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

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.

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, DAAM2, 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, AVIL, CDK20, CUBN, DAAM2, 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.

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%.

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

This panel typically provides 99.8% 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. 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).