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

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: mouse all
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Genomic context

Location:: 6p12.3-p12.2

Exon count:: 75

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (51615299..52087615, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (51458672..51926294, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (51480097..51952411, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Rare variants in PKHD1 associated with Caroli syndrome: Two case reports.
Title: Rare variants in PKHD1 associated with Caroli syndrome: Two case reports.
Clinical features of autosomal recessive polycystic kidney disease in the Japanese population and analysis of splicing in PKHD1 gene for determination of phenotypes.
Title: Clinical features of autosomal recessive polycystic kidney disease in the Japanese population and analysis of splicing in PKHD1 gene for determination of phenotypes.
Cilia and polycystic kidney disease.
Title: Cilia and polycystic kidney disease.
Presence of compound heterozygous mutations in the PHKD1 gene in an asymptomatic patient.", trans "Presencia de mutaciones en heterocigosis compuesta en el gen PHKD1 en una paciente asintomatica.
Title: Presence of compound heterozygous mutations in the PHKD1 gene in an asymptomatic patient.
Refining genotype-phenotype correlations in 304 patients with autosomal recessive polycystic kidney disease and PKHD1 gene variants.
Title: Refining genotype-phenotype correlations in 304 patients with autosomal recessive polycystic kidney disease and PKHD1 gene variants.
Possible PKHD1 Hot-spot Mutations Related to Early Kidney Function Failure or Hepatofibrosis in Chinese Children with ARPKD: A Retrospective Single Center Cohort Study and Literature Review.
Title: Possible PKHD1 Hot-spot Mutations Related to Early Kidney Function Failure or Hepatofibrosis in Chinese Children with ARPKD: A Retrospective Single Center Cohort Study and Literature Review.
The carboxy-terminus of the human ARPKD protein fibrocystin can control STAT3 signalling by regulating SRC-activation.
Title: The carboxy-terminus of the human ARPKD protein fibrocystin can control STAT3 signalling by regulating SRC-activation.
Analysis of the polycystin complex (PCC) in human urinary exosome-like vesicles (ELVs).
Title: Analysis of the polycystin complex (PCC) in human urinary exosome-like vesicles (ELVs).
two novel compound heterozygous PKHD1 mutations were implicated in causing ARPKD in a Han Chinese family. The results expand the mutation spectrum of PKHD1 that leads to ARPKD, which may improve genetic counseling and prenatal diagnosis for families with ARPKD.
Title: Novel compound heterozygous PKHD1 mutations cause autosomal recessive polycystic kidney disease in a Han Chinese family.
PKHD1 mutations increased nonglycolytic acidification rate, consistent with an increase in tricarboxylic acid cycle activity or breakdown of intracellular glycogen. In addition, they increased basal and ATP-linked oxygen consumption rates. The PKHD1 and PKD2 mutations also altered mitochondrial morphology, resembling the effects of polycystin 1 deficiency.
Title: Truncating PKHD1 and PKD2 mutations alter energy metabolism.

Submit: New GeneRIF Correction See all GeneRIFs (68)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Polycystic kidney disease 4 MedGen: C4540575 OMIM: 263200 GeneReviews: Autosomal Recessive Polycystic Kidney Disease - PKHD1	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 EBI GWAS CatalogPubMed
Genome-wide association of single-nucleotide polymorphisms with weight loss outcomes after Roux-en-Y gastric bypass surgery. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study and meta-analysis of intraocular pressure. EBI GWAS Catalog EBI GWAS CatalogPubMed
NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH46288 (e-PCR)
- UniSTS:33063

SHGC-110670 (e-PCR)
- UniSTS:167975

RH37475 (e-PCR)
- UniSTS:7464

RH45221 (e-PCR)
- UniSTS:47151

D6S245 (e-PCR)
- UniSTS:147254

RH119735 (e-PCR)
- UniSTS:133187

SGC35102 (e-PCR)
- UniSTS:77387

D6S1344 (e-PCR)
- UniSTS:149327

RH120344 (e-PCR)
- UniSTS:132484

SHGC-148211 (e-PCR)
- UniSTS:176261

G62945 (e-PCR)
- UniSTS:139920

RH16344 (e-PCR)
- UniSTS:74650

D6S2010 (e-PCR)
- UniSTS:58786

G49556 (e-PCR)
- UniSTS:109226

D6S2390 (e-PCR)
- UniSTS:474560

D6S2391 (e-PCR)
- UniSTS:474561

SHGC-78840 (e-PCR)
- UniSTS:100832

stdJ136A8T7 (e-PCR)
- UniSTS:181729

RH121598 (e-PCR)
- UniSTS:134370

D6S1714 (e-PCR)
- UniSTS:74724

D6S1956 (e-PCR)
- UniSTS:75258

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 more info	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

