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Nephronophthisis and Senior-Loken Syndrome via the IQCB1/NPHP5 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
IQCB1 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
9937IQCB181479 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 type 5 (NPH5) (OMIM# 609254) is a form of juvenile nephronophthisis with Leber congenital amaurosis known as Senior-Loken syndrome (Otto et al. Nat Genet 37:282-288, 2005; Hildebrandt et al. 2009).


NPH5 is inherited in an autosomal recessive manner. Variants in the IQCB1/NPHP5 gene cause NPH5 (Otto et al. Nat Genet 37:282-288, 2005). IQCB1 encodes a protein called nephrocystin-5, which is localized to the connecting cilia of the photoreceptor in the retina and to the primary cilia in renal cells. Nephrocystin-5 contains an IQ domain, which directly interacts with calmodulin. It is found in a complex with retinitis pigmentosa GTPase regulator (RPGR) protein, responsible for X-linked retinitis pigmentosa, and also interacts with nephrocystin-6 (product of the CEP290 gene), suggesting that nephrocystin-5 has a role in photoreceptor homeostasis (Otto et al. 2005; Schafer et al. Hum Mol Genet 17:3655-3662, 2008; Hildebrandt et al. J Am Soc Nephrol 20:23-35, 2009). A mix of nonsense, frameshift, and splicing variants has been reported in IQCB1/NPHP5 (Otto et al. 2005; Otto et al. Hum Mut 29:418-426, 2008). 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 PGxome

Variants in IQCB1/NPHP5 gene are estimated to cause approximately ~3% of NPH cases (Hildebrandt et al. J Am Soc Nephrol 20:23-35, 2009). It has been predicted that variant in the IQCB1 gene are the most frequent cause of Senior-Loken syndrome (Otto et al. Nat Genet 37:282-8, 2005).

Testing Strategy

This test provides full coverage of all coding exons of the IQCB1 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 Senior-Loken syndrome, juvenile NPH with Leber congenital amaurosis, 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 IQCB1.


Official Gene Symbol OMIM ID
IQCB1 609237
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Senior-Loken Syndrome 5 609254


  • 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
  • Hildebrandt F. et al. 2009. Journal of the American Society of Nephrology : Jasn. 20: 23-35. PubMed ID: 19118152
  • Hildebrandt F. et al. 2009. Journal of the American Society of Nephrology : Jasn. 20: 23-35. PubMed ID: 19118152
  • Otto et al. 2005. PubMed ID: 15723066
  • Otto et al. 2005. PubMed ID: 15723066
  • Otto et al. 2005. PubMed ID: 15723066
  • Otto, E. A., et.al. (2008). "Mutation analysis in nephronophthisis using a combined approach of homozygosity mapping, CEL I endonuclease cleavage, and direct sequencing." Hum Mutat 29(3): 418-26. PubMed ID: 18076122
  • Schafer, T., et.al. (2008). "Genetic and physical interaction between the NPHP5 and NPHP6 gene products." Hum Mol Genet 17(23): 3655-62. PubMed ID: 18723859


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