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Nephronophthisis and Joubert Syndrome via the NPHP1 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
NPHP1 81406 81406,81405 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
15261NPHP181406 81406,81405 $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


  • Fang Xu, PhD, FACMG

Clinical Features and Genetics

Clinical Features

Juvenile or type 1 nephronophthisis (NPH1) (OMIM 256100) is the most common inherited cause of chronic renal failure in children. NPH1 is characterized by polyuria, growth retardation, and progressive deterioration of renal function during childhood or adolescence (Hildebrandt et al. Nat Genet 17:149-153, 1997; Hildebrandt et al. J Am Soc Nephrol 20:23-35, 2009).

Joubert syndrome (JS) (OMIM 213300, 609583) is marked by ataxia, hypotonia, abnormal eye movements, apraxia, neonatal respiratory anomalies, mental retardation, agenesis/hypoplasia of the cerebellar vermis, and a brain malformation known as the "molar tooth sign" (MTS) on cranial MRI. MTS is considered to be the most characteristic diagnostic feature. Some JS patients develop retinal dystrophy or progressive renal failure.


NPH1 and JS are both inherited in an autosomal recessive manner. It has been documented that variants in the NPHP1 gene may cause both NPH1 and JS (Hildebrandt et al. Nat Genet 17:149-53, 1997; Saunier et al. Am J Hum Genet 66:778-789, 2000; Heninger et al. Am J Kidney Dis 37:1131-1139, 2001; Parisi et al. Am J Hum Genet 75:82-91, 2004). Nephronophthisis (NPH) exhibits locus heterogeneity; nine NPH genes have been identified (NPHP1, INV/NPHP2, NPHP3, NPHP4, NPHP5/IQCB1, CEP260/NPHP6, NPHP7/GLIS2, RPGRIP1L/NPHP8, and NEK8/NPHP9) (Hildebrandt et al. J Am Soc Nephrol 20:23-35, 2009). JS likewise have also been linked to variants in the AHI1, CEP290, TMEM67/MKS3, RPGRIP1L, CC2D2A, INPP5E, ARL13B, and NPHP1 genes. PreventionGenetics performs tests for all of these genes.

Clinical Sensitivity - Sequencing with CNV PG-Select

Approximately two thirds of NPH1 patients have homozygous deletions of NPHP1 (Heninger et al. Am J Kidney Dis 37:1131-1139, 2001), and roughly 2% of JS patients have homozygous deletions of NPHP1 (Parisi and Glass GeneReviews, 2007). Other variants in NPHP1 gene contribute approximately 3% of the NPH1 cases.

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 NPHP1 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 NPH1 or JS 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 NPHP1.


Official Gene Symbol OMIM ID
NPHP1 607100
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


  • Heninger, E., et.al. (2001). "Improved strategy for molecular genetic diagnostics in juvenile nephronophthisis." Am J Kidney Dis 37(6): 1131-9. PubMed ID: 11382680
  • 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
  • Parisi M, Glass I. 2013. Joubert Syndrome and Related Disorders. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews(®), Seattle (WA): University of Washington, Seattle. PubMed ID: 20301500
  • Parisi, M. A., et.al. (2004). "The NPHP1 gene deletion associated with juvenile nephronophthisis is present in a subset of individuals with Joubert syndrome." Am J Hum Genet 75(1): 82-91. PubMed ID: 15138899
  • Saunier, S., et.al. (2000). "Characterization of the NPHP1 locus: mutational mechanism involved in deletions in familial juvenile nephronophthisis." Am J Hum Genet 66(3): 778-89. PubMed ID: 10712196


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

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