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Deafness, Autosomal Dominant 2B (DFNA2B) via the GJB3 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
Order Kits
TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
1552 GJB3$490.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

The sensitivity of our sequencing assay for this gene is currently unknown. However, since only missense, nonsense and small deletion variants have been described for this gene in association with nonsyndromic hearing loss, we believe that our sequencing assay will be able to identify all of these variants. Overall, pathogenic variants in GJB3 are thought to play a small role in nonsyndromic hearing loss due to the limited number of families that have been identified (Hilgert et al. 2009; Smith and Hildebrand 2015).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 GJB3$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Sensitivity

The sensitivity of our aCGH assay for this gene is currently unknown. No large deletions or duplications in GJB3 have been reported for nonsyndromic hearing loss.

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Clinical Features

Nonsyndromic hearing loss is characterized by difficulty or inability to hear that is not associated with any visible defects involving the external ear, other organs, or any other medical condition. Nonsyndromic hearing loss may be associated with abnormalities involving the middle ear and/or the inner ear (Ciuman 2013; Dodson et al. 2011; Hilgert et al. 2009). At least 70% of cases involving hearing loss are nonsyndromic (Van Camp et al. 1997).

The clinical features of nonsyndromic hearing loss and deafness due to pathogenic variants in the GJB3 gene vary widely with autosomal dominant variants causing bilateral sensorineural hearing loss with a downsloping audiogram and moderate hearing loss at high frequencies (Xia et al. 1998). Autosomal recessive variants cause early-onset moderate to severe bilateral sensorineural hearing loss with flat audiograms and normal vestibular function (Liu et al. 2000).

Genetics

The GJB3 gene encodes the gap junction protein beta 3, more commonly known as connexin 31. Connexins form gap junctions that facilitate metabolite and ion transport between adjacent cells. Connexin 31 is expressed in fibrocytes of the spiral ligament and spiral limbus of the mouse chochlea and auditory and peripheral nerves, although its role in auditory function remains unclear (Xia et al. 2000; López-Bigas et al. 2001).

The different gene loci for nonsyndromic hearing loss are designated DFN (for DeaFNess) and named on the mode of inheritance; DFNA for autosomal dominant, DFNB for autosomal recessive and DFNX for X-linked inheritance, respectively. The GJB3 gene is located in chromosomal region 1p34.3 and is associated with nonsyndromic hearing loss inherited in an autosomal dominant manner (DFNA2B), with some reports of autosomal recessive and digenic inheritance.

Autosomal dominant nonsyndromic hearing loss due to pathogenic variants in GJB3 has only been reported in two small Chinese families (Xia et al. 1998). However, these variants were found in both affected and unaffected individuals. Additionally, it is unlikely that hearing loss due to the nearby and at that time undiscovered KCNQ4 gene was excluded in these families. No subsequent reports have convincingly identified variants in GJB3 as causing autosomal dominant hearing loss in other families.

Autosomal dominant nonsyndromic hearing loss with peripheral neuropathy due to pathogenic variants in GJB3 has been reported in one multi-generation Spanish family (López-Bigas et al. 2001).

Autosomal recessive nonsyndromic hearing loss due to pathogenic variants in GJB3 has only been reported in two small Chinese families in which affected individuals were compound heterozygotes for two different missense variants (Liu et al. 2000). A Turkish family with one missense variant in GJB3 was reported to have autosomal recessive nonsyndromic hearing loss, although the second pathogenic variant was not identified (Uyguner et al. 2003).

Autosomal recessive nonsyndromic hearing loss has also been reported to be caused by digenic inheritance of variants in GJB3 and GJB2 (DFNA1A) in three Chinese families (Liu et al. 2009).

The role of GJB3 in causing nonsyndromic hearing loss is currently viewed as questionable due to limited evidence (Hilgert et al. 2009; Smith and Hildebrand 2015).

Heterozygous and homozygous variants in GJB3 are also known to cause erythrokeratodermia variabilis et progressiva, a skin disorder characterized by transient erythematous hyperkeratotic plaques (Gottfried et al. 2002).

Testing Strategy

This test involves bidirectional Sanger DNA sequencing of the single coding exon of GJB3. The entire coding region and ~20 bp of flanking non-coding DNA on either side of each splice site are sequenced. We will also sequence any portion (Test #100) or portions of the exon (Test #200) in family members of patients with known mutations or to confirm research results.

Indications for Test

Nonsyndromic hearing loss and deafness due to variants in GJB3 is suspected in individuals with the following: pre- or postlingual, moderate to severe, bilateral sensorineural hearing impairment; no related systemic findings identified by medical history and physical examination; or a family history of nonsyndromic hearing loss consistent with autosomal dominant or more rarely, autosomal recessive inheritance. Variants in GJB3 causative for Erythrokeratodermia Variabilis et Progressiva have not been reported to also cause hearing loss, and vice versa.

Gene

Official Gene Symbol OMIM ID
GJB3 603324
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
Nonsyndromic Hearing Loss and Deafness Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Ciuman R.R. 2013. Medical Science Monitor. 19: 1195-210. PubMed ID: 24362017
  • Dodson K.M. et al. 2011. American Journal of Medical Genetics. Part A. 155A: 993-1000. PubMed ID: 21465647
  • Gottfried I. et al. 2002. Human Molecular Genetics. 11: 1311-6. PubMed ID: 12019212
  • Hilgert N. et al. 2009. Current Molecular Medicine. 9: 546-64. PubMed ID: 19601806
  • Hilgert N. et al. 2009. Mutation Research. 681: 189-96. PubMed ID: 18804553
  • López-Bigas N. et al. 2001. Human Molecular Genetics. 10: 947-52. PubMed ID: 11309368
  • Liu X.Z. et al. 2000. Human Molecular Genetics. 9: 63-7. PubMed ID: 10587579
  • Liu X.Z. et al. 2009. Human Genetics. 125: 53-62. PubMed ID: 19050930
  • Smith R.J.H. and Hildebrand M. 2015. DFNA2 Nonsyndromic Hearing Loss. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301388
  • Uyguner et al. 2003. Clinical Genetics. 64: 65-9. PubMed ID: 12791041
  • Van Camp G. et al. 1997. American Journal of Human Genetics. 60: 758-64. PubMed ID: 9106521
  • Xia et al. 2000. Neuroreport. 11: 2449-53. PubMed ID: 10943702
  • Xia J.H. et al. 1998. Nature Genetics. 20: 370-3. PubMed ID: 9843210
Order Kits
TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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