Nephrotic Syndrome (NS)/Focal Segmental Glomerulosclerosis (FSGS) Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
10417 ACTN4 81406,81479 Order Options
ANKFY1 81479,81479
ANLN 81479,81479
APOL1 81479,81479
ARHGAP24 81479,81479
ARHGDIA 81479,81479
AVIL 81479,81479
CD2AP 81479,81479
CDK20 81479,81479
COL4A3 81408,81479
COL4A4 81407,81479
COL4A5 81408,81407
COL4A6 81479,81479
COQ2 81479,81479
COQ6 81479,81479
COQ8B 81479,81479
CRB2 81479,81479
CUBN 81479,81479
DGKE 81479,81479
DLC1 81479,81479
EMP2 81479,81479
FAT1 81479,81479
GAPVD1 81479,81479
GON7 81479,81479
INF2 81406,81479
ITGA3 81479,81479
ITGB4 81479,81479
ITSN1 81479,81479
ITSN2 81479,81479
KANK1 81479,81479
KANK2 81479,81479
KANK4 81479,81479
KAT2B 81479,81479
KIRREL1 81479,81479
LAGE3 81479,81479
LAMA5 81479,81479
LAMB2 81407,81479
LMX1B 81479,81479
MAFB 81479,81479
MAGI2 81479,81479
MYH9 81479,81479
MYO1E 81479,81479
NEU1 81479,81479
NFKB2 81479,81479
NPHS1 81407,81479
NPHS2 81405,81479
NUP107 81479,81479
NUP133 81479,81479
NUP160 81479,81479
NUP205 81479,81479
NUP93 81479,81479
OSGEP 81479,81479
PAX2 81406,81479
PDSS2 81479,81479
PLCE1 81407,81479
PTPRO 81479,81479
SCARB2 81479,81479
SGPL1 81479,81479
SMARCAL1 81479,81479
TBC1D8B 81479,81479
TNS2 81479,81479
TP53RK 81479,81479
TPRKB 81479,81479
TRIM8 81479,81479
TRPC6 81406,81479
TTC21B 81479,81479
WDR4 81479,81479
WDR73 81479,81479
WT1 81405,81479
XPO5 81479,81479
YRDC 81479,81479
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
10417 Genes x (71) 81479 81405, 81406, 81407, 81408, 81479 $990 Order Options

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our PGxome Custom Panel tool.

A 25% additional charge will be applied to STAT orders. View STAT turnaround times here.

For Reflex to PGxome pricing click here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

Turnaround Time

18 days on average

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Nephrotic syndrome (NS) is a genetically heterogeneous disease defined by proteinuria, hypoalbuminemia, hyperlipidemia, and edema (Benoit et al. 2010. PubMed ID: 20333530; Santín et al. 2011. PubMed ID: 21415313; Preston et al. 2019. PubMed ID: 29181713). It is the most common glomerular disease in children. Nephrotic syndrome in young adults and children is classified into steroid-sensitive NS (SSNS) versus steroid-resistant NS (SRNS) in terms of its response to a standardized steroid therapy. Approximately 20% of cases are 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. Hereditary FSGS can be either limited to the kidney or syndromic with features in other systems. Diffuse mesangial sclerosis (DMS) is the other important histological feature associated with SRNS. SRNS accounts for ~11% of early-onset chronic kidney disease (CKD) (Vivante and Hildebrandt. 2016. PubMed ID: 26750453). The clinical courses of NS vary greatly with a wide range of age at onset from birth to adulthood. A conclusive molecular diagnosis is necessary for better personalized treatment and accurate genetic counselling.

Genetics

The inheritance modes of NS/FSGS associated with the genes listed below can be autosomal dominant, autosomal recessive or X-linked (Sharif and Barua. 2018. PubMed ID: 29465426; Lovric et al. 2016. PubMed ID: 26507970; Preston et al. 2017. PubMed ID: 29181713). This panel also includes the genes for syndromic focal glomerulosclerosis, such as Galloway-Mowat syndrome (GAMOS) (see for example at Braun et al. 2017. PubMed ID: 28805828), and TRIM8-related early-onset epileptic encephalopathy (Assoum et al. 2018. PubMed ID: 30244534; Warren et al. 2020. PubMed ID: 32193649).

Defects in the COL4A3, COL4A4 and COL4A5 genes cause a wide spectrum of phenotypes from autosomal recessive or dominant Alport syndrome to autosomal dominant familial hematuria and thin basement membrane disease (TBMD) (see for example at Gast et al. 2016. PubMed ID: 26346198; Malone et al. 2014. PubMed ID: 25229338).

