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

Gene ID: 7827, updated on 18-Aug-2020

Summary

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

Genomic context

See NPHS2 in Genome Data Viewer
Location:
1q25.2
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (179550539..179575987, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (179519674..179545086, 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

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

NCBI Reference Sequences (RefSeq)

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_001297575.2NP_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:122276
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
  2. NM_014625.4NP_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:123287
    PHB; prohibitin homologues
    cd08827
    Location:122344
    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 109.20200815

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_017002298.1XP_016857787.1  podocin isoform X2

  2. XM_005245483.3XP_005245540.1  podocin isoform X1

    Conserved Domains (2) summary
    smart00244
    Location:90228
    PHB; prohibitin homologues
    cl19107
    Location:92285
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
  3. XM_017002299.1XP_016857788.1  podocin isoform X3

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