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

Gene ID: 5314, updated on 17-Jun-2019

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
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; 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

Genomic context

See PKHD1 in Genome Data Viewer
Location:
6p12.3-p12.2
Exon count:
75
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (51614685..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 WT1 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

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 
signaling receptor activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cell-cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
 
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 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cilium IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA 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 

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)

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_138694.4NP_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)
    AL355997, AY074797
    Consensus CDS
    CCDS4935.1
    UniProtKB/Swiss-Prot
    P08F94
    Related
    ENSP00000360158.3, ENST00000371117.7
    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 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, 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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    51614685..52087625 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010944.2XP_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_017010945.2XP_016866434.1  fibrocystin isoform X2

  3. XM_017010947.2XP_016866436.1  fibrocystin isoform X5

  4. XM_011514683.3XP_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_017010946.2XP_016866435.1  fibrocystin isoform X4

  6. XM_011514682.3XP_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_011514680.3XP_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_011514684.3XP_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_017010948.2XP_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_017010949.2XP_016866438.1  fibrocystin isoform X8

  11. XM_011514690.3XP_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_011514691.3XP_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

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