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    PKHD1 PKHD1 ciliary IPT domain containing fibrocystin/polyductin [ Homo sapiens (human) ]

    Gene ID: 5314, updated on 2-Nov-2024

    Summary

    Official Symbol
    PKHD1provided by HGNC
    Official Full Name
    PKHD1 ciliary IPT domain containing fibrocystin/polyductinprovided by HGNC
    Primary source
    HGNC:HGNC:9016
    See related
    Ensembl:ENSG00000170927 MIM:606702; AllianceGenome:HGNC:9016
    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; PCYT; PKD4; 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]
    Expression
    Biased expression in kidney (RPKM 4.0), pancreas (RPKM 0.7) and 2 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PKHD1 in Genome Data Viewer
    Location:
    6p12.3-p12.2
    Exon count:
    75
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (51615299..52087615, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (51458672..51926294, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (51480097..51952411, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD66 Neighboring gene ribosomal protein S15a pseudogene 20 Neighboring gene uncharacterized LOC101927082 Neighboring gene uncharacterized LOC124900615 Neighboring gene uncharacterized LOC105375087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:51608450-51608950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:51608951-51609451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:51719291-51719815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:51719816-51720339 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:51739224-51739950 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:51739951-51740677 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:51846961-51847687 Neighboring gene RNA, 7SL, cytoplasmic 580, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:51888848-51890047 Neighboring gene uncharacterized LOC124901327 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:51941398-51941968 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:51941969-51942537 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:51961188-51962387 Neighboring gene long intergenic non-protein coding RNA, muscle differentiation 1 Neighboring gene microRNA 133b Neighboring gene microRNA 206

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    Associated conditions

    Description Tests
    Polycystic kidney disease 4 Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study.
    EBI GWAS Catalog
    Genome-wide association of single-nucleotide polymorphisms with weight loss outcomes after Roux-en-Y gastric bypass surgery.
    EBI GWAS Catalog
    Genome-wide association study and meta-analysis of intraocular pressure.
    EBI GWAS Catalog
    NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ46150, DKFZp686C01112

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_positive_effect branching morphogenesis of an epithelial tube ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in branching morphogenesis of an epithelial tube ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell-cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_positive_effect cell-cell junction organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cilium assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in epithelial cell morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in establishment of centrosome localization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in establishment of mitotic spindle orientation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in homeostatic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in intracellular calcium ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in kidney development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of epithelial cell apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of epithelial cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of ERK1 and ERK2 cascade IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of TOR signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cell-cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cell-matrix adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of centrosome duplication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of cholangiocyte proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of establishment of planar polarity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in 9+0 non-motile cilium IEA
    Inferred from Electronic Annotation
    more info
     
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cilium IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in external side of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in extracellular exosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in mitotic spindle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    fibrocystin
    Names
    PKHD1, fibrocystin/polyductin
    TIG multiple domains 1
    fibrocystin/polyductin complex
    polycystic kidney and hepatic disease 1 (autosomal recessive)
    polycystic kidney and hepatic disease 1 protein
    polyductin
    tigmin

    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_008753.1 RefSeqGene

      Range
      5013..477327
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_138694.4NP_619639.3  fibrocystin isoform 1

      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)
      AL355997, AY074797
      Consensus CDS
      CCDS4935.1
      UniProtKB/Swiss-Prot
      P08F94, Q86Z26
      Related
      ENSP00000360158.3, ENST00000371117.8
      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_170724.3NP_733842.2  fibrocystin isoform 2

      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, ENST00000340994.4
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      51615299..52087615 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017010944.3XP_016866433.1  fibrocystin isoform X1

      UniProtKB/Swiss-Prot
      P08F94, Q86Z26
      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_017010945.3XP_016866434.1  fibrocystin isoform X2

    3. XM_017010947.3XP_016866436.1  fibrocystin isoform X5

    4. XM_011514683.4XP_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_017010946.3XP_016866435.1  fibrocystin isoform X4

      Conserved Domains (2) 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 ...
      TIGR04247
      Location:29623129
      NosD_copper_fam; nitrous oxide reductase family maturation protein NosD
    6. XM_011514682.4XP_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_011514680.4XP_011512982.1  fibrocystin isoform X1

      See identical proteins and their annotated locations for XP_011512982.1

      UniProtKB/Swiss-Prot
      P08F94, Q86Z26
      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_011514684.4XP_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_017010948.3XP_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_017010949.3XP_016866438.1  fibrocystin isoform X8

    11. XM_011514690.4XP_011512992.1  fibrocystin isoform X17

      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_011514691.4XP_011512993.1  fibrocystin isoform X17

      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_011514687.2XP_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_011514686.3XP_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_017010950.2XP_016866439.1  fibrocystin isoform X10

    16. XM_011514685.2XP_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_011514688.3XP_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_017010951.2XP_016866440.1  fibrocystin isoform X14

    19. XM_047418895.1XP_047274851.1  fibrocystin isoform X15

    20. XM_017010952.2XP_016866441.1  fibrocystin isoform X16

      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_001743469.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      51458672..51926294 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355644.1XP_054211619.1  fibrocystin isoform X1

    2. XM_054355645.1XP_054211620.1  fibrocystin isoform X2

    3. XM_054355648.1XP_054211623.1  fibrocystin isoform X5

    4. XM_054355649.1XP_054211624.1  fibrocystin isoform X6

    5. XM_054355647.1XP_054211622.1  fibrocystin isoform X4

    6. XM_054355646.1XP_054211621.1  fibrocystin isoform X3

    7. XM_054355643.1XP_054211618.1  fibrocystin isoform X1

    8. XM_054355650.1XP_054211625.1  fibrocystin isoform X7

    9. XM_054355651.1XP_054211626.1  fibrocystin isoform X7

    10. XM_054355652.1XP_054211627.1  fibrocystin isoform X8

    11. XM_054355662.1XP_054211637.1  fibrocystin isoform X17

    12. XM_054355661.1XP_054211636.1  fibrocystin isoform X17

    13. XM_054355656.1XP_054211631.1  fibrocystin isoform X12

    14. XM_054355655.1XP_054211630.1  fibrocystin isoform X11

    15. XM_054355654.1XP_054211629.1  fibrocystin isoform X10

    16. XM_054355653.1XP_054211628.1  fibrocystin isoform X9

    17. XM_054355657.1XP_054211632.1  fibrocystin isoform X13

    18. XM_054355658.1XP_054211633.1  fibrocystin isoform X14

    19. XM_054355659.1XP_054211634.1  fibrocystin isoform X15

    20. XM_054355660.1XP_054211635.1  fibrocystin isoform X16

    RNA

    1. XR_008487347.1 RNA Sequence