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Deafness, Autosomal Dominant 9 (DFNA9) and Autosomal Recessive Hearing Loss via the COCH 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
11185 COCH 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
11185COCH81479 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

Deafness, autosomal dominant 9 (DFNA9) is characterized by high-frequency, progressive, postlingual (adult-onset) sensorineural nonsyndromic hearing loss that is associated with variable vestibular dysfunction associated with histological alterations in the temporal bone as well as mucopolysaccharide deposition in the cochlear channels and vestibular nerves. This can result in vestibular hypofunction, vertigo or tinnitus (Robertson et al. 1998. PubMed ID: 9806553, Robertson et al. 2006. PubMed ID: 16481359).

Hearing in individuals with DFNA9 generally deteriorates at age 20 and progresses to anacusis (total deafness) by the age of 50 (Hildebrand et al. 2009. PubMed ID: 19161137). The progression of deafness is often slow. The most pronounced hearing loss in DFNA9 involves high-frequency sound. By age 30, DNFNA9 individuals may develop a sudden drop in word recognition, which in turn corresponds to a sharp decline in communication ability, yet can be resolved to a certain degree using cochlear implants (Manolis et al. 1996. PubMed ID: 8817345).

Autosomal recessive inheritance has also been reported in two individuals from a single family with moderate prelingual sensorineural hearing loss with vestibular dysfunction (JanssensdeVarebeke et al. 2018. PubMed ID: 29449721).

Genetics

Pathogenic variants in the cochlin (COCH) gene cause autosomal dominant (DFNA9) and autosomal recessive hearing loss. The COCH gene is located in chromosome 14q11.2-13, and consists of 11 coding exons that encode a 550-amino acid cochlin protein (Robertson et al. 2001. PubMed ID: 11709536). The COCH gene is mainly expressed in the spiral ligament, limbus, and channels of the osseous spirallamina, which are components of the cochlea (Robertson et al. 1998. PubMed ID: 9806553).

To date, a total of ~25 pathogenic COCH sequence variants have been reported to cause DFNA9, all of which are missense and small in-frame deletions (Human Gene Mutation Database), suggestive of a dominant negative or gain-of-function effect. Autosomal recessive hearing loss has been described in one family with a homozygous premature termination variant, suggestive of a loss-of-function effect (JanssensdeVarebeke et al. 2018. PubMed ID: 29449721).

Clinical Sensitivity - Sequencing with CNV PGxome

The clinical sensitivity of this test has been reported to range from about 1% to 6%. For example, an investigation conducted in China indicated that pathogenic sequence variants in the COCH gene accounted for ~1% (1/125) of families with nonsyndromic hearing loss that tested negative for causative variants in the GJB2, SLC26A4, and MT-RNR1 genes (Yang et al. 2013. PubMed ID: 23767834). In a study involving Japanese deafness patients, 0.09% (1/1,120) harbored causative COCH sequence variants (Nishio and Usami. 2015. PubMed ID: 25788563). In two independent studies, disease-causing COCH variants were detected in ~3% (1/32) and ~6% (2/32) of Korean patients with nonsyndromic sensorineural hearing loss (Chang and Choi. 2014. PubMed ID: 25279224; Choi et al. 2013. PubMed ID: 23990876).

No large deletions or duplications involving COCH have been reported (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the COCH 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 COCH test candidates are individuals who present with high-frequency, progressive, postlingual (adult-onset), autosomal dominant or congenital, moderate, autosomal recessive sensorineural hearing loss, with variable vestibular dysfunction.

Gene

Official Gene Symbol OMIM ID
COCH 603196
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Deafness, Autosomal Dominant 9 AD 601369

Citations

  • Chang and Choi. 2014. PubMed ID: 25279224
  • Choi et al. 2013. PubMed ID: 23990876
  • Hildebrand et al. 2009. PubMed ID: 19161137
  • Human Gene Mutation Database (Bio-base).
  • JanssensdeVarebeke et al. 2018. PubMed ID: 29449721
  • Manolis et al. 1996. PubMed ID: 8817345
  • Nishio and Usami. 2015. PubMed ID: 25788563
  • Robertson et al. 1998. PubMed ID: 9806553
  • Robertson et al. 2001. PubMed ID: 11709536
  • Robertson et al. 2006. PubMed ID: 16481359
  • Yang et al. 2013. PubMed ID: 23767834

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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