We also include the APOL1 gene in this panel, whose kidney risk alleles have a significant effect on disease susceptibility (Genovese et al. 2010. PubMed ID: 20647424; Friedman and Pollak. 2019. PubMed ID: 31710572).

The spectrum of pathogenic variants throughout these genes includes all types of genetic changes. Of note, large deletions are relatively commonly found in the COL4A3, COL4A4 and COL4A5 genes. De novo variants are common in the WT1 and TRIM8 genes.

Autosomal dominant: ACTN4, ANLN, ARHGAP24, COL4A3, COL4A4, INF2, LMX1B, MAFB, MYH9, NFKB2, PAX2, TRIM8, TRPC6, and WT1

Autosomal dominant or recessive: CD2AP

Autosomal recessive: ANKFY1, ARHGDIA, AVIL, CDK20, COQ2, COQ6, COQ8B/ADCK4, CRB2, CUBN, DGKE, DLC1, EMP2, FAT1, GAPVD1, GON7, ITGA3, ITGB4, ITSN1, ITSN2, KANK1, KANK2, KANK4, KAT2B, KIRREL1, LAMA5, LAMB2, MAGI2, MYO1E, NEU1, NPHS1, NPHS2, NUP107, NUP133, NUP160, NUP205, NUP93, OSGEP, PDSS2, PLCE1, PTPRO, SCARB2, SGPL1, SMARCAL1, TBC1D8B, TNS2, TP53RK, TPRKB, TTC21B, WDR4, WDR73, XPO5 and YRDC

X-linked dominant: COL4A5, COL4A6 and TBC1D8B

X-linked recessive: LAGE3

Risk gene: APOL1

Proteins encoded by the majority of NS-associated genes in the current panel are localized to the podocytes, which are essential in maintaining the glomerular filtration barrier. Regarding protein function and location in podocytes, the proteins encoded by associated genes can be divided into several subgroups as listed below (Preston et al. 2017. PubMed ID: 29181713).

Slit diaphragm-associated proteins: CD2AP, CRB2, FAT1, KIRREL1, NPHS1, NPHS2, PLCE1, and TRPC6

Nuclear proteins/transcription factors: LMX1B, MAFB, NFKB2, NUP107, NUP133, NUP160, NUP205, NUP93, PAX2, SMARCAL1, WDR4, WDR73, WT1, XPO5, and YRDC

Cytoskeletal, scaffold and membrane proteins: ACTN4, ANLN, ARHGAP24, ARHGDIA, AVILCDK20, CUBN, DLC1, EMP2, GON7, INF2, ITSN1, ITSN2 KANK1, KANK2, KANK4, KAT2B, LAGE3, MYO1E, MAGI2, OSGEP, PTPRO, TNS2, TP53RK, and TPRKB

Glomerular basement membrane-associated: COL4A3, COL4A4, COL4A5, COL4A6, ITGA3, ITGB4, LAMA5 and LAMB2

Mitochondrial proteins: COQ2, COQ6, COQ8B/ADCK4 and PDSS2

Lysosome-associated proteins: SCARB2

Metabolic and cytosolic proteins: DGKE, SGPL1 and TTC21B

Endosomal regulator RAB5 regulation: ANKFY1 and GAPVD1

Other: APOL1, MYH9, NEU1 and TRIM8

See individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

Testing Strategy

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

This panel typically provides 99.4% coverage of all coding exons of the genes 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 coverage as ≥20X NGS reads or Sanger sequencing.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Clinical Sensitivity - Sequencing with CNV PGxome

In the largest international cohort study to date, sequencing for 27 genes known to cause steroid-resistant nephrotic syndrome (SRNS) detected a single-gene cause across 21 genes in 29.5% (526 of 1783) of families with SRNS that manifested before 25 years of age (Sadowski et al. 2015. PubMed ID: 25349199).

In our laboratory, the positive rate (i.e. test yield) is ~23%. The major positive genes (~55%) are NPHS1, NPHS2, and WT1. The COL4A3, COL4A4 and COL4A5 genes together account for ~20% of positive cases. Other less frequently found causative genes (~20%) are PLCE1, TRPC6, INF2, and LMX1B. The remaining genes together only account for ~5.0%.

Indications for Test

Candidates for this test are patients with nephrotic syndrome (NS) or focal segmental glomerulosclerosis (FSGS). This test especially aids in a differential diagnosis of similar phenotypes by analyzing multiple genes simultaneously.

