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Nephronophthisis via the NPHP4 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
15265 NPHP4 81479 81479,81479 $990 Order Options and Pricing
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
15265NPHP481479 81479,81479 $990 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.

Testing run on PG-Select capture probes does not include exome-wide CNV analysis. Reflex is available to PGxome or an exome-based panel, or you can use this gene list to create a custom panel (click here).

Click here for costs to reflex to whole PGxome.

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

  • Fang Xu, PhD, FACMG

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 4 (NPH4) (OMIM 606966) results in chronic renal failure in children after five years of age and in adolescents (Mollet et al. Nat Genet 32:300-305, 2002; Otto et al. Am J Hum Genet 71:1161-1169, 2002).

Genetics

NPH4 is inherited in an autosomal recessive manner, and is caused by variants in the NPHP4 gene (Mollet et al. Nat Genet 32:300-305, 2002; Otto et al. Am J Hum Genet 71:1161-1169, 2002). NPHP4 encodes the protein nephrocystin-4, which is localized to primary cilia, basal bodies, centrosomes, and cortical actin cytoskeleton. It has been reported that nephrocystin-4 interacts with nephrocystin-1 and nephrocystin-3 (products of NPHP1 and NPHP3 genes respectively) and might have a role in cilia function and or maintenance (Mollet et al. 2002; Otto et al. 2002; Olbrich et al. Nat Genet 34:455-459, 2003; Hildebrandt et al. J Am Soc Nephrol 20:23-35, 2009). A mix of nonsense, frameshift, splicing and missense variants have been reported in NPHP4 (Mollet et al. 2002; Otto et al. 2002). 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. 2009).

Clinical Sensitivity - Sequencing with CNV PG-Select

Variants in NPHP4 are estimated to cause approximately ~2% of NPH cases (Hildebrandt et al. J Am Soc Nephrol 20:23-35, 2009).

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the NPHP4 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.

Indications for Test

Candidates for this test are patients with symptoms consistent with juvenile or adolescent 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 NPHP4.

Gene

Official Gene Symbol OMIM ID
NPHP4 607215
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Nephronophthisis 4 AR 606966

Citations

  • 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
  • Mollet, G., et.al. (2002). "The gene mutated in juvenile nephronophthisis type 4 encodes a novel protein that interacts with nephrocystin." Nat Genet 32(2): 300-5. PubMed ID: 12244321
  • Olbrich, H., et.al. (2003). "Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis." Nat Genet 34(4): 455-9. PubMed ID: 12872122
  • Otto, E., et.al. (2002). "A gene mutated in nephronophthisis and retinitis pigmentosa encodes a novel protein, nephroretinin, conserved in evolution." Am J Hum Genet 71(5): 1161-7. PubMed ID: 12205563

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

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ORDER OPTIONS

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View Ordering Instructions

1) Select Test Method (Platform)


1) 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.

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