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Nphs2 nephrosis 2, podocin [ Mus musculus (house mouse) ]

Gene ID: 170484, updated on 2-Nov-2024

Summary

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Official Symbol
Nphs2provided by MGI
Official Full Name
nephrosis 2, podocinprovided by MGI
Primary source
MGI:MGI:2157018
See related
Ensembl:ENSMUSG00000026602 AllianceGenome:MGI:2157018
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
PDCN; SRN1
Summary
Acts upstream of or within gene expression. Located in cytoplasmic side of plasma membrane. Is active in cell periphery. Colocalizes with slit diaphragm. Is expressed in liver; metanephros; and ureter. Used to study nephrotic syndrome. Human ortholog(s) of this gene implicated in nephrotic syndrome type 2. Orthologous to human NPHS2 (NPHS2 stomatin family member, podocin). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Restricted expression toward kidney adult (RPKM 17.5) See more
Orthologs
human all
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Genomic context

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See Nphs2 in Genome Data Viewer
Location:
1 G3; 1 67.71 cM
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (156138105..156155605)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (156310535..156328035)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 30472 Neighboring gene STARR-seq mESC enhancer starr_02734 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:158194711-158194894 Neighboring gene STARR-seq mESC enhancer starr_02735 Neighboring gene tudor domain containing 5 Neighboring gene axonemal dynein light chain domain containing 1 Neighboring gene ribosomal protein L35, retrotransposed Neighboring gene STARR-seq mESC enhancer starr_02736 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:158338195-158338508 Neighboring gene STARR-positive B cell enhancer ABC_E3317 Neighboring gene STARR-positive B cell enhancer ABC_E9485 Neighboring gene sterol O-acyltransferase 1 Neighboring gene STARR-positive B cell enhancer ABC_E2571 Neighboring gene STARR-positive B cell enhancer mm9_chr1:158404407-158404707

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. A missense mutation in podocin leads to early and severe renal disease in mice. Philippe A, et al. Kidney Int, 2008 May. PMID 18288100
  2. Podocin inactivation in mature kidneys causes focal segmental glomerulosclerosis and nephrotic syndrome. Mollet G, et al. J Am Soc Nephrol, 2009 Oct. PMID 19713307, Free PMC Article
  3. Calpain activation and secretion promote glomerular injury in experimental glomerulonephritis: evidence from calpastatin-transgenic mice. Peltier J, et al. J Am Soc Nephrol, 2006 Dec. PMID 17082241
  4. An inducible mouse model of podocin-mutation-related nephrotic syndrome. Tabatabaeifar M, et al. PLoS One, 2017. PMID 29049388, Free PMC Article
  5. Mapping of the podocin proximity-dependent proteome reveals novel components of the kidney podocyte foot process. Gerlach GF, et al. Front Cell Dev Biol, 2023. PMID 37325559, Free PMC Article

See all (95) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. c-Cbl induced podocin ubiquitination contributes to the podocytes injury in diabetic nephropathy.
    Title: c-Cbl induced podocin ubiquitination contributes to the podocytes injury in diabetic nephropathy.
  2. Deletion of protein tyrosine phosphatase SHP-1 restores SUMOylation of podocin and reverses the progression of diabetic kidney disease.
    Title: Deletion of protein tyrosine phosphatase SHP-1 restores SUMOylation of podocin and reverses the progression of diabetic kidney disease.
  3. Proteolytic cleavage of Podocin by Matriptase exacerbates podocyte injury.
    Title: Proteolytic cleavage of Podocin by Matriptase exacerbates podocyte injury.
  4. While R140Q podocin mRNA expression was elevated, protein abundance was reduced by more than 50% within one week following induction
    Title: An inducible mouse model of podocin-mutation-related nephrotic syndrome.
  5. Ubiquitin ligase Ubr4 is a key component of the podocin interactome purified from cultured podocytes and native glomeruli. Ubiquitylomic analysis of mouse glomeruli revealed that podocin is ubiquitylated at two lysine residues. Ubiquitylation of one podocin site, K301, do not only target podocin for proteasomal degradation, but may also affect stability and disassembly of the multimeric complex.
    Title: The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes.
  6. ATP evokes activation of TRPC6 channels in podocytes through P2Y receptors, podocin, and generation of reactive oxygen species.
    Title: ATP acting through P2Y receptors causes activation of podocyte TRPC6 channels: role of podocin and reactive oxygen species.
  7. the carboxyl terminus of podocin/MEC-2 has to be placed at the inner leaflet of the plasma membrane to mediate cholesterol binding and contribute to ion channel activity.
    Title: A disease-causing mutation illuminates the protein membrane topology of the kidney-expressed prohibitin homology (PHB) domain protein podocin.
  8. Podocin is necessary for assembly of the NOX2-TRPC6 complex in lipid rafts.
    Title: NOX2 interacts with podocyte TRPC6 channels and contributes to their activation by diacylglycerol: essential role of podocin in formation of this complex.
  9. study shows a variety of mechanical stimuli cause activation of endogenously expressed TRPC6 channels of podocytes; also that podocin reduces sensitivity of TRPC6 channels to mechanical stimuli, so that a loss of podocin function would result in hyperactivation of TRPC6 channels in foot processes
    Title: Opposing effects of podocin on the gating of podocyte TRPC6 channels evoked by membrane stretch or diacylglycerol.
  10. These data descrived the importance of concomitant decreases in podocin, CD2AP and tensin2 during septic acute renal failure-associated proteinuria.
    Title: Decreases in podocin, CD2-associated protein (CD2AP) and tensin2 may be involved in albuminuria during septic acute renal failure.
Submit: New GeneRIF Correction See all GeneRIFs (20)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (5) 
  • Targeted (6)  1 citation

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 MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in actin cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
  
involved_in actin cytoskeleton organization ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in metanephric podocyte development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cell periphery IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cell-cell junction ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasmic side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic side of plasma membrane ISO
Inferred from Sequence Orthology
more info
  
located_in membrane raft IEA
Inferred from Electronic Annotation
more info
  
located_in membrane raft ISO
Inferred from Sequence Orthology
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
part_of protein-containing complex IEA
Inferred from Electronic Annotation
more info
  
part_of protein-containing complex ISO
Inferred from Sequence Orthology
more info
  
colocalizes_with slit diaphragm IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with slit diaphragm ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
podocin
Names
nephrosis 2 homolog, 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.

mRNA and Protein(s)

  1. NM_130456.4 → NP_569723.1  podocin

    See identical proteins and their annotated locations for NP_569723.1

    Status: VALIDATED

    Source sequence(s)
    AC161414, FJ715770
    Consensus CDS
    CCDS15391.1
    UniProtKB/Swiss-Prot
    Q8BWE6, Q91X05, Q91Z95
    UniProtKB/TrEMBL
    C0LL94, C0LL95
    Related
    ENSMUSP00000027896.5, ENSMUST00000027896.10
    Conserved Domains (1) summary
    cd08827
    Location:124 → 346
    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: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    156138105..156155605
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011238765.2 → XP_011237067.1  podocin isoform X3

    Conserved Domains (1) summary
    cl19107
    Location:124 → 179
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

  2. XM_006496683.4 → XP_006496746.1  podocin isoform X1

    Conserved Domains (1) summary
    cl19107
    Location:124 → 267
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily

  3. XM_006496684.3 → XP_006496747.1  podocin isoform X2

    Conserved Domains (1) summary
    cl19107
    Location:2 → 203
    SPFH_like; core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q91X05.2 GenPept UniProtKB/Swiss-Prot:Q91X05

Gene LinkOut

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