Diseases

Name Inheritance OMIM ID
Alport Syndrome, Autosomal Dominant AD 104200
Alport Syndrome, Autosomal Recessive AR 203780
Alport Syndrome, X-Linked Recessive XL 301050
Cerebral Palsy, Spastic Quadriplegic, 2 612900
Coenzyme Q10 Deficiency AR 607426
Coenzyme Q10 deficiency, primary, 3 AR 614652
Coenzyme Q10 deficiency, primary, 6 AR 614650
Deafness, X-linked 6 XL 300914
Duane retraction syndrome 3 AD 617041
Epidermolysis Bullosa With Pyloric Atresia AR 226730
Epilepsy, Progressive Myoclonic 4, With Or Without Renal Failure AR 254900
Familial Colorectal Cancer AR 114500
Finnish Congenital Nephrotic Syndrome AR 256300
Focal Segmental Glomerulosclerosis 1 AD 603278
Focal Segmental Glomerulosclerosis 2 AD 603965
Focal Segmental Glomerulosclerosis 3, Susceptibility To 607832
Focal Segmental Glomerulosclerosis 4, Susceptibility To AR 612551
Focal Segmental Glomerulosclerosis 5 AD 613237
Focal Segmental Glomerulosclerosis 6 AR 614131
Focal Segmental Glomerulosclerosis 8 AD 616032
Focal Segmental Glomerulosclerosis 9 AR 616220
Galloway-Mowat Syndrome AR 251300
Galloway-Mowat Syndrome 2, X-linked XL 301006
Galloway-Mowat Syndrome 3 AR 617729
Galloway-Mowat Syndrome 4 AR 617730
Galloway-Mowat Syndrome 5 AR 617731
Galloway-Mowat syndrome 6 AR 618347
Galloway-Mowat syndrome 7 AR 618348
Galloway-Mowat syndrome 8 AR 618349
Glomerulosclerosis, Focal Segmental, 7 AD 616002
Immunodeficiency, common variable, 10 AD 615577
Interstitial Lung Disease, Nephrotic Syndrome, and Epidermolysis Bullosa, Congenital AR 614748
May-Hegglin Anomaly AD 155100
Megaloblastic Anemia Due To Inborn Errors Of Metabolism AR 261100
Microcephaly, growth deficiency, seizures, and brain malformations AR 618346
Multicentric carpotarsal osteolysis syndrome AD 166300
Nail-Patella Syndrome AD 161200
Nephronophthisis 12 AD 613820
Nephrotic Syndrome, Idiopathic, Steroid-Resistant AR 600995
Nephrotic Syndrome, Type 10 AR 615861
Nephrotic Syndrome, Type 11 AR 616730
Nephrotic Syndrome, Type 12 AR 616892
Nephrotic Syndrome, Type 13 AR 616893
Nephrotic Syndrome, Type 14 AR 617575
Nephrotic Syndrome, Type 15 AR 617609
Nephrotic syndrome, type 18 AR 618177
Nephrotic syndrome, type 19 AR 618178
Nephrotic syndrome, type 20 XL 301028
Nephrotic syndrome, type 21 AR 618594
Nephrotic Syndrome, Type 3 AR 610725
Nephrotic syndrome, type 4 AD 256370
Nephrotic Syndrome, Type 5, With Or Without Ocular Abnormalities AR 614199
Nephrotic Syndrome, Type 6 AR 614196
Nephrotic Syndrome, Type 7 AR 615008
Nephrotic Syndrome, Type 8 AR 615244
Nephrotic syndrome, type 9 AR 615573
Palmoplantar Keratoderma and Woolly Hair AR 616099
Schimke Immunoosseous Dysplasia AR 242900
Sialidosis, Type II AR 256550

Related Test

Name
PGxome®

Citations

  • Assoum et al. 2018. PubMed ID: 30244534
  • Benoit et al. 2010. PubMed ID: 20333530
  • Braun et al. 2017. PubMed ID: 28805828
  • Friedman and Pollak. 2019. PubMed ID: 31710572
  • Gast et al. 2016. PubMed ID: 26346198
  • Genovese et al. 2010. PubMed ID: 20647424
  • Lovric et al. 2016. PubMed ID: 26507970
  • Malone et al. 2014. PubMed ID: 25229338
  • Preston et al. 2017. PubMed ID: 29181713
  • Sadowski et al. 2015. PubMed ID: 25349199
  • Santín et al. 2011. PubMed ID: 21415313
  • Sharif and Barua. 2018. PubMed ID: 29465426
  • Vivante and Hildebrandt. 2016. PubMed ID: 26750453
  • Warren et al. 2020. PubMed ID: 32193649

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.

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


Specimen Types

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