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Congenital Nephrotic Syndrome via the NPHS1 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
NPHS1 81407 81407,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
3097NPHS181407 81407,81479 $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


  • Wuyan Chen, PhD

Clinical Features and Genetics

Clinical Features

Nephrotic syndrome is a renal disease defined by proteinuria, hypoalbuminemia, hyperlipidemia, and edema (Benoit et al. Pediatr Nephrol 25(9):1621–1632, 2010). Approximately 20% of cases are steroid-resistant nephrotic syndrome (SRNS), characterized by resistance to steroid treatment and rapid progression to end-stage renal failure. The prevalent histological feature of SRNS is focal segmental glomerulosclerosis (FSGS), which has been seen in approximately 60% of SRNS cases. SRNS presents with a wide range of age at onset from birth to adulthood. Congenital nephrotic syndrome (OMIM# 256300) is characterized by prenatal onset of massive proteinuria and severe SRNS in the first three months of life (Benoit et al., 2010; Tryggvason et al. N Engl J Med 354(13):1387-1401, 2006). Other features include radial dilatations of the proximal tubules, mesangial expansion, and capillary obliteration. The most common type is congenital nephrotic syndrome of the Finnish type, which has a high incidence in Finland and the Old Order Mennonites in Lancaster, Pennsylvania.


Congenital nephrotic syndrome is an autosomal recessive disorder. NPHS1 defects are the primary cause of congenital nephrotic syndrome in both familial and sporadic cases (Kestilä et al. Mol Cell 1(4):575-582, 1998; Lenkkeri et al. Am J Hum Genet 64(1):51-61, 1999; Santín et al. Clin J Am Soc Nephrol 6(5):1139-1148, 2011). The NPHS1 gene with 29 exons encodes nephrin that is crucial in the function of the glomerular filtration barrier in the kidneys. Missense, nonsense, splicing site mutations, small deletion/insertions have been found across the whole coding region of the NPHS1 gene. A multi-exon deletion within NPHS1 has also been reported, but is very rare (Machuca et al. J Am Soc Nephrol 21(7):1209-1217, 2010). Notably, NPHS1 mutations also represent a minor cause of infantile, childhood- and adult-onset SRNS (Philippe et al. J Am Soc Nephrol 19(10):1871-1878, 2008; Santín et al. Kidney Int 76(12):1268-1276, 2009; Santín et al., 2011). Congenital nephrotic syndrome can also be caused by defects in the NPHS2, WT1 and PLCE1 genes, but these genes only represent a minor cause of the disease (Santín et al., 2011).

Clinical Sensitivity - Sequencing with CNV PG-Select

NPHS1 mutations were found in 80% of patients with nephrotic syndrome in the first three months of life (83% in familiar cases and 78% in sporadic cases) (Santín et al. Clin J Am Soc Nephrol. 6(5):1139-1148, 2011).

Testing Strategy

This test provides full coverage of all coding exons of the NPHS1 gene, plus ~10 bases of flanking noncoding DNA. We define full coverage as >20X NGS reads or Sanger sequencing.

Indications for Test

Candidates for this test are patients with nephrotic syndrome in the first three months of life as well as in those with typical proximal tubular radial dilatation (Benoit et al., 2010). Candidates for this test are also patients with infantile, childhood and adult-onset SRNS when NPHS2 is normal (Santín et al., 2011). Testing is also indicated for family members of patients who have known NPHS1 mutations. This test may also be considered for the reproductive partners of individuals who carry pathogenic variants in NPHS1.


Official Gene Symbol OMIM ID
NPHS1 602716
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT


Name Inheritance OMIM ID
Finnish Congenital Nephrotic Syndrome AR 256300


  • Benoit, G. et al. (2010). “Hereditary nephrotic syndrome: a systematic approach for genetic testing and a review of associated podocyte gene mutations.” Pediatr Nephrol 25(9):1621-1632. PubMed ID: 20333530
  • Kestilä, M. et al. (1998) "Positionally cloned gene for a novel glomerular protein--nephrin--is mutated in congenital nephrotic syndrome." Mol Cell. 1(4):575-82. PubMed ID: 9660941
  • Lenkkeri, U. et al. (1999). "Structure of the gene for congenital nephrotic syndrome of the finnish type (NPHS1) and characterization of mutations." Am J Hum Genet 64(1):51-61. PubMed ID: 9915943
  • Machuca, E. et al. (2010). "Genotype-phenotype correlations in non-Finnish congenital nephrotic syndrome." J Am Soc Nephrol 21(7):1209-1217. PubMed ID: 20507940
  • Philippe, A. et al. (2008). “Nephrin mutations can cause childhood-onset steroid-resistant nephrotic syndrome.” J Am Soc Nephrol 19(10):1871-1878. PubMed ID: 18614772
  • Santín, S. et al. (2009) "Nephrin mutations cause childhood- and adult-onset focal segmental glomerulosclerosis." Kidney Int 76(12):1268-1276. PubMed ID: 19812541
  • Santín, S. et al. (2011). "Clinical utility of genetic testing in children and adults with steroid-resistant nephrotic syndrome." Clin J Am Soc Nephrol 6(5):1139-1148.  PubMed ID: 21415313
  • Tryggvason, K. et al. (2006). "Hereditary proteinuria syndromes and mechanisms of proteinuria." N Engl J Med 354(13):1387-1401. PubMed ID: 16571882


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