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

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; AllianceGenome:HGNC:9009
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: mouse all
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Genomic context

Location:: 4q22.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (88007635..88077777)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (91334123..91404269)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (88928787..88998929)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Polycystin-2, mechanosensing, and left-right asymmetry in autosomal dominant polycystic kidney disease.
Title: Polycystin-2, mechanosensing, and left-right asymmetry in autosomal dominant polycystic kidney disease.
Targeted Next Generation Sequencing Revealed Novel Variants in the PKD1 and PKD2 Genes of Iranian Patients with Autosomal Dominant Polycystic Kidney Disease.
Title: Targeted Next Generation Sequencing Revealed Novel Variants in the PKD1 and PKD2 Genes of Iranian Patients with Autosomal Dominant Polycystic Kidney Disease.
Identified eleven exon variants in PKD1 and PKD2 genes that altered RNA splicing by minigene assay.
Title: Identified eleven exon variants in PKD1 and PKD2 genes that altered RNA splicing by minigene assay.
The diverse effects of pathogenic point mutations on ion channel activity of a gain-of-function polycystin-2.
Title: The diverse effects of pathogenic point mutations on ion channel activity of a gain-of-function polycystin-2.
circPKD2 inhibits the glioma cell proliferation, invasion and glycolytic metabolism through regulating the miR-1278/LATS2 axis.
Title: circPKD2 inhibits the glioma cell proliferation, invasion and glycolytic metabolism through regulating the miR-1278/LATS2 axis.
Regulation of PKD2 channel by TACAN: how does it link to cystogenesis in autosomal dominant polycystic kidney disease?
Title: Regulation of PKD2 channel by TACAN: how does it link to cystogenesis in autosomal dominant polycystic kidney disease?
Detection of PKD1 and PKD2 Somatic Variants in Autosomal Dominant Polycystic Kidney Cyst Epithelial Cells by Whole-Genome Sequencing.
Title: Detection of PKD1 and PKD2 Somatic Variants in Autosomal Dominant Polycystic Kidney Cyst Epithelial Cells by Whole-Genome Sequencing.
Polycystin-2 (TRPP2): Ion channel properties and regulation.
Title: Polycystin-2 (TRPP2): Ion channel properties and regulation.
Identification of novel single-nucleotide variants altering RNA splicing of PKD1 and PKD2.
Title: Identification of novel single-nucleotide variants altering RNA splicing of PKD1 and PKD2.
c-Jun N-terminal kinase (JNK) signaling contributes to cystic burden in polycystic kidney disease.
Title: c-Jun N-terminal kinase (JNK) signaling contributes to cystic burden in polycystic kidney disease.

Submit: New GeneRIF Correction See all GeneRIFs (199)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Polycystic kidney disease 2 MedGen: C2751306 OMIM: 613095 GeneReviews: Polycystic Kidney Disease, Autosomal Dominant	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

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption. EBI GWAS Catalog EBI GWAS CatalogPubMed
GWAS of dental caries patterns in the permanent dentition. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-67606 (e-PCR)
- UniSTS:46393

PKD2_477 (e-PCR)
- UniSTS:280910

SHGC-24101 (e-PCR)
- UniSTS:9043

SHGC-8591 (e-PCR)
- UniSTS:27987

D4S2796 (e-PCR)
- UniSTS:24407

SHGC-67224 (e-PCR)
- UniSTS:77401

SHGC-67908 (e-PCR)
- UniSTS:11876

G59384 (e-PCR)
- UniSTS:136549

SHGC-148257 (e-PCR)
- UniSTS:176285

SHGC-50276 (e-PCR)
- UniSTS:56245

G63630 (e-PCR)
- UniSTS:140741

SHGC-111600 (e-PCR)
- UniSTS:168425

STS-R48232 (e-PCR)
- UniSTS:12782

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
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 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 monoatomic cation channel activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables muscle alpha-actinin binding	IBA Inferred from Biological aspect of Ancestor more info
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
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
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription regulator inhibitor activity	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
enables voltage-gated calcium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated monoatomic cation channel activity	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated monoatomic 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
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 calcium-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in cell surface receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in cell surface receptor signaling pathway via JAK-STAT	ISO Inferred from Sequence Orthology more info
involved_in cell surface receptor signaling pathway via JAK-STAT	ISS Inferred from Sequence or Structural Similarity more info
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 detection of mechanical stimulus	IBA Inferred from Biological aspect of Ancestor more info
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 establishment of localization in cell	IEA Inferred from Electronic Annotation 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 intracellular calcium ion homeostasis	IEA Inferred from Electronic Annotation more info
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
acts_upstream_of 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 cytosolic calcium ion concentration	IEA Inferred from Electronic Annotation more info
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
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 regulation of calcium ion import	IDA Inferred from Direct Assay 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
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	ISO Inferred from Sequence Orthology more info
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 side of endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay 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 more info	PubMed
located_in extracellular exosome	IDA Inferred from Direct Assay more info	PubMed
located_in lamellipodium	IDA Inferred from Direct Assay more info	PubMed
located_in lumenal side of endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in migrasome	IDA Inferred from Direct Assay 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
located_in plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
part_of polycystin complex	IPI Inferred from Physical Interaction more info	PubMed
part_of polycystin complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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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)

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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.

Genomic

NG_008604.1 RefSeqGene

Range

4968..75110

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000297.4 → NP_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

O60441, Q13563, Q15764, Q2M1Q3, Q2M1Q5

Related

ENSP00000237596.2, ENST00000237596.7

Conserved Domains (4) summary

cd15902
Location:754 → 782

EFh_HEF; EF-hand motif [structural motif]

cl23634
Location:724 → 792

EFh_HEF; EF-hand, calcium binding motif, found in the hexa-EF hand proteins family

pfam08016
Location:269 → 687

PKD_channel; Polycystin cation channel

pfam18109
Location:834 → 868

Fer4_24; Ferredoxin I 4Fe-4S cluster domain

RNA

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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

88007635..88077777

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011532028.3 → XP_011530330.1 polycystin-2 isoform X1

Conserved Domains (2) summary

pfam08016
Location:267 → 612

PKD_channel; Polycystin cation channel

cl08302
Location:657 → 703

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 ...
XM_011532029.2 → XP_011530331.1 polycystin-2 isoform X2

Conserved Domains (2) summary

pfam08016
Location:27 → 447

PKD_channel; Polycystin cation channel

cl08302
Location:492 → 538

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 ...
XM_011532030.3 → XP_011530332.1 polycystin-2 isoform X3

Conserved Domains (2) summary

pfam08016
Location:2 → 407

PKD_channel; Polycystin cation channel

cl08302
Location:452 → 498

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 ...