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NPHS2 NPHS2 stomatin family member, podocin [ Homo sapiens (human) ]

Gene ID: 7827, updated on 12-Sep-2021

Summary

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Official Symbol
NPHS2provided by HGNC
Official Full Name
NPHS2 stomatin family member, podocinprovided by HGNC
Primary source
HGNC:HGNC:13394
See related
Ensembl:ENSG00000116218 MIM:604766
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PDCN; SRN1
Summary
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]
Expression
Restricted expression toward kidney (RPKM 45.3) See more
Orthologs
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Genomic context

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See NPHS2 in Genome Data Viewer
Location:
1q25.2
Exon count:
8
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (179550539..179575987, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (179519674..179545083, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene axonemal dynein light chain domain containing 1 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 54 Neighboring gene myocyte enhancer factor 2A pseudogene 1 Neighboring gene RNA, U5F small nuclear 2, pseudogene Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A Study of the Risk Factors and Urinary Podocin as an Early Prognostic Indicator of Renal Injury in Diabetic Nephropathy. Kondapi K, et al. J Assoc Physicians India, 2021 Jun. PMID 34472785
  2. Analysis of the clinical characteristics of arthritis with renal disease caused by a NPHS2 gene mutation. Shi D, et al. Clin Rheumatol, 2021 Aug. PMID 33428103
  3. Prevalence of the NPHS2 variants p.R229Q, p.A242V, and p.R138Q in patients with focal segmental glomerulosclerosis. de Almeida R, et al. Clin Nephrol, 2020 Oct. PMID 32691731
  4. Generation of an induced pluripotent stem cell (iPSC) line (IMAGINi007) from a patient with steroid-resistant nephrotic syndrome carrying the homozygous p.R138Q mutation in the podocin-encoding NPHS2 gene. Menara G, et al. Stem Cell Res, 2020 Jul. PMID 32585588
  5. Detection of Podocin in Human Urine Sediment Samples by Charge Derivatization and LC-MS-MRM Method. Bąchor R, et al. Int J Mol Sci, 2020 May 2. PMID 32370166, Free PMC Article

See all (157) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A Study of the Risk Factors and Urinary Podocin as an Early Prognostic Indicator of Renal Injury in Diabetic Nephropathy.
    Title: A Study of the Risk Factors and Urinary Podocin as an Early Prognostic Indicator of Renal Injury in Diabetic Nephropathy.
  2. Generation of an induced pluripotent stem cell (iPSC) line (IMAGINi007) from a patient with steroid-resistant nephrotic syndrome carrying the homozygous p.R138Q mutation in the podocin-encoding NPHS2 gene.
    Title: Generation of an induced pluripotent stem cell (iPSC) line (IMAGINi007) from a patient with steroid-resistant nephrotic syndrome carrying the homozygous p.R138Q mutation in the podocin-encoding NPHS2 gene.
  3. Analysis of the clinical characteristics of arthritis with renal disease caused by a NPHS2 gene mutation.
    Title: Analysis of the clinical characteristics of arthritis with renal disease caused by a NPHS2 gene mutation.
  4. Detection of Podocin in Human Urine Sediment Samples by Charge Derivatization and LC-MS-MRM Method.
    Title: Detection of Podocin in Human Urine Sediment Samples by Charge Derivatization and LC-MS-MRM Method.
  5. NPHS2 gene mutations in azerbaijani children with steroid-resistant nephrotic syndrome.
    Title: NPHS2 gene mutations in azerbaijani children with steroid-resistant nephrotic syndrome.
  6. Prevalence of the NPHS2 variants p.R229Q, p.A242V, and p.R138Q in patients with focal segmental glomerulosclerosis.
    Title: Prevalence of the <i>NPHS2</i> variants p.R229Q, p.A242V, and p.R138Q in patients with focal segmental glomerulosclerosis.
  7. Urinary podocyte mRNA is a potent biomarker of anti-neutrophil cytoplasmic antibody-associated glomerulonephritis.
    Title: Urinary podocyte mRNA is a potent biomarker of anti-neutrophil cytoplasmic antibody-associated glomerulonephritis.
  8. ULK-1 with EGFR can predict early impairment in DN while PDCN can highlight progressive diabetic nephropathy (DN) risk EGFR and PDCN may interact synergistically with ULK-1 in autophagy dysregulation as a pathogenic mechanism of DN induction and progression.
    Title: Epidermal growth factor receptor and podocin predict nephropathy progression in type 2 diabetic patients through interaction with the autophagy influencer ULK-1.
  9. Haplotype analysis suggests a single mutation origin for V260E and it was associated with a decline in kidney function over a 60-month period (p = 0.026). The V260E variant is a good predictor of autosomal recessive SRNS in black South African children and could provide useful information in a clinical setting.
    Title: The podocin V260E mutation predicts steroid resistant nephrotic syndrome in black South African children with focal segmental glomerulosclerosis.
  10. Study identified three different polymorphisms in the NPHS2 gene in 7 patients with focal segmental glomerulosclerosis but none was detected in the Iranian cohort with steroid-resistant nephrotic syndrome.
    Title: TRPC6 and NPHS2 gene variants in adult patients with steroid-resistant nephrotic syndrome in North-West of Iran.
Submit: New GeneRIF Correction See all GeneRIFs (127)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in actin cytoskeleton reorganization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in excretion TAS
Traceable Author Statement
more info
 PubMed 
involved_in metanephric glomerular visceral epithelial cell development IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
located_in cell-cell junction IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular exosome HDA PubMed 
located_in integral component of plasma membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in intrinsic component of the cytoplasmic side of the plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane raft IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with slit diaphragm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
podocin
Names
NPHS2, podocin
nephrosis 2, idiopathic, steroid-resistant (podocin)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007535.1 RefSeqGene

    Range
    4998..30411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_887

mRNA and Protein(s)

  1. NM_001297575.2 → NP_001284504.1  podocin isoform 2

    See identical proteins and their annotated locations for NP_001284504.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AL160286, BC029141, BI831348, BX095913
    Consensus CDS
    CCDS72988.1
    UniProtKB/Swiss-Prot
    Q9NP85
    Related
    ENSP00000356588.4, ENST00000367616.4
    Conserved Domains (1) summary
    cl19107
    Location:122 → 276
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

  2. NM_014625.4 → NP_055440.1  podocin isoform 1

    See identical proteins and their annotated locations for NP_055440.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AJ279254, AL160286, BC029141, BX095913
    Consensus CDS
    CCDS1331.1
    UniProtKB/Swiss-Prot
    Q9NP85
    Related
    ENSP00000356587.4, ENST00000367615.9
    Conserved Domains (2) summary
    smart00244
    Location:123 → 287
    PHB; prohibitin homologues
    cd08827
    Location:122 → 344
    SPFH_podocin; Podocin, a subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    179550539..179575987 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002298.1 → XP_016857787.1  podocin isoform X2

  2. XM_005245483.3 → XP_005245540.1  podocin isoform X1

    Conserved Domains (2) summary
    smart00244
    Location:90 → 228
    PHB; prohibitin homologues
    cl19107
    Location:92 → 285
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

  3. XM_017002299.1 → XP_016857788.1  podocin isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NP85.1 GenPept UniProtKB/Swiss-Prot:Q9NP85

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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