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Aliases for PKHD1 Gene

Aliases for PKHD1 Gene

  • Polycystic Kidney And Hepatic Disease 1 (Autosomal Recessive) 2 3
  • Polyductin 2 3 4
  • Tigmin 2 3 4
  • FCYT 3 4 6
  • Polycystic Kidney And Hepatic Disease 1 Protein 3 4
  • TIG Multiple Domains 1 2 3
  • Fibrocystin 2 3
  • TIGM1 3 4
  • ARPKD 3 6

External Ids for PKHD1 Gene

Previous HGNC Symbols for PKHD1 Gene

  • TIGM1

Previous GeneCards Identifiers for PKHD1 Gene

  • GC06M051482
  • GC06M051526
  • GC06M051480
  • GC06M051314

Summaries for PKHD1 Gene

Entrez Gene Summary for PKHD1 Gene

  • 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]

GeneCards Summary for PKHD1 Gene

PKHD1 (Polycystic Kidney And Hepatic Disease 1 (Autosomal Recessive)) is a Protein Coding gene. Diseases associated with PKHD1 include polycystic kidney and hepatic disease and congenital hepatic fibrosis. GO annotations related to this gene include receptor activity. An important paralog of this gene is CEMIP.

UniProtKB/Swiss-Prot for PKHD1 Gene

  • May be required for correct bipolar cell division through the regulation of centrosome duplication and mitotic spindle assembly. May be a receptor protein that acts in collecting-duct and biliary differentiation.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PKHD1 Gene

Genomics for PKHD1 Gene

Regulatory Elements for PKHD1 Gene

Genomic Location for PKHD1 Gene

Start:
51,615,300 bp from pter
End:
52,087,625 bp from pter
Size:
472,326 bases
Orientation:
Minus strand

Genomic View for PKHD1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PKHD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PKHD1 Gene

Proteins for PKHD1 Gene

  • Protein details for PKHD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P08F94-PKHD1_HUMAN
    Recommended name:
    Fibrocystin
    Protein Accession:
    P08F94
    Secondary Accessions:
    • Q5VUA2
    • Q5VUA3
    • Q5VWV1
    • Q86Z26
    • Q8TCZ9

    Protein attributes for PKHD1 Gene

    Size:
    4074 amino acids
    Molecular mass:
    446702 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PKHD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PKHD1 Gene

Proteomics data for PKHD1 Gene at MOPED

Post-translational modifications for PKHD1 Gene

  • Glycosylation at Asn54, Asn226, Asn276, Asn357, Asn387, Asn507, Asn520, Asn529, Asn641, Asn711, Asn830, Asn869, Asn967, Asn977, Asn1065, Asn1084, Asn1116, Asn1135, Asn1234, Asn1241, Asn1312, Asn1323, Asn1346, Asn1377, Asn1460, Asn1475, Asn1494, Asn1527, Asn1532, Asn1564, Asn1582, Asn1602, Asn1631, Asn1698, Asn1764, Asn1779, Asn1879, Asn1883, Asn1919, Asn1945, Asn1959, Asn2034, Asn2115, Asn2144, Asn2350, Asn2385, Asn2435, Asn2471, Asn2509, Asn2535, Asn2553, Asn2595, Asn2633, Asn2753, Asn2768, Asn3008, Asn3140, Asn3169, Asn3225, Asn3488, Asn3528, Asn3707, Asn3726, and Asn3838
  • Modification sites at PhosphoSitePlus

Other Protein References for PKHD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PKHD1 Gene

Domains for PKHD1 Gene

Protein Domains for PKHD1 Gene

Suggested Antigen Peptide Sequences for PKHD1 Gene

Graphical View of Domain Structure for InterPro Entry

P08F94

UniProtKB/Swiss-Prot:

PKHD1_HUMAN :
  • P08F94
Domain:
  • Contains 2 G8 domains.
  • Contains 12 IPT/TIG domains.
Similarity:
  • Contains 9 PbH1 repeats.
genes like me logo Genes that share domains with PKHD1: view

No data available for Gene Families for PKHD1 Gene

Function for PKHD1 Gene

Molecular function for PKHD1 Gene

UniProtKB/Swiss-Prot Function: May be required for correct bipolar cell division through the regulation of centrosome duplication and mitotic spindle assembly. May be a receptor protein that acts in collecting-duct and biliary differentiation.

Gene Ontology (GO) - Molecular Function for PKHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity NAS 11919560
GO:0005515 protein binding IPI 16243292
genes like me logo Genes that share ontologies with PKHD1: view
genes like me logo Genes that share phenotypes with PKHD1: view

Animal Models for PKHD1 Gene

MGI Knock Outs for PKHD1:

Animal Model Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PKHD1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for PKHD1 Gene

Localization for PKHD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PKHD1 Gene

Membrane; Single-pass type I membrane protein. Cytoplasm, cytoskeleton, cilium basal body. Cell projection, cilium. Cytoplasm, cytoskeleton, spindle. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PKHD1 Gene COMPARTMENTS Subcellular localization image for PKHD1 gene
Compartment Confidence
cytoskeleton 5
plasma membrane 5
extracellular 1

