Tchem PKD2 Polycystin-2

Protein Classes

PANTHER Classes

Protein / Transporter / Ion Channel / Polycystin-2

Protein / Signaling Molecule / Membrane-bound Signaling Molecule / Polycystin-2

Protein / Enzyme Modulator / G-protein Modulator / Polycystin-2

Protein / ... / Protease / Polycystin-2

DTO Classes

Protein / Ion Channel / Polycystin Cation Channel (Pcc) Family / Polycystin-2

Protein Summary

Description

Component of a heteromeric calcium-permeable ion channel formed by PKD1 and PKD2 that is activated by interaction between PKD1 and a Wnt family member, such as WNT3A and WNT9B (PubMed:27214281). Can also form a functional, homotetrameric ion channel (PubMed:29899465). Functions as a cation channel involved in fluid-flow mechanosensation by the primary cilium in renal epithelium (PubMed:18695040). Functions as outward-rectifying K(+) channel, but is also permeable to Ca(2+), and to a much lesser degree also to Na(+) (PubMed:11854751, PubMed:15692563, PubMed:27071085, PubMed:27991905). May contribute to the release of Ca(2+) stores from the endoplasmic reticulum (PubMed:11854751, PubMed:20881056). Together with TRPV4, forms mechano- and thermosensitive channels in cilium (PubMed:18695040). PKD1 and PKD2 may function through a common signaling pathway that is necessary to maintain the normal, differentiated state of renal tubule cells. Acts as a regulator of cilium length, together with PKD1. The dynamic control of cilium length is essential in the regulation of mechanotransductive signaling. The cilium length response creates a negative feedback loop whereby fluid shear-mediated deflection of the primary cilium, which decreases intracellular cAMP, leads to cilium shortening and thus decreases flow-induced signaling. Also involved in left-right axis specification via its role in sensing nodal flow; forms a complex with PKD1L1 in cilia to facilitate flow detection in left-right patterning. Detection of asymmetric nodal flow gives rise to a Ca(2+) signal that is required for normal, asymmetric expression of genes involved in the specification of body left-right laterality (By similarity). 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]

Uniprot Accession IDs

• Q13563
• O60441
• Q15764
• Q2M1Q3
• Q2M1Q5
• PC2

Gene Name

• PKD2

Ensembl ID

• ENST00000237596
• ENSP00000237596
• ENSG00000118762

Symbol

• TRPP2
• PC2
• PKD4
• Pc-2
• APKD2
• TRPP2

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
biological process	1
molecular function	1
microRNA	0.82
cell type or tissue	0.81
kinase	0.78

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 367.8   (req: < 5)

Gene RIFs: 156   (req: <= 3)

Antibodies: 302   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 367.8   (req: >= 5)

Gene RIFs: 156   (req: > 3)

Antibodies: 302   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 75

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 1

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Active Ligands (1)

Explore Active Ligands

1 – 1 of 1

Ca²⁺

PKD2Tchem IC

- : 6

GWAS Traits (4)

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1 – 4 of 4

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
gout	EFO_0004274	4	3	0	1.7	98.7
renal system measurement	EFO_0004742	1	1	1		87.5
uric acid measurement	EFO_0004761	1	1	1		87.5
hyperuricemia	EFO_0009104	1	1	0	1.5	34.2

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
gout	EFO_0004274	0	1.7	98.7
renal system measurement	EFO_0004742	1		87.5
uric acid measurement	EFO_0004761	1		87.5
hyperuricemia	EFO_0009104	0	1.5	34.2

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Orthologs (14)

1 – 5 of 14

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	polycystin 2, transient receptor potential cation channel	VGNC:7424	461367
Macaque	polycystin 2, transient receptor potential cation channel		702179
Mouse	polycystic kidney disease 2	MGI:1099818	18764
Rat	polycystin 2, transient receptor potential cation channel	RGD:1559992	498328
Dog	polycystin 2, transient receptor potential cation channel	VGNC:44600	487852

Species	Name	OMA	EggNOG	Inparanoid
Chimp	polycystin 2, transient receptor potential cation channel
Macaque	polycystin 2, transient receptor potential cation channel
Mouse	polycystic kidney disease 2
Rat	polycystin 2, transient receptor potential cation channel
Dog	polycystin 2, transient receptor potential cation channel

Protein Structure (12 Structures, 1 AlphaFold Model)

Representation

  axes   backbone   ball+stick   cartoon   rocket   rope   spacefill

Color Scheme

  target   atomindex   bfactor   chainname   electrostatic   element   hydrophobicity   resname   sstruc

Click on a row in the table to change the structure displayed.
More information can be found at RCSB PDB

