GENE REFERENCE / HGNC:13394

NPHS2

NPHS2 stomatin family member, podocin

protein-coding gene1q25.2Gene information

What does this gene do?

The NPHS2 gene provides instructions for making a protein called podocin. Podocin is primarily found in the kidneys, which are organs that filter waste products from the blood and remove them in urine. Specifically, podocin is found in cells called podocytes, which are located in specialized kidney structures called glomeruli. Podocin is located at the cell surface in the area between two podocytes called the slit diaphragm. The slit diaphragm is known as a filtration barrier because it captures proteins in blood so that they remain in the body while allowing other molecules like sugars and salts to be excreted in urine. Podocin likely helps bring other proteins that are needed for a functional slit diaphragm to the podocyte cell surface. The protein also is involved with podocyte cell signaling, helping the cell adapt to changes that occur during the filtration process.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-04-18. Source review: 2016-07.

ClinGen reviews

We found no matching ClinGen review in the data used here. This does not rule out a link between the gene and a condition.

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 674
Submissions for variants in or overlapping this gene: 1,451
Submissions explicitly reporting this gene: 1,406
Alleles reported pathogenic / likely pathogenic: 174
VariationIDs with uncertain significance: 170
VariationIDs with conflicting classifications: 35

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about NPHS2?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 174 alleles in NPHS2 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in NPHS2.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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