NPHS2

Chr 1

NPHS2 stomatin family member, podocin

Also known as: PDCN, SRN1

NCBI Gene: 7827ENSG00000116218UniProt: Q9NP85

This gene encodes a protein that plays a role in the regulation of glomerular permeability. Mutations in this gene cause steroid-resistant nephrotic syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtNephrotic syndrome 2

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
43
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
1.18
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — NPHS2
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
1.18LOEUF
pLI 0.000
Z-score 0.97
OE 0.76 (0.51–1.18)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?
0.69Z-score
OE missense 0.86 (0.76–0.98)
174 obs / 201.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.76 (0.51–1.18)
0≤0.351.4
Missense OE?0.86 (0.76–0.98)
0≤0.61.4
Synonymous OE?1.01
0≤1.21.6
LoF obs/exp: 15 / 19.7Missense obs/exp: 174 / 201.4Syn Z: -0.08

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

NPHS2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients