Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 5310, updated on 8-Jul-2021

    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
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PKD1 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    51
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (2088708..2135898, complement)
    105.20201022 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-06-10)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-06-10)

    ClinGen Genome Curation PagePubMed

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables Wnt-activated receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to calcium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables calcium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transmembrane transporter binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in branching morphogenesis of an epithelial tube IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in calcium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in calcium-independent cell-matrix adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cartilage condensation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cartilage development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in cell-cell signaling by wnt IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell-matrix adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cytoplasmic sequestering of transcription factor ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in detection of mechanical stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in digestive tract development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in embryonic placenta development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in establishment of cell polarity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in genitalia development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in heart development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in in utero embryonic development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in kidney development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in liver development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lung epithelium development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in lymph vessel morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    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 ascending thin limb development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in metanephric collecting duct development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in metanephric distal tubule morphogenesis IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in metanephric proximal tubule development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in neural tube development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in peptidyl-serine phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cytosolic calcium ion concentration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein export from nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein heterotetramerization 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 G1/S transition of mitotic cell cycle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of mitotic spindle organization IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within regulation of proteasomal protein catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to fluid shear stress IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in skin development IEP
    Inferred from Expression Pattern
    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 Golgi membrane TAS
    Traceable Author Statement
    more info
     
    located_in Golgi-associated vesicle membrane TAS
    Traceable Author Statement
    more info
     
    located_in basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of calcium channel complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of cation channel complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
     
    located_in ciliary membrane TAS
    Traceable Author Statement
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in integral component of membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in integral component of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lateral plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in motile cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleus 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-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)

    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_008617.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_000296.4NP_000287.4  polycystin-1 isoform 2 precursor

      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)
      AC009065, AC093513
      Consensus CDS
      CCDS45385.1
      Related
      ENSP00000399501.1, ENST00000423118.5
      Conserved Domains (6) summary
      TIGR00864
      Location:972728
      PCC; polycystin cation channel protein
      smart00303
      Location:30113060
      GPS; G-protein-coupled receptor proteolytic site domain
      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]
      pfam08016
      Location:37124112
      PKD_channel; Polycystin cation channel
    2. NM_001009944.3NP_001009944.3  polycystin-1 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC009065, AC093513
      Consensus CDS
      CCDS32369.1
      Related
      ENSP00000262304.4, ENST00000262304.9
      Conserved Domains (6) summary
      TIGR00864
      Location:972728
      PCC; polycystin cation channel protein
      smart00303
      Location:30113060
      GPS; G-protein-coupled receptor proteolytic site domain
      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]
      pfam08016
      Location:37134113
      PKD_channel; Polycystin cation channel

    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_000016.10 Reference GRCh38.p13 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

    Reference GRCh38.p13 ALT_REF_LOCI_1

    Genomic

    1. NT_187607.1 Reference GRCh38.p13 ALT_REF_LOCI_1

      Range
      705067..760109 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Support Center