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PKD1 polycystin 1, transient receptor potential channel interacting [ Homo sapiens (human) ]

Gene ID: 5310, updated on 4-Nov-2018

Summary

Official Symbol
PKD1provided by HGNC
Official Full Name
polycystin 1, transient receptor potential channel interactingprovided by HGNC
Primary source
HGNC:HGNC:9008
See related
Ensembl:ENSG00000008710 MIM:601313; Vega:OTTHUMG00000155795
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
PBP; PC1; Pc-1; TRPP1
Summary
This gene encodes a member of the polycystin protein family. The encoded glycoprotein contains a large N-terminal extracellular region, multiple transmembrane domains and a cytoplasmic C-tail. It is an integral membrane protein that functions as a regulator of calcium permeable cation channels and intracellular calcium homoeostasis. It is also involved in cell-cell/matrix interactions and may modulate G-protein-coupled signal-transduction pathways. It plays a role in renal tubular development, and mutations in this gene cause autosomal dominant polycystic kidney disease type 1 (ADPKD1). ADPKD1 is characterized by the growth of fluid-filled cysts that replace normal renal tissue and result in end-stage renal failure. Splice variants encoding different isoforms have been noted for this gene. Also, six pseudogenes, closely linked in a known duplicated region on chromosome 16p, have been described. [provided by RefSeq, Oct 2008]
Expression
Ubiquitous expression in endometrium (RPKM 11.1), fat (RPKM 9.6) and 25 other tissues See more
Orthologs

Genomic context

See PKD1 in Genome Data Viewer
Location:
16p13.3
Exon count:
50
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (2088708..2135898, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2138709..2185899, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene SLC9A3 regulator 2 Neighboring gene nth like DNA glycosylase 1 Neighboring gene TSC complex subunit 2 Neighboring gene uncharacterized LOC105371049 Neighboring gene microRNA 1225 Neighboring gene microRNA 6511b-1 Neighboring gene microRNA 3180-5 Neighboring gene microRNA 4516 Neighboring gene RAB26, member RAS oncogene family

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-02-22)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-02-22)

ClinGen Genome Curation Page

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of polycystic kidney disease 1, autosomal dominant (PKD1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • 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...
  • Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway, organism-specific biosystem (from WikiPathways)
    Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway, organism-specific biosystemThis pathway Involved in chemo-resistance of cells in bladder cancer begins with LOXL2 activation of CDC37 and COL2A1. COL2A1 activates the complex NRF1/2 and two other complexes that trigger RTK/MAP...
  • 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 ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium channel activity ISS
Inferred from Sequence or Structural Similarity
more info
 
carbohydrate binding IEA
Inferred from Electronic Annotation
more info
 
ion channel binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
JAK-STAT cascade ISS
Inferred from Sequence or Structural Similarity
more info
 
anatomical structure morphogenesis TAS
Traceable Author Statement
more info
PubMed 
branching morphogenesis of an epithelial tube IDA
Inferred from Direct Assay
more info
PubMed 
calcium ion transmembrane transport ISS
Inferred from Sequence or Structural Similarity
more info
 
calcium-independent cell-matrix adhesion TAS
Traceable Author Statement
more info
PubMed 
cartilage condensation IEA
Inferred from Electronic Annotation
more info
 
cartilage development IEP
Inferred from Expression Pattern
more info
PubMed 
cell cycle arrest ISS
Inferred from Sequence or Structural Similarity
more info
 
cell-matrix adhesion TAS
Traceable Author Statement
more info
PubMed 
cytoplasmic sequestering of transcription factor ISS
Inferred from Sequence or Structural Similarity
more info
 
detection of mechanical stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
digestive tract development IEP
Inferred from Expression Pattern
more info
PubMed 
embryonic placenta development ISS
Inferred from Sequence or Structural Similarity
more info
 
establishment of cell polarity IEA
Inferred from Electronic Annotation
more info
 
genitalia development IEP
Inferred from Expression Pattern
more info
PubMed 
heart development IEP
Inferred from Expression Pattern
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules TAS
Traceable Author Statement
more info
PubMed 
in utero embryonic development ISS
Inferred from Sequence or Structural Similarity
more info
 
kidney development ISS
Inferred from Sequence or Structural Similarity
more info
 
liver development IEA
Inferred from Electronic Annotation
more info
 
lung epithelium development IEP
Inferred from Expression Pattern
more info
PubMed 
lymph vessel morphogenesis IEA
Inferred from Electronic Annotation
more info
 
