HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
26 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
NPHS2
NPHS2 stomatin family member, podocin
Chromosome 1 Β· 1q25.2
NCBI Gene: 7827Ensembl: ENSG00000116218.14HGNC: HGNC:13394UniProt: Q9NP85
166PubMed Papers
21Diseases
0Drugs
157Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cytoplasmic side of plasma membraneextracellular exosomeprotein-containing complexactin cytoskeleton organizationnephrotic syndromenephrotic syndrome, type 2familial idiopathic steroid-resistant nephrotic syndromesteroid-resistant nephrotic syndrome
✦AI Summary

NPHS2 encodes podocin, an integral membrane protein of the glomerular slit diaphragm that plays a critical role in regulating glomerular permeability 1. Podocin functions as a linker between the plasma membrane and the cytoskeleton, contributing to the structural integrity of the glomerular filtration barrier 2. NPHS2 is expressed in differentiated podocytes alongside other slit diaphragm proteins including nephrin, CD2AP, and synaptopodin 2. Mutations in NPHS2 are a significant cause of steroid-resistant nephrotic syndrome (SRNS), accounting for a substantial proportion of genetic cases, particularly in early-onset disease 3. NPHS2 mutations manifest in both familial and sporadic forms of SRNS and focal segmental glomerulosclerosis (FSGS) 1. The common R229Q variant shows population-specific associations, with increased FSGS risk in European-derived populations but not African-derived populations 1. Homozygous R229Q carriers have significantly elevated SRNS risk compared to non-carriers 4. Other pathogenic mutations including missense variants (P20L, P316S) and frameshift mutations (42delG) have been identified in SRNS patients 5. Recent organoid studies demonstrate that NPHS2 mutations result in reduced protein expression and abnormal NPHS1 localization, contributing to podocyte dysfunction 6. Molecular diagnosis of NPHS2 mutations enables accurate etiologic classification and personalized treatment strategies for SRNS patients.

Sources cited
1
Podocin is expressed in differentiated podocytes and is part of the slit diaphragm complex along with nephrin and other associated proteins
PMID: 11856766
2
NPHS2 encodes podocin, an integral membrane protein at the slit diaphragm involved in glomerular permeability regulation; mutations cause familial and sporadic SRNS/FSGS
PMID: 16481888
3
NPHS2 mutations are identified in 29.5% of SRNS cases in early-onset disease, with frequency inversely correlating with age of onset
PMID: 25349199
4
Homozygous R229Q variant carriers show significantly higher SRNS risk compared to non-carriers
PMID: 24715228
5
NPHS2 mutations including P20L, P316S, R229Q, and 42delG frameshift mutations are detected in SRNS patients and affect clinical management
PMID: 27885584
6
NPHS2 mutations result in reduced podocin expression and aberrant NPHS1 localization in podocytes, reversible with genetic correction
PMID: 35417019
Disease Associationsβ“˜21
nephrotic syndromeOpen Targets
0.80Strong
nephrotic syndrome, type 2Open Targets
0.75Strong
familial idiopathic steroid-resistant nephrotic syndromeOpen Targets
0.62Moderate
steroid-resistant nephrotic syndromeOpen Targets
0.55Moderate
idiopathic nephrotic syndromeOpen Targets
0.52Moderate
focal segmental glomerulosclerosisOpen Targets
0.49Moderate
genetic disorderOpen Targets
0.49Moderate
Nephrotic range proteinuriaOpen Targets
0.42Moderate
congenital nephrotic syndrome, Finnish typeOpen Targets
0.38Weak
ProteinuriaOpen Targets
0.38Weak
chronic kidney diseaseOpen Targets
0.35Weak
goutOpen Targets
0.35Weak
post term pregnancyOpen Targets
0.31Weak
kidney diseaseOpen Targets
0.13Weak
IGA glomerulonephritisOpen Targets
0.10Suggestive
familial juvenile hyperuricemic nephropathy type 1Open Targets
0.07Suggestive
nephrotic syndrome, type 24Open Targets
0.07Suggestive
clear cell renal carcinomaOpen Targets
0.07Suggestive
Dent diseaseOpen Targets
0.07Suggestive
COVID-19Open Targets
0.07Suggestive
Nephrotic syndrome 2UniProt
Pathogenic Variants157
NM_014625.4(NPHS2):c.979C>T (p.Leu327Phe)Likely pathogenic
Nephrotic syndrome, type 2|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 327
NM_014625.4(NPHS2):c.502C>T (p.Arg168Cys)Pathogenic
Nephrotic syndrome, type 2|not provided|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 168
NM_014625.4(NPHS2):c.259G>T (p.Glu87Ter)Pathogenic
