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Gyrate Atrophy of Choroid and Retina via the OAT 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
8339 OAT 81479 81479,81479 $890 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8339OAT81479 81479,81479 $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

  • Dana Talsness, PhD

Clinical Features and Genetics

Clinical Features

Gyrate atrophy (GA) is an autosomal recessive eye disorder characterized by progressive chorioretinal degeneration that leads to loss of vision. Other symptoms include hyperornithinemia, progressive centripetal loss of vision, minor central and peripheral nervous system abnormalities, and type II muscle fiber atrophy with accumulation of tubular aggregates (Mitchell et al. 1988; Peltola et al. 2002). However, the clinical phenotype is largely confined to the eye (Ramesh et al. 1991).

Genetics

Pathogenic variants in OAT have been reported to be causative for autosomal-recessive Gyrate atrophy (GA). The OAT gene on chromosome 10 encodes Ornithine delta-aminotransferase, which is a nuclear-encoded mitochondrial matrix enzyme (OATase). This enzyme catalyzes the reversible interconversion of ornithine and alpha-ketoglutarate to glutamate semialdehyde and glutamate. Functional studies have shown that the majority of the causative variants inactivate enzyme activity. These studies also suggested allelic heterogeneity causing both pyridoxine responsive and non-responsive forms of GA, reflecting the clinical and biochemical heterogeneity in this disease (Ramesh et al. 1991; Brody et al. 1992). OAT gene sequences are also found on the X chromosome (Xp11.2) that map to the same region as L1.28 (Xp11.0-p11.3), a marker closely linked to X-linked recessive retinitis pigmentosa. However, the functional OAT gene is on chromosome 10 (Barrett et al. 1987). So far, about 70 causative variants (Missense/nonsense, splicing and small and large deletions and insertions) have been reported in OAT-associated disorders (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

Mashima et al. identified causative variants (missense, nonsense, small deletions and splice-site variants) in 95.5% (21/22) mutant OAT alleles from 11 patients, which indicates that large copy number variants are a rare cause of the disease (Mashima et al. 1994).

Testing Strategy

This test provides full coverage of all coding exons of the OAT 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

All patients with symptoms suggestive of Gyrate Atrophy of Choroid and Retina are candidates. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in OAT.

Gene

Official Gene Symbol OMIM ID
OAT 613349
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Citations

  • Barrett D.J. et al. 1987. Investigative Ophthalmology & Visual Science. 28: 1037-42. PubMed ID: 3596985
  • Brody L.C. et al. 1992. The Journal of Biological Chemistry. 267: 3302-7. PubMed ID: 1737786
  • Human Gene Mutation Database (Bio-base).
  • Mashima Y. et al. 1994. Investigative Ophthalmology & Visual Science. 35: 1065-70. PubMed ID: 8125717
  • Mitchell G.A. et al. 1988. The Journal of Clinical Investigation. 81: 630-3. PubMed ID: 3339136
  • Peltola K.E. et al. 2002. Neurology 59:735-40. PubMed ID: 12221166
  • Ramesh V. et al. 1991. Molecular Biology & Medicine. 8:81-93. PubMed ID: 1682785

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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