Gene Ontology (GO) - Cellular Components for PKHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 20709014
GO:0005813 centrosome IDA 20554582
GO:0016021 integral component of membrane IEA --
GO:0016324 apical plasma membrane IDA 16243292
GO:0031362 anchored component of external side of plasma membrane TAS 11919560
genes like me logo Genes that share ontologies with PKHD1: view

Pathways for PKHD1 Gene

SuperPathways for PKHD1 Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Interacting Proteins for PKHD1 Gene

STRING Interaction Network Preview (showing 2 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000360158%0d%0a9606.ENSP00000297156%0d%0a9606.ENSP00000368516%0d%0a
Selected Interacting proteins: ENSP00000360158 P08F94-PKHD1_HUMAN for PKHD1 Gene via STRING I2D

Gene Ontology (GO) - Biological Process for PKHD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001822 kidney development ISS --
GO:0006874 cellular calcium ion homeostasis IMP 17669261
GO:0008284 positive regulation of cell proliferation IMP 19943112
GO:0010824 regulation of centrosome duplication IMP 20554582
GO:0016337 single organismal cell-cell adhesion ISS --
genes like me logo Genes that share ontologies with PKHD1: view

No data available for Pathways by source for PKHD1 Gene

Compounds for PKHD1 Gene

(1) Novoseek inferred chemical compound relationships for PKHD1 Gene

Compound -log(P) Hits PubMed IDs
calcium 0 4
genes like me logo Genes that share compounds with PKHD1: view

Transcripts for PKHD1 Gene

Unigene Clusters for PKHD1 Gene

Polycystic kidney and hepatic disease 1 (autosomal recessive):
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PKHD1

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for PKHD1
  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PKHD1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^
SP1:
SP2:
SP3:

ExUns: 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45 ^ 46 ^ 47 ^ 48 ^ 49 ^ 50 ^ 51 ^ 52 ^
SP1: -
SP2: -
SP3: -

ExUns: 53 ^ 54 ^ 55 ^ 56 ^ 57 ^ 58 ^ 59 ^ 60 ^ 61 ^ 62 ^ 63 ^ 64 ^ 65 ^ 66 ^ 67 ^ 68 ^ 69 ^ 70
SP1: - -
SP2:
SP3: -

Relevant External Links for PKHD1 Gene

GeneLoc Exon Structure for
PKHD1
ECgene alternative splicing isoforms for
PKHD1

Expression for PKHD1 Gene

mRNA expression in normal human tissues for PKHD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PKHD1 Gene

This gene is overexpressed in Kidney - Cortex (25.0) and Pancreas (18.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for PKHD1 Gene

SOURCE GeneReport for Unigene cluster for PKHD1 Gene Hs.662050

mRNA Expression by UniProt/SwissProt for PKHD1 Gene

P08F94-PKHD1_HUMAN
Tissue specificity: Predominantly expressed in fetal and adult kidney. In the kidney, it is found in the cortical and medullary collecting ducts. Also present in the adult pancreas, but at much lower levels. Detectable in fetal and adult liver. Rather indistinct signal in fetal brain.
genes like me logo Genes that share expressions with PKHD1: view

In Situ Assay Products

Orthologs for PKHD1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PKHD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PKHD1 35
  • 99.33 (n)
  • 98.94 (a)
PKHD1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LOC537895 35
  • 83.74 (n)
  • 78.76 (a)
PKHD1 36
  • 79 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PKHD1 35
  • 85.14 (n)
  • 80.01 (a)
PKHD1 36
  • 80 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pkhd1 35
  • 79.37 (n)
  • 72.74 (a)
Pkhd1 16
Pkhd1 36
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PKHD1 36
  • 62 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PKHD1 36
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves PKHD1 35
  • 61.09 (n)
  • 51.8 (a)
PKHD1 36
  • 49 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pkhd1 35
  • 54.63 (n)
  • 45.24 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3786 36
  • 22 (a)
OneToMany
Species with no ortholog for PKHD1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PKHD1 Gene

ENSEMBL:
Gene Tree for PKHD1 (if available)
TreeFam:
Gene Tree for PKHD1 (if available)

Paralogs for PKHD1 Gene

Paralogs for PKHD1 Gene

genes like me logo Genes that share paralogs with PKHD1: view

Variants for PKHD1 Gene

Sequence variations from dbSNP and Humsavar for PKHD1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs481642 -- 51,704,018(+) CATCA(G/T)CCATG intron-variant
rs481795 -- 51,704,073(+) TTCTA(C/T)CTTTC intron-variant
rs488063 -- 51,649,664(-) TTGGT(A/G)GTATT intron-variant
rs488913 -- 51,649,612(+) AGCTT(C/T)CCAAA intron-variant
rs509107 -- 51,666,249(+) acaca(A/T)ttatg intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PKHD1 Gene