mesonephric duct development IEP
Inferred from Expression Pattern
more info
PubMed 
mesonephric tubule development IEP
Inferred from Expression Pattern
more info
PubMed 
metanephric ascending thin limb development IEP
Inferred from Expression Pattern
more info
PubMed 
metanephric collecting duct development IEP
Inferred from Expression Pattern
more info
PubMed 
metanephric distal tubule morphogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
metanephric proximal tubule development IEP
Inferred from Expression Pattern
more info
PubMed 
neural tube development IEP
Inferred from Expression Pattern
more info
PubMed 
peptidyl-serine phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
placenta blood vessel development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cytosolic calcium ion concentration IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
protein export from nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell adhesion IEA
Inferred from Electronic Annotation
more info
 
regulation of mitotic spindle organization IEA
Inferred from Electronic Annotation
more info
 
regulation of proteasomal protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
response to fluid shear stress IEA
Inferred from Electronic Annotation
more info
 
skin development IEP
Inferred from Expression Pattern
more info
PubMed 
spinal cord development IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane TAS
Traceable Author Statement
more info
 
Golgi-associated vesicle membrane TAS
Traceable Author Statement
more info
 
basolateral plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
cell surface IEA
Inferred from Electronic Annotation
more info
 
ciliary membrane TAS
Traceable Author Statement
more info
 
cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular exosome HDA PubMed 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
lateral plasma membrane IEA
Inferred from Electronic Annotation
more info
 
motile cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleus 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
 

General protein information

Preferred Names
polycystin-1
Names
autosomal dominant polycystic kidney disease 1 protein
polycystic kidney disease 1 (autosomal dominant)
polycystic kidney disease-associated protein
transient receptor potential cation channel, subfamily P, member 1

NCBI Reference Sequences (RefSeq)

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_008617.1 RefSeqGene

    Range
    5001..54511
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000296.3NP_000287.3  polycystin-1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_000287.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate acceptor splice site, 3 nt downstream of that used by transcript variant 1, at the junction of one of the coding exons. This results in an isoform (2) that is 1 aa shorter than isoform 1.
    Source sequence(s)
    AC093513, L33243, U24497
    Consensus CDS
    CCDS45385.1
    UniProtKB/Swiss-Prot
    P98161
    Related
    ENSP00000399501.1, OTTHUMP00000208670, ENST00000423118.5, OTTHUMT00000341689
    Conserved Domains (12) summary
    TIGR00864
    Location:972728
    PCC; polycystin cation channel protein
    smart00303
    Location:30113060
    GPS; G-protein-coupled receptor proteolytic site domain
    smart00034
    Location:406531
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    smart00082
    Location:125177
    LRRCT; Leucine rich repeat C-terminal domain
    smart00089
    Location:11281209
    PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins
    smart00321
    Location:177271
    WSC; present in yeast cell wall integrity and stress response component proteins
    COG4886
    Location:50126
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    cd01752
    Location:31183237
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    sd00031
    Location:7092
    LRR_1; leucine-rich repeat [structural motif]
    pfam00801
    Location:17231792
    PKD; PKD domain
    pfam04479
    Location:38743956
    RTA1; RTA1 like protein
    pfam08016
    Location:37104112
    PKD_channel; Polycystin cation channel
  2. NM_001009944.2NP_001009944.2  polycystin-1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001009944.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC093513, L33243, U24497
    Consensus CDS
    CCDS32369.1
    UniProtKB/Swiss-Prot
    P98161
    Related
    ENSP00000262304.4, OTTHUMP00000208669, ENST00000262304.8, OTTHUMT00000341688
    Conserved Domains (12) summary
    TIGR00864
    Location:972728
    PCC; polycystin cation channel protein
    smart00303
    Location:30113060
    GPS; G-protein-coupled receptor proteolytic site domain
    smart00034
    Location:406531
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    smart00082
    Location:125177
    LRRCT; Leucine rich repeat C-terminal domain
    smart00089
    Location:11281209
    PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins
    smart00321
    Location:177271
    WSC; present in yeast cell wall integrity and stress response component proteins
    COG4886
    Location:50126
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    cd01752
    Location:31183237
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    sd00031
    Location:7092
    LRR_1; leucine-rich repeat [structural motif]
    pfam00801
    Location:17231792
    PKD; PKD domain
    pfam04479
    Location:38753957
    RTA1; RTA1 like protein
    pfam08016
    Location:37114113
    PKD_channel; Polycystin cation channel

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    2088708..2135898 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450299.1XP_024306067.1  polycystin-1 isoform X4

    Conserved Domains (5) summary
    TIGR00864
    Location:732744
    PCC; polycystin cation channel protein
    smart00303
    Location:30273076
    GPS; G-protein-coupled receptor proteolytic site domain
    cd01752
    Location:31343253
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    sd00031
    Location:4868
    LRR_1; leucine-rich repeat [structural motif]
    cl27887
    Location:37274129
    PKD_channel; Polycystin cation channel
  2. XM_024450298.1XP_024306066.1  polycystin-1 isoform X1

