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    PKD2 polycystin 2, transient receptor potential cation channel [ Homo sapiens (human) ]

    Gene ID: 5311, updated on 25-Jun-2017
    Official Symbol
    PKD2provided by HGNC
    Official Full Name
    polycystin 2, transient receptor potential cation channelprovided by HGNC
    Primary source
    HGNC:HGNC:9009
    See related
    Ensembl:ENSG00000118762 MIM:173910; Vega:OTTHUMG00000160982
    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
    PC2; PKD4; Pc-2; APKD2; TRPP2
    Summary
    This gene encodes a member of the polycystin protein family. The encoded protein is a multi-pass membrane protein that functions as a calcium permeable cation channel, and is involved in calcium transport and calcium signaling in renal epithelial cells. This protein interacts with polycystin 1, and they may be partners in a common signaling cascade involved in tubular morphogenesis. Mutations in this gene are associated with autosomal dominant polycystic kidney disease type 2. [provided by RefSeq, Mar 2011]
    Orthologs
    Location:
    4q22.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 4 NC_000004.12 (88007647..88077779)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (88928799..88998931)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377325 Neighboring gene secreted phosphoprotein 1 Neighboring gene RNA, U1 small nuclear 36, pseudogene Neighboring gene ATP binding cassette subfamily G member 2 (Junior blood group) Neighboring gene ribosomal protein L31 pseudogene 24 Neighboring gene RNA, U6 small nuclear 818, pseudogene

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Polycystic kidney disease 2
    MedGen: C2751306 OMIM: 613095 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-07-06)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-06)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption.
    NHGRI GWA Catalog
    GWAS of dental caries patterns in the permanent dentition.
    NHGRI GWA Catalog
    Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.
    NHGRI GWA Catalog
    • Cargo trafficking to the periciliary membrane, organism-specific biosystem (from REACTOME)
      Cargo trafficking to the periciliary membrane, organism-specific biosystemProteomic studies suggest that the cilium is home to approximately a thousand proteins, and has a unique protein and lipid make up relative to the bulk cytoplasm and plasma membrane (Pazour et al, 20...
    • Cilium Assembly, organism-specific biosystem (from REACTOME)
      Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
    • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
      Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
    • VxPx cargo-targeting to cilium, organism-specific biosystem (from REACTOME)
      VxPx cargo-targeting to cilium, organism-specific biosystemA number of membrane proteins destined for the ciliary membrane are recognized by ARF4 in the trans-Golgi network, initiating the formation of a ciliary targeting complex that directs the passage of ...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC138466, MGC138468

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATPase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    HLH domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    actinin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    calcium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    calcium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    calcium-induced calcium release activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoskeletal protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    identical protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    ion channel binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    muscle alpha-actinin binding IEA
    Inferred from Electronic Annotation
    more info
     
    outward rectifier potassium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    phosphoprotein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    potassium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    potassium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    voltage-gated calcium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    voltage-gated cation channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    voltage-gated ion channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    voltage-gated potassium channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    voltage-gated sodium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    voltage-gated sodium channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    JAK-STAT cascade ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    aorta development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    branching involved in ureteric bud morphogenesis IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    calcium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    calcium ion transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    calcium ion transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell cycle arrest ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular response to cAMP IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to calcium ion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular response to fluid shear stress IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cellular response to hydrostatic pressure IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to osmotic stress IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to reactive oxygen species NAS
    Non-traceable Author Statement
    more info
    PubMed 
    centrosome duplication NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cytoplasmic sequestering of transcription factor IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    detection of mechanical stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    detection of mechanical stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    detection of nodal flow ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    determination of left/right symmetry ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    determination of liver left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    embryonic placenta development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    heart development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    heart looping IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    liver development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    mesonephric duct development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    mesonephric tubule development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    metanephric S-shaped body morphogenesis IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    metanephric ascending thin limb development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    metanephric cortex development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    metanephric cortical collecting duct development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    metanephric distal tubule development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    metanephric mesenchyme development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    metanephric part of ureteric bud development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    metanephric smooth muscle tissue development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    negative regulation of G1/S transition of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of cell proliferation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    negative regulation of ryanodine-sensitive calcium-release channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    neural tube development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    placenta blood vessel development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of cell cycle arrest IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of nitric oxide biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    potassium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    potassium ion transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    potassium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein homotetramerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of cAMP metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of calcium ion import IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of postsynaptic membrane potential IEA
    Inferred from Electronic Annotation
    more info
     
    release of sequestered calcium ion into cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    release of sequestered calcium ion into cytosol IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    renal artery morphogenesis IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    renal tubule morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    sodium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    sodium ion transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    spinal cord development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    Component Evidence Code Pubs
    basal cortex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    basal plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with cell-cell junction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    ciliary basal body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ciliary membrane IEA
    Inferred from Electronic Annotation
    more info
     
    cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
     
    endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endoplasmic reticulum IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with filamentous actin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of cytoplasmic side of endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of lumenal side of endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lamellipodium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitotic spindle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    motile cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    non-motile cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    polycystin complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Preferred Names
    polycystin-2
    Names
    autosomal dominant polycystic kidney disease type II protein
    polycystic kidney disease 2 (autosomal dominant)
    transient receptor potential cation channel subfamily P member 2

    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_008604.1 RefSeqGene

      Range
      4980..75112
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000297.3NP_000288.1  polycystin-2

      See identical proteins and their annotated locations for NP_000288.1

      Status: REVIEWED

      Source sequence(s)
      AF054992, AF113693, AW600307, BC112263
      Consensus CDS
      CCDS3627.1
      UniProtKB/Swiss-Prot
      Q13563
      UniProtKB/TrEMBL
      Q9UEU6
      Related
      ENSP00000237596.2, OTTHUMP00000161169, ENST00000237596.6, OTTHUMT00000253042
      Conserved Domains (2) summary
      pfam08016
      Location:267687
      PKD_channel; Polycystin cation channel
      cl08302
      Location:732778
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p7 Primary Assembly

      Range
      88007647..88077779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011532028.2XP_011530330.1  polycystin-2 isoform X1

      Conserved Domains (2) summary
      pfam08016
      Location:267612
      PKD_channel; Polycystin cation channel
      cl08302
      Location:657703
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    2. XM_011532029.1XP_011530331.1  polycystin-2 isoform X2

      Conserved Domains (2) summary
      pfam08016
      Location:27447
      PKD_channel; Polycystin cation channel
      cl08302
      Location:492538
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    3. XM_011532030.2XP_011530332.1  polycystin-2 isoform X3

      Conserved Domains (2) summary
      pfam08016
      Location:2407
      PKD_channel; Polycystin cation channel
      cl08302
      Location:452498
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    RNA

    1. XR_001741236.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018915.2 Alternate CHM1_1.1

      Range
      88905594..88975728
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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