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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)

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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

NG_008753.1 RefSeqGene

Range

5013..477327

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_138694.4 → NP_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:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:3004 → 3176

Beta_helix; Right handed beta helix region
NM_170724.3 → NP_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:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:3004 → 3176

Beta_helix; Right handed beta helix region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

51615299..52087615 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017010944.3 → XP_016866433.1 fibrocystin isoform X1

UniProtKB/Swiss-Prot

P08F94, Q86Z26

Conserved Domains (4) summary

cd00603
Location:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:3004 → 3176

Beta_helix; Right handed beta helix region
XM_017010945.3 → XP_016866434.1 fibrocystin isoform X2
XM_017010947.3 → XP_016866436.1 fibrocystin isoform X5
XM_011514683.4 → XP_011512985.1 fibrocystin isoform X6

Conserved Domains (4) summary

cd00603
Location:1197 → 1294

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:931 → 1004

TIG; IPT/TIG domain

pfam10162
Location:1719 → 1835

G8; G8 domain

pfam13229
Location:2790 → 2962

Beta_helix; Right handed beta helix region
XM_017010946.3 → XP_016866435.1 fibrocystin isoform X4

Conserved Domains (2) summary

cd00603
Location:1197 → 1294

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:2962 → 3129

NosD_copper_fam; nitrous oxide reductase family maturation protein NosD
XM_011514682.4 → XP_011512984.1 fibrocystin isoform X3

Conserved Domains (4) summary

cd00603
Location:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:2958 → 3130

Beta_helix; Right handed beta helix region
XM_011514680.4 → XP_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:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:3004 → 3176

Beta_helix; Right handed beta helix region
XM_011514684.4 → XP_011512986.1 fibrocystin isoform X7

Conserved Domains (4) summary

cd00603
Location:960 → 1057

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:1249 → 1332

TIG; IPT/TIG domain

pfam10162
Location:1696 → 1812

G8; G8 domain

pfam13229
Location:2767 → 2939

Beta_helix; Right handed beta helix region
XM_017010948.3 → XP_016866437.1 fibrocystin isoform X7

Conserved Domains (4) summary

cd00603
Location:960 → 1057

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:1249 → 1332

TIG; IPT/TIG domain

pfam10162
Location:1696 → 1812

G8; G8 domain

pfam13229
Location:2767 → 2939

Beta_helix; Right handed beta helix region
XM_017010949.3 → XP_016866438.1 fibrocystin isoform X8
XM_011514690.4 → XP_011512992.1 fibrocystin isoform X17

See identical proteins and their annotated locations for XP_011512992.1

Conserved Domains (2) summary

pfam10162
Location:774 → 897

G8; G8 domain

pfam13229
Location:1029 → 1201

Beta_helix; Right handed beta helix region
XM_011514691.4 → XP_011512993.1 fibrocystin isoform X17

See identical proteins and their annotated locations for XP_011512993.1

Conserved Domains (2) summary

pfam10162
Location:774 → 897

G8; G8 domain

pfam13229
Location:1029 → 1201

Beta_helix; Right handed beta helix region
XM_011514687.2 → XP_011512989.1 fibrocystin isoform X12

Conserved Domains (4) summary

cd00603
Location:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:3004 → 3176

Beta_helix; Right handed beta helix region
XM_011514686.3 → XP_011512988.1 fibrocystin isoform X11

Conserved Domains (4) summary

cd00603
Location:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:3004 → 3176

Beta_helix; Right handed beta helix region
XM_017010950.2 → XP_016866439.1 fibrocystin isoform X10
XM_011514685.2 → XP_011512987.1 fibrocystin isoform X9

Conserved Domains (4) summary

cd00603
Location:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:3004 → 3176

Beta_helix; Right handed beta helix region
XM_011514688.3 → XP_011512990.1 fibrocystin isoform X13

Conserved Domains (4) summary

cd00603
Location:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:3004 → 3176

Beta_helix; Right handed beta helix region
XM_017010951.2 → XP_016866440.1 fibrocystin isoform X14
XM_047418895.1 → XP_047274851.1 fibrocystin isoform X15
XM_017010952.2 → XP_016866441.1 fibrocystin isoform X16

Conserved Domains (4) summary

cd00603
Location:1197 → 1294

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:1486 → 1569

TIG; IPT/TIG domain

pfam10162
Location:1933 → 2049

G8; G8 domain

pfam13229
Location:2290 → 2446

Beta_helix; Right handed beta helix region