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Deafness, Autosomal Dominant 15 (DFNA15) via the POU4F3 Gene

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

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
2934 POU4F3$540.00 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 clinical sensitivity of this test has been reported to range from 0.5% to 12%. For example, in two independent studies conducted in Japan, disease-causing POU4F3 sequence variants were detected in 0.5% (1/216) of randomly selected deafness patients (Miyagawa et al. 2013) and 6.7% (1/15) of unrelated hearing loss families (Mutai et al. 2013). In Korea, 12.5% (1/8) of families with autosomal dominant nonsyndromic sensorineural hearing loss harbored pathogenic sequence variants in the POU4F3 gene (Baek et al. 2012). In China, causative POU4F3 sequence variants were identified 0.8% (1/125) of deaf patients who tested negative for pathogenic sequence variants in the deafness genes GJB2, SLC26A4, and MT-RNR1 (Yang et al. 2013) and in 4.3% (1/23) of families with nonsyndromic hearing loss (Wei et al. 2014).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 POU4F3$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 Features

Autosomal dominant deafness 15 (DFNA15) is a late-onset (postlingual), bilateral, high-frequency, progressive, nonsyndromic hearing loss disorder that begins in the first to third decades and results in severe to profound hearing impairment by the fifth to sixth decades of life. The audioprofile of most nonsyndromic hearing loss cases can be distinct, thus assisting in the development of an evaluation strategy for molecular genetic testing and in generating a prognosis on the rate of hearing loss per year (Hildebrand et al. 2008). Pure tone audiograms of DFNA15 individuals generally show gently downward-sloping to flat pure tone audiograms, indicating mid-/high-frequency to all-frequency hearing impairment, with a progression rate of around 0.8 decibels/year across most frequencies (Collin et al. 2008: Frydman et al. 2000; Pauw et al. 2008). DFNA15 patients may show variable rates of progression, age of onset, as well as vestibular defects (Freitas et al. 2014). Other rare symptoms include instability, vertigo, and higher risk for falls.

Genetics

DFNA15 is an autosomal dominant hearing disorder that is caused by pathogenic sequence variants in the POU domain, class 4, transcription factor 3 (POU4F3) gene (also known as the BRN3C gene), which is located on chromosome 5q32 (Vahava et al. 1998). The POU4F3 gene consists of two coding exons that encode a 338-amino acid transcription factor, which plays an essential role in the embryonic development of the cochlea, particularly in the maturation, differentiation, as well as survival of inner ear sensory hair cells (Xiang et al. 1995, 1997, 1998; Hertzano et al. 2004; Yoshimura et al. 2014). Functional studies indicate that the POU4F3 protein regulates gene expression of nuclear receptors, neutrophins, cytoplasmic phosphoproteins, and other transcription factors (Hertzano et al. 2004; Clough et al. 2004; Towers et al. 2010; Tornari et al. 2014). To date, a total of about 10 pathogenic POU4F3 sequence variants have been reported, which include 6 missense and 4 frame shift sequence variants that disrupt the functioning of the POU4F3 protein by eliminating its ability to bind to DNA. One entire gene deletion has also been reported (Weiss et al. 2003; Human Gene Mutation Database).

Testing Strategy

Testing is accomplished by amplifying the coding exons of the POU4F3 gene and ~20 bp of adjacent noncoding sequence, then determining the nucleotide sequence using standard dideoxy Sanger sequencing methods and a capillary electrophoresis instrument. We will also sequence any single exon (Test #100) in family members of patients with a known mutation or to confirm research results.

Indications for Test

The ideal POU4F3 test candidates are individuals who present with late-onset, bilateral, high-frequency, progressive, autosomal dominant nonsyndromic hearing loss.

Gene

Official Gene Symbol OMIM ID
POU4F3 602460
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Deafness, Autosomal Dominant 15 AD 602459

Related Test

Name
Nonsyndromic Hearing Loss and Deafness Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Baek J.I. et al. 2012. Orphanet Journal of Rare Diseases. 7: 60. PubMed ID: 22938506
  • Clough R.L. et al. 2004. Biochemical and Biophysical Research Communications. 324: 372-81. PubMed ID: 15465029
  • Collin R.W. et al. 2008. Human Mutation. 29: 545-54. PubMed ID: 18228599
  • Freitas É.L. et al. 2014. European Journal of Medical Genetics. 57: 125-8. PubMed ID: 24556497
  • Frydman M. et al. 2000. Archives of Otolaryngology--head & Neck Surgery. 126: 633-7. PubMed ID: 10807331
  • Hertzano R. et al. 2004. Human Molecular Genetics. 13: 2143-53. PubMed ID: 15254021
  • Hildebrand M.S. et al. 2008. Genetics in Medicine. 10: 797-804. PubMed ID: 18941426
  • Human Gene Mutation Database (Bio-base).
  • Miyagawa M. et al. 2013. PLoS One. 8: e71381. PubMed ID: 23967202
  • Mutai H. et al. 2013. Orphanet Journal of Rare Diseases. 8: 172. PubMed ID: 24164807
  • Pauw R.J. et al. 2008. Archives of Otolaryngology--head & Neck Surgery. 134: 294-300. PubMed ID: 18347256
  • Tornari C. et al. 2014. Plos One. 9: e112247. PubMed ID: 25372459
  • Towers E.R. et al. 2011. Journal of Cell Science. 124: 1145-55. PubMed ID: 21402877
  • Vahava O. et al. 1998. Science (new York, N.y.). 279: 1950-4. PubMed ID: 9506947
  • Wei Q. et al. 2014. Journal of Translational Medicine. 12: 311. PubMed ID: 25388789
  • Weiss S. et al. 2003. Molecular and Cellular Biology. 23: 7957-64. PubMed ID: 14585957
  • Xiang M. et al. 1995. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 15: 4762-85. PubMed ID: 7623109
  • Xiang M. et al. 1997. Proceedings of the National Academy of Sciences of the United States of America. 94: 9445-50. PubMed ID: 9256502
  • Xiang M. et al. 1998. Development (cambridge, England). 125: 3935-46. PubMed ID: 9735355
  • Yang T. et al. 2013. Orphanet Journal of Rare Diseases. 8: 85. PubMed ID: 23767834
  • Yoshimura H. et al. 2014. Plos One. 9: e92547. PubMed ID: 24676347
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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