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Epilepsy: SCN3A-Related Epilepsy via the SCN3A Gene

Summary and Pricing

Test Method

Sequencing and CNV Detection via NextGen Sequencing using PG-Select Capture Probes
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
SCN3A 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7993SCN3A81479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Testing run on PG-select capture probes includes CNV analysis for the gene(s) on the panel but does not permit the optional add on of exome-wide CNV analysis. Any of the NGS platforms allow reflex to other clinically relevant genes, up to whole exome or whole genome sequencing depending upon the base platform selected for the initial test.

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

This test is also offered via a custom panel (click here) on our exome or genome backbone which permits the optional add on of exome-wide CNV or genome-wide SV analysis.

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.


Genetic Counselors


  • Eric Bend, PhD

Clinical Features and Genetics

Clinical Features

Patients with a pathogenic variant in SCN3A present complex focal seizures with secondary generalization, or simple febrile seizures, or unprovoked generalized tonic clonic seizures with onset from infantile to early childhood. Other clinical symptoms include learning disability, mild speech delay, and attention deficit hyperactivity disorder (ADHD) with or without developmental delay (Holland et al 2008; Meisler et al 2010; Vanoye et al 2014).


SCN3A-related infantile epilepsy is caused by a heterozygous pathogenic variant in the patient. The penetrance is variable (Holland et al 2008; Vanoye et al 2014). SCN3A encodes a pore-forming, voltage-gated sodium channel, type III, α subunit which is expressed highly in the brain. Biophysical characterization of epilepsy-associated SCN3A variants suggests that certain gain- and loss-of-function SCN3A pathogenic variants may only lead to increased seizure susceptibility (Lamar et al. 2017).

The reported SCN3A pathogenic variants are missense and only one nonsense (Human Gene Mutation Database). Large duplications including SCN2A and SCN3A have been reported to be causative for infantile epilepsy (Vecchi et al 2011; Goeggel Simonetti et al. 2012).

Clinical Sensitivity - Sequencing with CNV PG-Select

Infantile epilepsy is clinically and genetically heterogeneous. Clinical sensitivity cannot be estimated because only a small number of patients have been reported.

Testing Strategy

This test provides full coverage of all coding exons of the SCN3A gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Sequencing is recommended for cases who are suspected to have SCN3A-related epilepsy.


Official Gene Symbol OMIM ID
SCN3A 182391
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Epileptic Encephalopathy, Early Infantile, 62 AD 617938


  • Goeggel Simonetti B. et al. 2012. Epilepsia. 53: 2128-34. PubMed ID: 23016767
  • Holland K.D. et al. 2008. Neuroscience Letters. 433: 65-70. PubMed ID: 18242854
  • Human Gene Mutation Database (Bio-base).
  • Lamar T. et al. 2017. Neurobiology of Disease. 102: 38-48. PubMed ID: 28235671
  • Meisler M.H. et al. 2010. The Journal of Physiology. 588: 1841-8. PubMed ID: 20351042
  • Vanoye C.G. et al. 2014. Neurobiology of Disease. 62: 313-22. PubMed ID: 24157691
  • Vecchi M. et al. 2011. Seizure. 20: 813-6. PubMed ID: 21893419


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

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View Ordering Instructions

1) Select Test Method (Platform)

1) Select Test Type

2) Select Additional Test Options

No Additional Test Options are available for this test.

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