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Long QT Syndrome via the SNTA1 Gene

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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
SNTA1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9961SNTA181479 81479,81479 $990 Order Options and Pricing

EMAIL CONTACTS

Genetic Counselors

Geneticist

  • Chun-An Chen, PhD

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 platform).

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

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

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks 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

  • Chun-An Chen, PhD

Clinical Features and Genetics

Indications for Test

All patients with symptoms suggestive of Long QT syndrome are candidates for this test.

Clinical Features

Long QT syndrome (LQTS) is a heritable channelopathy characterized by an exceedingly prolonged cardiac repolarization that may trigger ventricular arrhythmias (torsade de pointes), recurrent syncopes, seizure, or sudden cardiac death (SCD) (Cerrone et al. 2012). The incidence of LQTS has been estimated between 1 in 2500 and 1 in 7000 in the general population.  LQTS can manifest with syncope and cardiac arrest that is commonly triggered by adrenergic stress, often precipitated by emotion or exercise. Roughly 10% to 15% of patients experience symptoms at rest or during the night (Schwartz et al. 2001). The mean age of onset of symptoms is 12 years, and earlier onset usually is associated with a more severe form of the disease (Priori et al 2004). Inherited LQTS occurs due to mutations in multiple genes such as KCNQ1 (LQT1), KCNH2 (LQT2), SCN5A (LQT3), ANK2(LQT4), KCNE1 (LQT5), KCNE2 (LQT6), KCNJ2(LQT7), CACNA1C(LQT8), CAV3(LQT9), SCN4B(LQT10), AKAP9(LQT11), SNTA1(LQT12) and KCNJ5 (LQT13), but it can also be acquired (acquired LQTS), usually as a result of pharmacological therapy. A small percentage of cases of LQTS occur in people who have an underlying pathogenic variation in the SNTA1 gene.

Genetics

Long QT 12 is caused by mutation in the SNTA1 gene and is inherited in an autosomal dominant manner. SNTA1 encodes a cytoplasmic cytoskeletal protein α1-syntrophin, which acts as a molecular scaffold for neuronal Nitric Oxide Synthase (nNOS) and plasma membrane Ca-ATPase (PMCA) (Ahn et al. 1996). SNTA1 protein is also known to interact with the pore-forming α subunit (SCN5A, known as NaV1.5) of the cardiac sodium channel complex. PMCA inhibits nitric oxide synthesis through NOS, and nitric oxide increases channel activation by inducing nitrosylation of Nav1.5 proteins. One causative variant in SNTA1 disrupts the interaction between Nav1.5 and PMCA, and consequently increase Nav1.5 nitrosylation and late sodium current (I Na) (Ueda et al. 2008). All known causative variants in SNTA1 are missense variants (Human Gene Mutation Database).

Clinical Sensitivity - Sequencing with CNV PGxome

Up to 70 % of patients with a clinical diagnosis of Long QT syndrome have identifiable causative variants (Beckmann et al. 2013). The majority of LQTS cases are caused by mutations in one of three genes: KCNQ1, KCNH2 and SCN5A. Approximately 5% total of LQTS causative variants are contributed by the following genes: ANK2, KCNE1, KCNE2, KCNJ2, CACNA1C, CAV3, SCN4B, AKAP9, SNTA1 and KCNJ5 (Lieve et al. 2012; Kapplinger et al. 2009).

To date, no gross deletions or duplications have been reported in the SNTA1 gene (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the SNTA1 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 Long QT syndrome are candidates for this test.

Gene

Official Gene Symbol OMIM ID
SNTA1 601017
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Long QT Syndrome 12 612955

Related Test

Name
Long QT Syndrome via the SCN4B Gene

Citations

  • Ahn AH, Freener CA, Gussoni E, Yoshida M, Ozawa E, Kunkel LM. 1996. The three human syntrophin genes are expressed in diverse tissues, have distinct chromosomal locations, and each bind to dystrophin and its relatives. J. Biol. Chem. 271: 2724–2730. PubMed ID: 8576247
  • Beckmann B-M, Wilde AAM, Kääb S. 2013. Clinical utility gene card for: long-QT syndrome (types 1-13). Eur. J. Hum. Genet. 21: PubMed ID: 23511927
  • Cerrone M. et al. 2012. Circulation. Cardiovascular genetics. 5: 581-90. PubMed ID: 23074337
  • Human Gene Mutation Database (Bio-base).
  • Human Gene Mutation Database (Bio-base).
  • Kapplinger JD, Tester DJ, Salisbury BA, Carr JL, Harris-Kerr C, Pollevick GD, Wilde AAM, Ackerman MJ. 2009. Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. Heart Rhythm 6: 1297–1303. PubMed ID: 19716085
  • Lieve KV, Williams L, Daly A, Richard G, Bale S, Macaya D, Chung WK. 2013. Results of genetic testing in 855 consecutive unrelated patients referred for long QT syndrome in a clinical laboratory. Genet Test Mol Biomarkers 17: 553–561. PubMed ID: 23631430
  • Priori et al. 2004. PubMed ID: 15367556
  • Schwartz et al. 2001. PubMed ID: 11136691
  • Ueda K, Valdivia C, Medeiros-Domingo A, Tester DJ, Vatta M, Farrugia G, Ackerman MJ, Makielski JC. 2008. Syntrophin mutation associated with long QT syndrome through activation of the nNOS-SCN5A macromolecular complex. Proc. Natl. Acad. Sci. U.S.A. 105: 9355–9360. PubMed ID: 18591664

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

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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