    Conserved Domains (6) summary
    TIGR00864
    Location:972768
    PCC; polycystin cation channel protein
    smart00303
    Location:30513100
    GPS; G-protein-coupled receptor proteolytic site domain
    COG4886
    Location:50126
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    cd01752
    Location:31583277
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    sd00031
    Location:7092
    LRR_1; leucine-rich repeat [structural motif]
    cl27887
    Location:37514153
    PKD_channel; Polycystin cation channel
  3. XM_024450300.1XP_024306068.1  polycystin-1 isoform X5

    Conserved Domains (5) summary
    TIGR00864
    Location:272698
    PCC; polycystin cation channel protein
    smart00303
    Location:29813030
    GPS; G-protein-coupled receptor proteolytic site domain
    cd01752
    Location:30883207
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    sd00031
    Location:2346
    LRR_1; leucine-rich repeat [structural motif]
    cl27887
    Location:36814083
    PKD_channel; Polycystin cation channel
  4. XM_011522529.2XP_011520831.1  polycystin-1 isoform X3

    Conserved Domains (11) summary
    TIGR00864
    Location:1152746
    PCC; polycystin cation channel protein
    smart00303
    Location:30293078
    GPS; G-protein-coupled receptor proteolytic site domain
    smart00034
    Location:424549
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    smart00082
    Location:143195
    LRRCT; Leucine rich repeat C-terminal domain
    smart00089
    Location:11461227
    PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins
    smart00321
    Location:195289
    WSC; present in yeast cell wall integrity and stress response component proteins
    cd01752
    Location:31363255
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    sd00031
    Location:111134
    LRR_1; leucine-rich repeat [structural motif]
    pfam00801
    Location:17411810
    PKD; PKD domain
    pfam04479
    Location:38923974
    RTA1; RTA1 like protein
    pfam08016
    Location:37284130
    PKD_channel; Polycystin cation channel
  5. XM_011522528.3XP_011520830.1  polycystin-1 isoform X2

    Conserved Domains (11) summary
    TIGR00864
    Location:1152746
    PCC; polycystin cation channel protein
    smart00303
    Location:30293078
    GPS; G-protein-coupled receptor proteolytic site domain
    smart00034
    Location:424549
    CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)
    smart00082
    Location:143195
    LRRCT; Leucine rich repeat C-terminal domain
    smart00089
    Location:11461227
    PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins
    smart00321
    Location:195289
    WSC; present in yeast cell wall integrity and stress response component proteins
    cd01752
    Location:31363255
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    sd00031
    Location:111134
    LRR_1; leucine-rich repeat [structural motif]
    pfam00801
    Location:17411810
    PKD; PKD domain
    pfam04479
    Location:38933975
    RTA1; RTA1 like protein
    pfam08016
    Location:37294131
    PKD_channel; Polycystin cation channel
  6. XM_024450301.1XP_024306069.1  polycystin-1 isoform X6

    Conserved Domains (4) summary
    TIGR00864
    Location:12060
    PCC; polycystin cation channel protein
    smart00303
    Location:23432392
    GPS; G-protein-coupled receptor proteolytic site domain
    cd01752
    Location:24502569
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    cl27887
    Location:30433445
    PKD_channel; Polycystin cation channel
  7. XM_005255370.3XP_005255427.1  polycystin-1 isoform X8

    Conserved Domains (8) summary
    smart00303
    Location:19962045
    GPS; G-protein-coupled receptor proteolytic site domain
    smart00089
    Location:113194
    PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins
    COG3291
    Location:40266
    COG3291; PKD repeat [Function unknown]
    cd01752
    Location:21032222
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    pfam00801
    Location:708777
    PKD; PKD domain
    pfam02010
    Location:11561599
    REJ; REJ domain
    pfam04479
    Location:28602942
    RTA1; RTA1 like protein
    pfam08016
    Location:26963098
    PKD_channel; Polycystin cation channel
  8. XM_011522537.2XP_011520839.1  polycystin-1 isoform X7

    Conserved Domains (8) summary
    smart00303
    Location:20372086
    GPS; G-protein-coupled receptor proteolytic site domain
    smart00089
    Location:154235
    PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins
    COG3291
    Location:81307
    COG3291; PKD repeat [Function unknown]
    cd01752
    Location:21442263
    PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...
    pfam00801
    Location:749818
    PKD; PKD domain
    pfam02010
    Location:11971640
    REJ; REJ domain
    pfam04479
    Location:29012983
    RTA1; RTA1 like protein
    pfam08016
    Location:27373139
    PKD_channel; Polycystin cation channel
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