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

    Gene ID: 5311, updated on 4-Jul-2021

    Summary

    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
    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]
    Annotation information
    Note: PKD2 (GeneID: 5311) and PRKD2 (GeneID: 25865) share the PKD2 symbol/alias in common. PKD2 is a widely used alternative name for protein kinase D2 (PRKD2), which can be confused with the official symbol for PKD2/polycystin-2/polycystic kidney disease 2. [19 Jun 2018]
    Expression
    Ubiquitous expression in endometrium (RPKM 27.5), kidney (RPKM 19.2) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See PKD2 in Genome Data Viewer
    Location:
    4q22.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (88007635..88077779)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (88928787..88998929)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene SPP1 5' regulatory region 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

    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?

    Phenotypes

    Associated conditions

    Description Tests
    Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption.
    GeneReviews: Not available
    GWAS of dental caries patterns in the permanent dentition.
    GeneReviews: Not available
    Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.
    GeneReviews: Not available
    Polycystic kidney disease 2 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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC138466, MGC138468

    Gene Ontology Provided by GOA

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

    General protein information

    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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      4968..75110
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000297.4NP_000288.1  polycystin-2

      See identical proteins and their annotated locations for NP_000288.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC084732, AF054992, AF113693, AW600307, BC112263
      Consensus CDS
      CCDS3627.1
      UniProtKB/Swiss-Prot
      Q13563
      UniProtKB/TrEMBL
      Q9UEU6
      Related
      ENSP00000237596.2, ENST00000237596.7
      Conserved Domains (3) summary
      pfam08016
      Location:267687
      PKD_channel; Polycystin cation channel
      cd15902
      Location:754782
      EFh_HEF; EF-hand motif [structural motif]
      cl23634
      Location:724792
      EFh_HEF; EF-hand, calcium binding motif, found in the hexa-EF hand proteins family

    RNA

    1. NR_156488.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC084732

    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_000004.12 Reference GRCh38.p13 Primary Assembly

      Range
      88007635..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 ...
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