Nephronophthisis via the GLIS2/NPHP7 Gene
Summary and Pricing 
Test Method
Exome Sequencing with CNV Detection
| Test Code | Test Copy Genes | Test CPT Code | Gene CPT Codes Copy CPT Code | Base Price | |
|---|---|---|---|---|---|
| 8787 | GLIS2 | 81479 | 81479,81479 | $990 | 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 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.
Clinical Features and Genetics
Clinical Features
Nephronophthisis (NPH) is the most common genetic cause of progressive renal failure in children and young adults. NPH is characterized by polyuria, growth retardation, and progressive deterioration of renal function with normal or slightly reduced kidney size (Hildebrandt et al. Nat Genet 17:149-153, 1997; Hildebrandt et al. J Am Soc Nephrol 20:23-35, 2009). Nephronophthisis type 7 (NPH7) (OMIM 611498) is a form of juvenile nephronophthisis (Attanasio et al. Nat Genet 39:1018-1024, 2007; Hildebrandt et al. 2009).
Genetics
NPH7 is inherited in an autosomal recessive manner. Variants in the GLIS2/NPHP7 gene cause NPH7 (Attanasio et al. Nat Genet 39:1018-1024, 2007). GLIS2 encodes a Gli-similar protein 2 (GLIS2), which is localized to the primary cilia. GLIS2 is a Kruppel-like zinc finger transcription factor essential for normal renal cell maintenance (Attanasio et al. 2007; Kim et al. Mol Cell Biol 28:2358-2367, 2008). Only a single splicing variant has been reported in the GLIS2/NPHP7 gene (Attanasio et al. 2007). Nephronophthisis exhibits locus heterogeneity. Nine NPH genes have been identified (NPHP1, INVS/NPHP2, NPHP3, NPHP4, IQCB1/NPHP5, CEP260/NPHP6, GLIS2/NPHP7, RPGRIP1L/NPHP8, and NEK8/NPHP9) (Hildebrandt et al. J Am Soc Nephrol 20:23-35, 2009).
Clinical Sensitivity - Sequencing with CNV PGxome
Variants in GLIS2/NPHP7 gene are estimated to cause less than 1% of the NPH cases (Hildebrandt et al. J Am Soc Nephrol 20:23-35, 2009).
Testing Strategy
This test provides full coverage of all coding exons of the GLIS2/NPHP7 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
Candidates for this test are patients with symptoms consistent with juvenile NPH and the family members of patients who have known variants. Conclusive connections between clinical features and individual mutated genes have not yet been made. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in GLIS2.
Candidates for this test are patients with symptoms consistent with juvenile NPH and the family members of patients who have known variants. Conclusive connections between clinical features and individual mutated genes have not yet been made. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in GLIS2.
Gene
| Official Gene Symbol | OMIM ID |
|---|---|
| GLIS2 | 608539 |
| Inheritance | Abbreviation |
|---|---|
| Autosomal Dominant | AD |
| Autosomal Recessive | AR |
| X-Linked | XL |
| Mitochondrial | MT |
Disease
| Name | Inheritance | OMIM ID |
|---|---|---|
| Nephronophthisis 7 | 611498 |
Citations
- Attanasio, M., et.al. (2007). "Loss of GLIS2 causes nephronophthisis in humans and mice by increased apoptosis and fibrosis." Nat Genet 39(8): 1018-24. PubMed ID: 17618285
- Hildebrandt et al. 1997. PubMed ID: 9326933
- Hildebrandt F. et al. 2009. Journal of the American Society of Nephrology : Jasn. 20: 23-35. PubMed ID: 19118152
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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ORDER OPTIONS
View Ordering Instructions1) Select Test Type
2) Select Additional Test Options
No Additional Test Options are available for this test.