrome type 2

AR

AD, autosomal dominant; AR, autosomal recessive; NSHL, nonsyndromic hearing loss; XL, X-linked

Clinical Sensitivity

Varies by gene

Analytical Sensitivity/Specificity

For massively parallel sequencing:

Variant Class Analytical Sensitivity (PPA) Estimatea (%)
and 95% Credibility Region (%)
Analytical Specificity (NPA) (%)

SNVs

>99 (96.9-99.4)

>99.9

Deletions 1-10 bpb

93.8 (84.3-98.2)

>99.9

Insertions 1-10 bpb

94.8 (86.8-98.5)

>99.9

aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived.

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

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 and intron-exon boundaries of the targeted genes
    • Regulatory region variants and deep intronic variants
    • Breakpoints of large deletions/duplications
    • Deletions/duplications in ESPN, GIPC3, ILDR1, LOXHD1, LRTOMT, MT-RNR1, OTOA, PDZD7, SIX1
    • Noncoding transcripts
    • The following exons are not sequenced due to technical limitations of the assay:
      • COCH (NM_001347720) 2
      • DNMT1 (NM_001130823) 5
      • OTOA (NM_144672) 20, 21, 22, 23, 24, 25, 26, 27, 28
      • MT-RNR1: targeted sequencing is performed for m.1555A>G only; other variants in this gene will not be detected.
  • The following may not be detected:
    • Deletions/duplications/insertions of any size by massively parallel sequencing
    • Deletions/duplications less than 1kb in the targeted genes by array
    • Some variants due to technical limitations in the presence of pseudogenes, repetitive, or homologous regions
    • Low-level somatic variants
    • Variants in MT-RNR1 other than the targeted m.1555A>G variant
    • Heteroplasmy present at less than 25% for the MT-RNR1 m.1555A>G variant
    • Single exon deletions/duplications in the following exons:
    • Gene Exon(s)
      CCDC50 (NM_178335) 1, 12
      CDH23 (NM_022124) 28, 63
      CLRN1 (NM_001195794) 3
      CLRN1 (NM_001256819) 2
      CLRN1 (NM_052995) 1, 4
      COL11A2 (NM_080680) 62
      DIAPH1 (NM_001314007) 29
      DIAPH1 (NM_005219) 18, 28
      DNMT1 (NM_001130823) 1, 5, 41
      HARS2 (NM_012208) 1
      HSD17B4 (NM_000414) 24
      HSD17B4 (NM_001199291) 1
      KCNQ4 (NM_004700) 9
      MASP1 (NM_139125) 1
      MYH14 (NM_024729) 3, 13, 17, 24, 25, 30, 34
      MYH9 (NM_002473) 13, 23, 29, 30, 39
      MYO15A (NM_016239) 25, 26, 33, 49, 62
      MYO7A (NM_000260) 17, 26, 29
      OTOF (NM_194248) 26
      PCDH15 (NM_001142769) 13
      RDX (NM_001260495) 3
      RDX (NM_001260496) 5
      RDX (NM_002906) 6, 10
      SLC26A4 (NM_000441) 21
      SLC26A5 (NM_001321787) 19
      SLC26A5 (NM_206884) 15
      TMC1 (NM_138691) 6, 24
      TMIE (NM_147196) 1
      TMPRSS3 (NM_024022) 4
      TRIOBP (NM_001039141) 14, 21
      TRIOBP (NM_138632) 8
      USH1C (NM_005709) 1
      USH1C (NM_153676) 26

References

Additional Resources