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 Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 7529 | NPRL2 | 81479 | 81479,81479 | $640 | Order Options and Pricing |
Pricing Comments
This test is also offered via our exome backbone with CNV detection (click here). The exome-based test may be higher priced, but permits reflex to the entire exome or to any other set of clinically relevant genes.
An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.
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.
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).
Genetics
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.
NPRL2 sequencing is recommended for patients who are suspected to have familial focal epilepsy with variable foci 2 and focal cortical dysplasia.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| NPRL2 | 607072 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Epilepsy, Familial Focal, with Variable Foci 2 | AD | 617116 |
Citations
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
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ORDER OPTIONS
View Ordering Instructions1) 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.