AF-Q13563-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 5 of 12

PDB Structure Id	Ligand	Method	Resolution (Å)	Residues	Fraction of Total Protein	Pub Year	Title

PDB Structure Id	Fraction of Total Protein	Resolution	Pub Year

Pathways (4)

Reactome (4)

Cargo trafficking to the periciliary membrane (R-HSA-5620920)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Cargo trafficking to the periciliary membrane	51 targets	R-HSA-5620920
Reactome	Cilium Assembly	187 targets	R-HSA-5617833
Reactome	Organelle biogenesis and maintenance	276 targets	R-HSA-1852241
Reactome	VxPx cargo-targeting to cilium	21 targets	R-HSA-5620916

Name	Explore in Pharos	Explore in Source
Cargo trafficking to the periciliary membrane	51 targets	R-HSA-5620920
Cilium Assembly	187 targets	R-HSA-5617833
Organelle biogenesis and maintenance	276 targets	R-HSA-1852241
VxPx cargo-targeting to cilium	21 targets	R-HSA-5620916

Gene Ontology Terms (97)

Functions (21)

Components (22)

Processes (54)

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Items per page:

10

1 – 10 of 21

GO Term	Evidence	Assigned by
actinin binding	Inferred from Direct Assay (IDA)	BHF-UCL
calcium ion binding	Inferred from Direct Assay (IDA)	UniProtKB
calcium-induced calcium release activity	Inferred from Direct Assay (IDA)	BHF-UCL
cytoskeletal protein binding	Inferred from Direct Assay (IDA)	BHF-UCL
potassium channel activity	Inferred from Direct Assay (IDA)	UniProtKB
protein homodimerization activity	Inferred from Direct Assay (IDA)	BHF-UCL
voltage-gated calcium channel activity	Inferred from Direct Assay (IDA)	BHF-UCL
voltage-gated cation channel activity	Inferred from Direct Assay (IDA)	BHF-UCL
voltage-gated ion channel activity	Inferred from Direct Assay (IDA)	BHF-UCL
voltage-gated sodium channel activity	Inferred from Direct Assay (IDA)	BHF-UCL

Protein-Protein Interactions (141)

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1 – 10 of 141

• See Interactions on String-DB

PKD2L2

Tbio

Family: IC

Novelty: 0.12399184

p_int: 0.999988736

p_ni: 0.000011264

Score: 0.221

Data Source: BioPlex,STRINGDB

COG7

Tbio

Novelty: 0.07137701

p_int: 0.999985303

p_ni: 0.000014697

Data Source: BioPlex

FAM3D

Tbio

Novelty: 0.11834339

p_int: 0.999924722

p_ni: 0.000075278

Score: 0.455

Data Source: BioPlex,STRINGDB

PICK1

Tbio

Novelty: 0.0058265

p_int: 0.999915865

p_ni: 0.000084135

Data Source: BioPlex

ATP6V1D

Tbio

Family: Enzyme

Novelty: 0.02298626

p_int: 0.99955135

p_ni: 0.000448644

p_wrong: 6e-9

Data Source: BioPlex

CYP2J2

Tchem

Novelty: 0.00534181

p_int: 0.999189282

p_ni: 0.000810718

Data Source: BioPlex

BCAS4

Tbio

Novelty: 0.11759439

p_int: 0.999170247

p_ni: 0.000829753

Score: 0.187

Data Source: BioPlex,STRINGDB

PTGIR

Tclin

Family: GPCR

Novelty: 0.0091906

p_int: 0.999120623

p_ni: 0.000879377

Data Source: BioPlex

CRYL1

Tbio

Family: Enzyme

Novelty: 0.04513297

p_int: 0.998234404

p_ni: 0.001765596

Data Source: BioPlex

CHRND

Tclin

Family: IC

Novelty: 0.0441685

p_int: 0.998047563

p_ni: 0.001952437

Score: 0.229

Data Source: BioPlex,STRINGDB

Publication Statistics

PubMed Score  367.80

PubMed score by year

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PubTator Score  587.15

PubTator score by year

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Patents

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Amino Acid Sequence

Residue Counts

Protein Sequence

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Find similar targets by:

UniProt Keyword Find Similar Targets

3D-structure
Alternative splicing
Calcium
Calcium channel
Calcium transport
Cell membrane
Cell projection
Ciliopathy
Cilium
Coiled coil

GWAS Trait Find Similar Targets

gout
hyperuricemia
renal system measurement
uric acid measurement

MGI Phenotype Find Similar Targets

cardiovascular system phenotype
cellular phenotype
digestive/alimentary phenotype
embryo phenotype
endocrine/exocrine gland phenotype
growth/size/body region phenotype
hematopoietic system phenotype
homeostasis/metabolism phenotype
immune system phenotype
liver/biliary system phenotype