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    PKHD1 PKHD1, fibrocystin/polyductin [ Homo sapiens (human) ]

    Gene ID: 5314, updated on 7-May-2017
    Official Symbol
    PKHD1provided by HGNC
    Official Full Name
    PKHD1, fibrocystin/polyductinprovided by HGNC
    Primary source
    HGNC:HGNC:9016
    See related
    Ensembl:ENSG00000170927 MIM:606702; Vega:OTTHUMG00000014841
    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
    FPC; FCYT; ARPKD; TIGM1
    Summary
    The protein encoded by this gene is predicted to have a single transmembrane (TM)-spanning domain and multiple copies of an immunoglobulin-like plexin-transcription-factor domain. Alternative splicing results in two transcript variants encoding different isoforms. Other alternatively spliced transcripts have been described, but the full length sequences have not been determined. Several of these transcripts are predicted to encode truncated products which lack the TM and may be secreted. Mutations in this gene cause autosomal recessive polycystic kidney disease, also known as polycystic kidney and hepatic disease-1. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    6p12.3-p12.2
    Exon count:
    76
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (51613291..52087625, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (51480145..51952423, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Wilms tumor 1 associated protein pseudogene Neighboring gene ribosomal protein S15a pseudogene 20 Neighboring gene uncharacterized LOC101927082 Neighboring gene uncharacterized LOC105375087 Neighboring gene RNA, 7SL, cytoplasmic 580, pseudogene Neighboring gene long intergenic non-protein coding RNA, muscle differentiation 1 Neighboring gene microRNA 133b Neighboring gene microRNA 206

    • 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

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    Description
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    NHGRI GWA Catalog
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    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ46150, DKFZp686C01112

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    receptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    cellular calcium ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    homeostatic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    kidney development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of cellular component movement ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of protein kinase B signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of ERK1 and ERK2 cascade IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of TOR signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of centrosome duplication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    single organismal cell-cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    anchored component of external side of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
     
    ciliary basal body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cilium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    mitotic spindle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    fibrocystin
    Names
    TIG multiple domains 1
    fibrocystin/polyductin complex
    polycystic kidney and hepatic disease 1 (autosomal recessive)
    polycystic kidney and hepatic disease 1 protein
    polyductin
    tigmin

    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_008753.1 RefSeqGene

      Range
      5001..477279
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_138694.3NP_619639.3  fibrocystin isoform 1 precursor

      See identical proteins and their annotated locations for NP_619639.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform of this protein.
      Source sequence(s)
      AY074797
      Consensus CDS
      CCDS4935.1
      UniProtKB/Swiss-Prot
      P08F94
      Related
      ENSP00000360158.3, OTTHUMP00000016598, ENST00000371117.7, OTTHUMT00000040893
      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:30043176
      Beta_helix; Right handed beta helix region
    2. NM_170724.2NP_733842.2  fibrocystin isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks several exons and includes an alternate exon in the 3' coding region and UTR, compared to variant 1. Isoform 2 is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL157774, AY074797
      Consensus CDS
      CCDS4936.1
      UniProtKB/Swiss-Prot
      P08F94
      Related
      ENSP00000341097.4, OTTHUMP00000016599, ENST00000340994.4, OTTHUMT00000040894
      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:30043176
      Beta_helix; Right handed beta helix region

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p7 Primary Assembly

      Range
      51613291..52087625 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017010944.1XP_016866433.1  fibrocystin isoform X1

      UniProtKB/Swiss-Prot
      P08F94
      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:30043176
      Beta_helix; Right handed beta helix region
    2. XM_017010945.1XP_016866434.1  fibrocystin isoform X2

    3. XM_017010947.1XP_016866436.1  fibrocystin isoform X5

    4. XM_011514683.2XP_011512985.1  fibrocystin isoform X6

      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:9311004
      TIG; IPT/TIG domain
      pfam10162
      Location:17191835
      G8; G8 domain
      pfam13229
      Location:27902962
      Beta_helix; Right handed beta helix region
    5. XM_017010946.1XP_016866435.1  fibrocystin isoform X4

    6. XM_011514682.2XP_011512984.1  fibrocystin isoform X3

      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:29583130
      Beta_helix; Right handed beta helix region
    7. XM_011514680.2XP_011512982.1  fibrocystin isoform X1

      See identical proteins and their annotated locations for XP_011512982.1

      UniProtKB/Swiss-Prot
      P08F94
      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:30043176
      Beta_helix; Right handed beta helix region
    8. XM_011514684.2XP_011512986.1  fibrocystin isoform X7

      Conserved Domains (4) summary
      cd00603
      Location:9601057
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:12491332
      TIG; IPT/TIG domain
      pfam10162
      Location:16961812
      G8; G8 domain
      pfam13229
      Location:27672939
      Beta_helix; Right handed beta helix region
    9. XM_017010948.1XP_016866437.1  fibrocystin isoform X7

      Conserved Domains (4) summary
      cd00603
      Location:9601057
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:12491332
      TIG; IPT/TIG domain
      pfam10162
      Location:16961812
      G8; G8 domain
      pfam13229
      Location:27672939
      Beta_helix; Right handed beta helix region
    10. XM_017010949.1XP_016866438.1  fibrocystin isoform X8

    11. XM_011514690.2XP_011512992.1  fibrocystin isoform X16

      See identical proteins and their annotated locations for XP_011512992.1

      Conserved Domains (2) summary
      pfam10162
      Location:774897
      G8; G8 domain
      pfam13229
      Location:10291201
      Beta_helix; Right handed beta helix region
    12. XM_011514691.2XP_011512993.1  fibrocystin isoform X16

      See identical proteins and their annotated locations for XP_011512993.1

      Conserved Domains (2) summary
      pfam10162
      Location:774897
      G8; G8 domain
      pfam13229
      Location:10291201
      Beta_helix; Right handed beta helix region
    13. XM_011514687.1XP_011512989.1  fibrocystin isoform X12

      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:30043176
      Beta_helix; Right handed beta helix region
    14. XM_011514686.2XP_011512988.1  fibrocystin isoform X11

      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:30043176
      Beta_helix; Right handed beta helix region
    15. XM_017010950.1XP_016866439.1  fibrocystin isoform X10

    16. XM_011514685.1XP_011512987.1  fibrocystin isoform X9

      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:30043176
      Beta_helix; Right handed beta helix region
    17. XM_011514688.2XP_011512990.1  fibrocystin isoform X13

      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:30043176
      Beta_helix; Right handed beta helix region
    18. XM_017010951.1XP_016866440.1  fibrocystin isoform X14

    19. XM_017010952.1XP_016866441.1  fibrocystin isoform X15

      Conserved Domains (4) summary
      cd00603
      Location:11971294
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      pfam01833
      Location:14861569
      TIG; IPT/TIG domain
      pfam10162
      Location:19332049
      G8; G8 domain
      pfam13229
      Location:22902446
      Beta_helix; Right handed beta helix region

    RNA

    1. XR_001743469.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018917.2 Alternate CHM1_1.1

      Range
      51482653..51954627 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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