Nephrotic syndrome, type 2|Steroid-resistant nephrotic syndrome|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 87
NM_014625.4(NPHS2):c.779T>A (p.Val260Glu)Pathogenic
not provided|Nephrotic syndrome, type 2|Steroid-resistant nephrotic syndrome|NPHS2-related disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 260
NM_014625.4(NPHS2):c.685C>T (p.Arg229Ter)Pathogenic
Nephrotic syndrome, type 2|not provided|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 229
NM_014625.4(NPHS2):c.851C>T (p.Ala284Val)Pathogenic
not provided|Nephrotic syndrome, type 2|Idiopathic nephrotic syndrome|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 284
NM_014625.4(NPHS2):c.714G>T (p.Arg238Ser)Pathogenic
Nephrotic syndrome, type 2|not provided|Steroid-resistant nephrotic syndrome|Focal segmental glomerulosclerosis
β˜…β˜…β˜†β˜†2026β†’ Residue 238
NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln)Pathogenic
Nephrotic syndrome, type 2|not provided|Nephrotic range proteinuria|Chronic kidney disease|Steroid-resistant nephrotic syndrome|Nephrotic syndrome|NPHS2-related disorder|See cases
β˜…β˜…β˜†β˜†2026β†’ Residue 138
NM_014625.4(NPHS2):c.353C>T (p.Pro118Leu)Pathogenic
Proteinuria|Nephrotic syndrome, type 2|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 118
NM_014625.4(NPHS2):c.586C>T (p.Arg196Ter)Pathogenic
Nephrotic syndrome, type 2|not provided|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 196
NM_014625.4(NPHS2):c.738+1G>APathogenic
not provided|Nephrotic syndrome, type 2|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025
NM_014625.4(NPHS2):c.436del (p.Arg146fs)Pathogenic
not provided|Nephrotic syndrome, type 2
β˜…β˜…β˜†β˜†2025β†’ Residue 146
NM_014625.4(NPHS2):c.643C>T (p.Gln215Ter)Pathogenic
Nephrotic syndrome, type 2|not provided|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 215
NM_014625.4(NPHS2):c.964C>G (p.Arg322Gly)Likely pathogenic
Nephrotic syndrome, type 2|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 322
NM_014625.4(NPHS2):c.538G>A (p.Val180Met)Pathogenic
Nephrotic syndrome, type 2|not provided|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 180
NM_014625.4(NPHS2):c.871C>T (p.Arg291Trp)Pathogenic
Nephrotic syndrome, type 2|not provided|Inborn genetic diseases|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 291
NM_014625.4(NPHS2):c.738+1G>CPathogenic
not provided|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025
NM_014625.4(NPHS2):c.890C>T (p.Ala297Val)Pathogenic
Nephrotic syndrome, type 2|not provided|Nephrotic syndrome|Idiopathic nephrotic syndrome|Inborn genetic diseases|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 297
NM_014625.4(NPHS2):c.873+2T>APathogenic
Nephrotic syndrome, type 2|not provided|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025
NM_014625.4(NPHS2):c.928G>A (p.Glu310Lys)Pathogenic
not provided|Nephrotic syndrome, type 2|Idiopathic nephrotic syndrome|Steroid-resistant nephrotic syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 310
View on ClinVar β†—
Related Genes
FAT1Protein interaction100%SYNPOProtein interaction98%ACTN4Protein interaction97%PODXLProtein interaction97%TRPC6Protein interaction97%WT1Protein interaction97%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
0%
Liver
0%
Heart
0%
Brain
0%
Lung
0%
Gene Interaction Network
Click a node to explore
NPHS2FAT1SYNPOACTN4PODXLTRPC6WT1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9NP85
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
1.32LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.99 [0.75–1.32]
RankingsWhere NPHS2 stands among ~20K protein-coding genes
  • #2,693of 20,598
    Most Researched166 Β· top quartile
  • #482of 5,498
    Most Pathogenic Variants157 Β· top 10%
  • #13,853of 17,882
    Most Constrained (LOEUF)1.32
Genes detectedNPHS2
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
A conditionally immortalized human podocyte cell line demonstrating nephrin and podocin expression.
PMID: 11856766
J Am Soc Nephrol Β· 2002
1.00
2
A single-gene cause in 29.5% of cases of steroid-resistant nephrotic syndrome.
PMID: 25349199
J Am Soc Nephrol Β· 2015
0.90
3
NPHS2 gene, nephrotic syndrome and focal segmental glomerulosclerosis: a HuGE review.
PMID: 16481888
Genet Med Β· 2006
0.80
4
Congenital nephrotic syndrome.
PMID: 17968594
Pediatr Nephrol Β· 2009
0.72
5
The p.R229Q variant of the NPHS2 (podocin) gene in focal segmental glomerulosclerosis and steroid-resistant nephrotic syndrome: a meta-analysis.
PMID: 24715228
Int Urol Nephrol Β· 2014
0.70