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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
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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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