Deafness, Autosomal Recessive 22 (DFNB22) via the OTOA Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
11547 OTOA 81479 81479,81479 $1420 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11547OTOA81479 81479(x2) $1420 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing backbone).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing backbone).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

18 days on average for standard orders or 13 days on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Ben Dorshorst, PhD

Clinical Features and Genetics

Clinical Features

Autosomal recessive deafness 22 (DFNB22) is a prelingual, bilateral, severe to profound, nonprogressive, nonsyndromic, sensorineural hearing loss disorder that involves disruption in the mechanotransduction of sound waves to the inner ear (Jovine et al. 2002; Zwaenepoel et al. 2002).. 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 audiometry of DFNB22 individuals generally show a flat audiogram, indicating all-frequency hearing loss (Lee et al. 2013).

Genetics

DFNB22 is an autosomal recessive hearing disorder that is caused by pathogenic sequence variants in the otoancorin (OTOA) gene, which is located on chromosome 16p12.2 (Zwaenepoel et al. 2002). The OTOA gene is 86 kb in size and consists of 28 coding exons that produce a 1,139-amino acid predominantly helical, noncollagenous glycoprotein that is mainly expressed on the surface of the spiral limbus in the cochlea of the inner ear (Sathyanarayana et al. 2009; Lukashin et al. 2012). The OTOA protein mediates the attachment of the tectorial membrane to the sensory epithelium of the inner hair cells of the cochlea, thereby deflecting the stereociliary bundle for the mechanotransduction of sound (Jovine et al. 2002; Zwaenepoel et al. 2002). The 7 OTOA variants implicated to date in hearing loss consist of 4 missense, 1 splicing and 2 gross deletions (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

The clinical sensitivity of this test has been reported to range up to 5%. In a cohort of multiethnic families with autosomal recessive nonsyndromic deafness, 0.6% (1/160) harbored pathogenic sequence variants in the OTOA gene (Bademci et al. 2015). Around 1.5% (1/65) of Algerian families tested positive for disease-causing OTOA sequence variants (Ammar-Kodja et al. 2015). Causative OTOA sequence variants were detected in 5% (1/20) of Palestinian families with prelingual nonsyndromic hearing loss (Shahin et al. 2010).

Testing Strategy

This test provides full coverage of most coding exons of the OTOA gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Exons 20-28 of the OTOA gene have paralogy, or high levels of sequence similarity to a second genomic locus. Inherent limitations of NGS reduce the ability to detect sequence variants and CNVs in paralogous regions. For this reason the paralogous exons are Sanger sequenced to ensure full coverage of all coding exons. Detection of CNVs is performed using NGS, and is able to detect CNVs that involve exons of OTOA with and without paralogy. In summary, all exons of the OTOA gene are included in this sequencing and CNV test.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Indications for Test

The ideal OTOA test candidates are individuals who present with prelingual (early-onset), bilateral, severe to profound, nonprogressive, autosomal recessive, sensorineural nonsyndromic hearing loss. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in OTOA.

Gene

Official Gene Symbol OMIM ID
OTOA 607038
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Deafness, Autosomal Recessive 22 AR 607039

Citations

  • Ammar-Khodja F. et al. 2015. Molecular Genetics & Genomic Medicine. 3: 189-96. PubMed ID: 26029705
  • Bademci G. et al. 2015. Genetics in Medicine : Official Journal of the American College of Medical Genetics. 0: N/A. PubMed ID: 26226137
  • Hildebrand M.S. et al. 2008. Genetics in Medicine. 10: 797-804. PubMed ID: 18941426
  • Human Gene Mutation Database (Bio-base).
  • Jovine L. et al. 2002. Bmc Cell Biology. 3: 28. PubMed ID: 12445334
  • Lee K. et al. 2013. Clinical Genetics. 84: 294-6. PubMed ID: 23173898
  • Lukashkin A.N. et al. 2012. Proceedings of the National Academy of Sciences of the United States of America. 109: 19351-6. PubMed ID: 23129639
  • Sathyanarayana B.K. et al. 2009. Bmc Structural Biology. 9: 1. PubMed ID: 19128473
  • Shahin H. et al. 2010. European Journal of Human Genetics. 18: 407-13. PubMed ID: 19888295
  • Zwaenepoel I. et al. 2002. Proceedings of the National Academy of Sciences of the United States of America. 99: 6240-5. PubMed ID: 11972037

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

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.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

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.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Method (Backbone)


1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

Note: acceptable specimen types are whole blood and DNA from whole blood only.
Total Price: $
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