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Epilepsy: Focal Epilepsy and Focal Cortical Dysplasia via the NPRL2 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
NPRL2 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
7529NPRL281479 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

Familial focal epilepsy with variable foci is a disorder characterized by focal seizures originally arising from different cortical regions, including the temporal, frontal, parietal, and occipital lobes. NPRL2-related familial focal epilepsy with variable foci 2 could present different symptoms such as focal seizure, frontal lobe epilepsy, nocturnal frontal lobe epilepsy, temporal lobe epilepsy and focal cortical dysplasia in different patients. Associated cognitive or psychiatric symptoms are not uncommon in patients. Image studies could reveal focal cortical dysplasia (Ricos et al. 2016. PubMed ID: 26505888; Weckhuysen et al. 2016. PubMed ID: 27173016).


Familial Focal Epilepsy with Variable foci 2 is inherited in autosomal dominant manner with incomplete penetrance and is caused by pathogenic variants in the NPRL2 gene. The NPRL2 gene encodes a subunit of the GAP Activity Towards Rags 1 (GATOR1) complex. NPRL2 (Nitrogen Permease Regulator-Like-2) and NPRL3 (Nitrogen Permease Regulator-Like-3) bind with DEPDC5 to form the GATOR1 protein complex, which negatively regulates the mammalian target of the Rapamycin (mTOR) signaling pathway. Loss of function of the GATOR1 complex is causative for a number of human brain malformations, including tuberous sclerosis, hemimegalencephaly, and focal cortical dysplasia (Ricos et al. 2016. PubMed ID: 26505888).

Pathogenic variants including nonsense, missense and a small frameshift deletion have been reported to be causative for familial focal epilepsy with variable foci 2 and focal cortical dysplasia (Ricos et al. 2016. PubMed ID: 26505888; Weckhuysen et al. 2016. PubMed ID: 27173016; Human Gene Mutation Database). No large deletions/duplications have been reported (HGMD database). Focal epilepsy is the most prevalent form of epilepsy observed in the general population. Penetrance is incomplete (Ricos et al. 2016. PubMed ID: 26505888).

Clinical Sensitivity - Sequencing with CNV PG-Select

In a cohort of 404 unrelated focal epilepsy patients, five patients had pathogenic variants in NPRL2 (Ricos et al. 2016. PubMed ID: 26505888).

Testing Strategy

This test provides full coverage of all coding exons of the NPRL2 gene, plus ~10 bases of flanking noncoding DNA. We define coverage as ≥20X NGS reads or Sanger sequencing.

Indications for Test

NPRL2 sequencing is recommended for patients who are suspected to have familial focal epilepsy with variable foci 2 and focal cortical dysplasia.


Official Gene Symbol OMIM ID
NPRL2 607072
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Epilepsy, Familial Focal, with Variable Foci 2 AD 617116


  • Human Gene Mutation Database (Bio-base).
  • Ricos et al. 2016. PubMed ID: 26505888
  • Weckhuysen et al. 2016. PubMed ID: 27173016


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)

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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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