Variant ID Type Subtype PubMed ID
esv2448462 CNV Deletion 19546169
esv2002849 CNV Deletion 18987734
esv3575 CNV Deletion 18987735
esv2732071 CNV Deletion 23290073
esv1002109 CNV Deletion 20482838
esv6562 CNV Loss 19470904
esv1140845 CNV Deletion 17803354
nsv526292 CNV Gain 19592680
nsv510899 CNV Complex 20534489
nsv510029 CNV Loss 20534489
esv2661375 CNV Deletion 23128226
esv24252 CNV Loss 19812545
esv33924 CNV Gain 17666407
nsv507329 CNV Insertion 20534489
esv33429 CNV Gain 17666407
nsv5303 CNV Loss 18451855
nsv511313 CNV Loss 21212237
nsv511882 CNV Loss 21212237
nsv820795 CNV Deletion 20802225
esv5268 CNV Deletion 18987735
esv2732072 CNV Deletion 23290073
esv2664845 CNV Deletion 23128226
esv23003 CNV Gain+Loss 19812545
esv2587934 CNV Deletion 19546169
nsv436518 CNV Deletion 17901297
esv2732074 CNV Deletion 23290073
nsv499787 CNV Loss 21111241
esv2657311 CNV Deletion 23128226
nsv349361 CNV Loss 16902084
nsv823689 CNV Loss 20364138
esv2732075 CNV Deletion 23290073
esv23422 CNV Gain 19812545
esv990745 CNV Deletion 20482838
esv2663435 CNV Deletion 23128226
nsv509134 CNV Insertion 20534489
esv1493351 CNV Insertion 17803354
esv1154861 CNV Insertion 17803354
esv2555448 CNV Insertion 19546169
esv2551556 CNV Deletion 19546169
dgv1052e201 CNV Deletion 23290073
esv2732077 CNV Deletion 23290073
esv2732079 CNV Deletion 23290073
esv271875 CNV Insertion 20981092
esv272475 CNV Insertion 20981092
nsv830662 CNV Gain 17160897

Relevant External Links for PKHD1 Gene

HapMap Linkage Disequilibrium report
PKHD1
Human Gene Mutation Database (HGMD)
PKHD1
Locus Specific Mutation Databases (LSDB)
PKHD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PKHD1 Gene

Disorders for PKHD1 Gene

(1) OMIM Diseases for PKHD1 Gene (606702)

UniProtKB/Swiss-Prot

PKHD1_HUMAN
  • Polycystic kidney disease, autosomal recessive (ARPKD) [MIM:263200]: A severe form of polycystic kidney disease affecting the kidneys and the hepatic biliary tract. The clinical spectrum is widely variable, with most cases presenting during infancy. The fetal phenotypic features classically include enlarged and echogenic kidneys, as well as oligohydramnios secondary to a poor urine output. Up to 50% of the affected neonates die shortly after birth, as a result of severe pulmonary hypoplasia and secondary respiratory insufficiency. In the subset that survives the perinatal period, morbidity and mortality are mainly related to severe systemic hypertension, renal insufficiency, and portal hypertension due to portal-tract fibrosis. {ECO:0000269 PubMed:11898128, ECO:0000269 PubMed:11919560, ECO:0000269 PubMed:12506140, ECO:0000269 PubMed:12846734, ECO:0000269 PubMed:12874454, ECO:0000269 PubMed:15108281, ECO:0000269 PubMed:16677362, ECO:0000269 PubMed:19914852}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for PKHD1 Gene

(13) Novoseek inferred disease relationships for PKHD1 Gene

Disease -log(P) Hits PubMed IDs
arpkd 98.8 187
congenital hepatic fibrosis 91.3 8
polycystic kidney diseases 91.1 20
adpkd 83 3
carolis disease 76.3 3

Relevant External Links for PKHD1

GeneTests
PKHD1
GeneReviews
PKHD1
Genetic Association Database (GAD)
PKHD1
Human Genome Epidemiology (HuGE) Navigator
PKHD1
genes like me logo Genes that share disorders with PKHD1: view

Publications for PKHD1 Gene

  1. PKHD1, the polycystic kidney and hepatic disease 1 gene, encodes a novel large protein containing multiple immunoglobulin-like-plexin- transcription-factor domains and parallel beta-helix 1 repeats. (PMID: 11898128) Onuchic L.F. … Germino G.G. (Am. J. Hum. Genet. 2002) 3 4 23
  2. The gene mutated in autosomal recessive polycystic kidney disease encodes a large, receptor-like protein. (PMID: 11919560) Ward C.J. … Harris P.C. (Nat. Genet. 2002) 3 4 23
  3. Spectrum of mutations in the gene for autosomal recessive polycystic kidney disease (ARPKD/PKHD1). (PMID: 12506140) Bergmann C. … Zerres K. (J. Am. Soc. Nephrol. 2003) 3 4 23
  4. A complete mutation screen of PKHD1 in autosomal-recessive polycystic kidney disease (ARPKD) pedigrees. (PMID: 12846734) Rossetti S. … Harris P.C. (Kidney Int. 2003) 3 4 23
  5. The autosomal recessive polycystic kidney disease protein is localized to primary cilia, with concentration in the basal body area. (PMID: 14978161) Wang S. … Zhou J. (J. Am. Soc. Nephrol. 2004) 3 4 23

Products for PKHD1 Gene

Sources for PKHD1 Gene

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