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Nephronophthisis-Like Nephropathy-1 (NPHPL1) via the XPNPEP3 Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
XPNPEP3 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8365XPNPEP381479 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.


Genetic Counselors


  • 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-like nephropathy-1 (NPHPL1) patients develop a renal disease reminiscent of nephronophthisis within the first three decades of life (O’Toole et al. J Clin Invest 120:791-802, 2010). Renal biopsies from NPHPL1 patients showed characteristic features of nephronophthisis, such as thickening, splitting, and attenuation of the tubular basement membrane, atrophic tubules, and mild interstitial fibrosis, while renal ultrasound revealed increased echogenicity and cysts (O’Toole et al. 2010). Extrarenal features of NPHPL1 include hypertension, essential tremor, high frequency sensorineural hearing loss, and arachnoid cysts on brain imaging. In addition, severe cases of NPHPL1 might develop a mitochondrial disorder with isolated complex I deficiency activity in muscle, seizures, mental retardation, hypertrophic dilated cardiomyopathy, and chronic pancreatitis with pancreatic cysts or hepatic involvement (O’Toole et al. 2010).


NPHPL1 is inherited in an autosomal recessive manner. Variants in the XPNPEP3 gene cause NPHPL1 (O’Toole et al. J Clin Invest 120:791-802, 2010). XPNPEP3 gene encodes a mitochondrial protein known as X-prolyl aminopeptidase 3 (XPNPEP3), which belongs to a family of X-prolyl aminopeptidases that utilize a metal cofactor and remove the N-terminal amino acid from peptides with a proline residue in the penultimate position (Ersahin et al. Arch Biochem Biophys 435:303-310, 2005). XPNPEP3 localizes to the mitochondria of the renal cells, yet it is predicted to have a cilia-related function. Biochemical studies demonstrated that several ciliary proteins are likely XPNPEP3 substrates (Ersahin et al. 2005; O’Toole et al. 2010). A frameshift variant and a splicing variant within the XPNPEP3 gene have been reported (O’Toole et al. 2010).

Clinical Sensitivity - Sequencing with CNV PGxome

Sensitivity of this test is currently unknown.

Testing Strategy

This test provides full coverage of all coding exons of the XPNPEP3 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 nephronophthisis-like nephropathy-1 and family members of patients who have known XPNPEP3 variants. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in XPNPEP3.


Official Gene Symbol OMIM ID
XPNPEP3 613553
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Nephronophthisis-Like Nephropathy 1 AR 613159


  • Ersahin, C., et.al. (2005). "Aminopeptidase P isozyme expression in human tissues and peripheral blood mononuclear cell fractions." Arch Biochem Biophys 435(2): 303-10. PubMed ID: 15708373
  • 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
  • O'Toole, J. F., et.al. (2010). "Individuals with mutations in XPNPEP3, which encodes a mitochondrial protein, develop a nephronophthisis-like nephropathy." J Clin Invest 120(3): 791-802. PubMed ID: 20179356


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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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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