Deafness, Autosomal Recessive 9 (DFNB9) via the OTOF 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
11549 OTOF 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11549OTOF81479 81479(x2) $890 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. If the Sanger option is selected, CNV detection may be ordered through Test #600.

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 9 (DFNB9) is characterized by two major features: prelingual, bilateral nonsyndromic hearing loss and less frequently, tempeture-sensitive nonsyndromic auditory neuropathy (TS-NSAN) (Iwasa et al. 2013). DFNB9-related deafness generally appears during the first two years of life as an auditory neuropathy, which is detected by electrophysiologic testing, wherein auditory brainstem responses (ABRs) are absent and otoacoustic emssions (OAEs) are present (Madden et al. 2012). However, OAEs eventually disappear, resulting in electrophysiologic testing that indicates a cochlear defect. It is important to distinguish auditory neuropathy from a cochlear defect because cochlear implants may be of marginal value in individuals with auditory neuropathy. TS-NSAN pertains to normal-to-mild hearing loss in the absence of fever or severe to profound hearing loss in the presence of fever. Hearing often returns to normal as fever resolves (Shearer et al. 2008). The global prevalence rate of DFNB9 remains unknown.

Genetics

DFNB9 is an autosomal recessive hearing disorder that is caused by pathogenic sequence variants in the otoferlin (OTOF) gene, which is mainly expressed in the inner hair cells of the cochlea and the brain, and plays a major role in synaptic exocytosis at the auditory ribbon synapse (Roux et al. 2006). The OTOF gene is 21 kb in size, located in chromosome 2p23.1, and consists of 48 coding exons that encode two isoforms. The long isoform contains six C2 domains and a C-terminal domain, whereas the short isoform comprises only the last three C2 domains (Chaib et al. 1993; Yasunaga et al. 1999, 2000). To date, a total of about 110 pathogenic OTOF sequence variants have been reported, which include missense/nonsense, splicing, small deletions, small insertions, small indels, and gross deletions (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

The clinical sensitivity of this test ranges from 2.3% to 10%, depending on the ethnicity of the patient. For example, pathogenic sequence variants in the OTOF gene account for 10% (16/160) of Japanese patients with severe to profound recessive nonsyndromic hearing loss who did not harbor causative variants in the GJB2 and SLC26A4 genes (Iwasa et a. 2013). On the other hand, pathogenic sequence variants in the OTOF gene may be responsible for 7% (7/52) of Brazilian families with prelingual autosomal recessive hearing loss (Romanos et al. 2009). In China, 6.8% (5/73) of families with temperature-sensitive auditory neuropathy were determined to have pathogenic sequence variants in the OTOF gene (Wang et al. 2010). In Turkey, 6.1% (3/49) of families with prelingual deafness and no detected pathogenic variants in the GJB2, GJB6, and MTRNR1 genes harbored disease-causing variants in OTOF (Duman et al. 2011). In Algeria, 6% (2/33) of families with recessive nonsyndromic hearing loss and no detected pathogenic variants in the GJB2 and TMC1 genes showed causative variants in the OTOF gene (Ammar-Khodja et al. 2015). In Korea, 3.2% (1/32) of families with nonsyndromic hearing loss and did not carry pathogenic sequence variants in the GJB2, SLC26A4, and POU3F4 genes or mitochondrial DNA were determined to have causative sequence variants in the OTOF gene (Choi et al. 2013). In Pakistan, disease-causing OTOF sequence variants have been detected in 2.3% (13/557) of patients with recessive congenital/prelingual severe to profound deafness (Choi et al. 2009).

Testing Strategy

This test provides full coverage of all coding exons of the OTOF 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).

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 OTOF test candidates are individuals who present with congenital, bilateral, severe-to-profound, autosomal recessive nonsyndromic hearing loss. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in OTOF.

Gene

Official Gene Symbol OMIM ID
OTOF 603681
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Deafness, Autosomal Recessive 9 AR 601071

Citations

  • Ammar-Khodja F. et al. 2015. Molecular Genetics and Genomic Medicine. 3: 189-96. PubMed ID: 26029705
  • Chaib H. et al. 1996. Human Molecular Genetics. 5: 155-8. PubMed ID: 8789454
  • Choi B.Y. et al. 2009. Clinical Genetics. 75(3): 237-43. PubMed ID: 19250381
  • Choi B.Y. et al. 2013. PLoS ONE. 8: e68692. PubMed ID: 23990876
  • Duman D. et al. 2011. Genetic Testing and Molecular Biomarkers. 15:29-33. PubMed ID: 21117948
  • Human Gene Mutation Database (Bio-base).
  • Iwasa Y. et al. 2013. BMC Medical Genetics. 14: 95. PubMed ID: 24053799
  • Madden C. et al. 2002. Archives of Otolaryngology, Head and Neck Surgery. 128:1026-30. PubMed ID: 12220206
  • Romanos J. et al. 2009. Journal of Human Genetics. 54: 382–385. PubMed ID: 19461658
  • Roux I. et al. 2006. Cell. 127: 277-89. PubMed ID: 17055430
  • Shearer A.E. et al. 2008. OTOF-Related Deafness. 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: 20301429
  • Wang D.Y. et al. 2010. BMC Medical Genetics. 11: 79. PubMed ID: 20504331
  • Yasunaga S. et al. 1999. Nature Genetics. 21: 363-9. PubMed ID: 10192385
  • Yasunaga S. et al. 2000. American Journal of Human Genetics. 67: 591-600. PubMed ID: 10903124

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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