Human Gene PKD1 (ENST00000262304.9_11) from GENCODE V47lift37
  Description: polycystin 1, transient receptor potential channel interacting, transcript variant 1 (from RefSeq NM_001009944.3)
Gencode Transcript: ENST00000262304.9_11
Gencode Gene: ENSG00000008710.20_18
Transcript (Including UTRs)
   Position: hg19 chr16:2,138,709-2,185,899 Size: 47,191 Total Exon Count: 46 Strand: -
Coding Region
   Position: hg19 chr16:2,139,728-2,185,690 Size: 45,963 Coding Exon Count: 46 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:2,138,709-2,185,899)mRNA (may differ from genome)Protein (4303 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PKD1_HUMAN
DESCRIPTION: RecName: Full=Polycystin-1; AltName: Full=Autosomal dominant polycystic kidney disease 1 protein; Flags: Precursor;
FUNCTION: Involved in renal tubulogenesis. Involved in fluid-flow mechanosensation by the primary cilium in renal epithelium (By similarity). Acts as a regulator of cilium length, together with PKD2 (By similarity). The dynamic control of cilium length is essential in the regulation of mechanotransductive signaling. The cilium length response creates a negative feedback loop whereby fluid shear-mediated deflection of the primary cilium, which decreases intracellular cAMP, leads to cilium shortening and thus decreases flow-induced signaling (By similarity). May be an ion- channel regulator. Involved in adhesive protein-protein and protein-carbohydrate interactions.
SUBUNIT: Interacts with PKD2. Interacts with PRKX; involved in differentiation and controlled morphogenesis of the kidney. Interacts with NPHP1 (via SH3 domain).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein. Cell projection, cilium (By similarity). Note=PKD1 localization to the plasma and ciliary membranes requires PKD2, is independent of PKD2 channel activity, and involves stimulation of PKD1 autoproteolytic cleavage at the GPS domain.
DOMAIN: The LDL-receptor class A domain is atypical; the potential calcium-binding site is missing.
PTM: After synthesis, undergoes cleavage between Leu-3048 and Thr- 3049 in the GPS domain. Cleavage at the GPS domain occurs through a cis-autoproteolytic mechanism involving an ester-intermediate via N-O acyl rearrangement. This process takes place in the early secretory pathway, depends on initial N-glycosylation, and requires the REJ domain. There is evidence that cleavage at GPS domain is incomplete. Uncleaved and cleaved products may have different functions in vivo.
DISEASE: Defects in PKD1 are the cause of polycystic kidney disease 1 (PKD1) [MIM:173900]. PKD1 is characterized by progressive formation and enlargement of cysts in both kidneys, typically leading to end-stage renal disease in adult life. Cysts also occurs in the liver and other organs. Its prevalence is estimated at about 1/1000.
SIMILARITY: Belongs to the polycystin family.
SIMILARITY: Contains 1 C-type lectin domain.
SIMILARITY: Contains 1 GPS domain.
SIMILARITY: Contains 1 LDL-receptor class A domain.
SIMILARITY: Contains 2 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 LRRCT domain.
SIMILARITY: Contains 1 LRRNT domain.
SIMILARITY: Contains 17 PKD domains.
SIMILARITY: Contains 1 PLAT domain.
SIMILARITY: Contains 1 REJ domain.
SIMILARITY: Contains 1 WSC domain.
CAUTION: Variant Cys-2379 has been originally described as a benign polymorphism (PubMed:10854095). However, it is a likely pathogenic mutation (PubMed:PubMed:22508176).
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/PKD1";
WEB RESOURCE: Name=Functional Glycomics Gateway - Glycan Binding; Note=Polycystin-1; URL="http://www.functionalglycomics.org/glycomics/GBPServlet?&operationType=view&cbpId=cbp_hum_Ctlect_204";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PKD1
Diseases sorted by gene-association score: polycystic kidney disease 1* (1288), cerebral aneurysms* (405), autosomal dominant polycystic kidney disease* (328), polycystic kidney disease 4, with or without hepatic disease* (247), hypertension, early-onset, autosomal dominant, with exacerbation in pregnancy* (231), polycystic kidney disease 1, autosomal dominant* (130), hypertension, essential* (121), polycystic kidney disease (103), kidney disease (78), chromosome 16p13.3 deletion syndrome* (71), cystic kidney disease (24), polycystic kidney disease 2 (19), intracranial berry aneurysm (19), tuberous sclerosis (16), polycystic liver disease (15), polycystic kidney disease, infantile severe, with tuberous sclerosis* (14), caroli disease (14), polycystic liver disease 1 (12), polycystic kidney disease 3 (11), intracranial aneurysm (9), steatocystoma multiplex (9), end stage renal failure (8), acrofacial dysostosis (7), nephronophthisis 1, juvenile (6), congenital hepatic fibrosis (6), autosomal genetic disease (5), bardet-biedl syndrome 17 (4), nephronophthisis (3), chronic kidney failure (2), bardet-biedl syndrome (2), autosomal dominant disease (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 191.58 RPKM in Brain - Cerebellum
Total median expression: 1092.47 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -121.60209-0.582 Picture PostScript Text
3' UTR -446.701019-0.438 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001304 - C-type_lectin
IPR016186 - C-type_lectin-like
IPR016187 - C-type_lectin_fold
IPR000483 - Cys-rich_flank_reg_C
IPR000203 - GPS_dom
IPR001611 - Leu-rich_rpt
IPR003591 - Leu-rich_rpt_typical-subtyp
IPR008976 - Lipase_LipOase
IPR001024 - LipOase_LH2
IPR000372 - LRR-contain_N
IPR022409 - PKD/Chitinase_dom
IPR002859 - PKD/REJ-like
IPR013122 - PKD1_2_channel
IPR000434 - PKD_1
IPR000601 - PKD_dom
IPR006228 - Polycystin_cat
IPR014010 - REJ-like
IPR002889 - WSC_carb-bd
IPR013994 - WSC_carb-bd_subgr

Pfam Domains:
PF00059 - Lectin C-type domain
PF00801 - PKD domain
PF01463 - Leucine rich repeat C-terminal domain
PF01477 - PLAT/LH2 domain
PF01822 - WSC domain
PF02010 - REJ domain
PF08016 - Polycystin cation channel
PF13855 - Leucine rich repeat
PF18911 - PKD domain

SCOP Domains:
48726 - Immunoglobulin
49265 - Fibronectin type III
49299 - PKD domain
49723 - Lipase/lipooxygenase domain (PLAT/LH2 domain)
50956 - Thermostable phytase (3-phytase)
52047 - RNI-like
52058 - L domain-like
52075 - Outer arm dynein light chain 1
55961 - Bet v1-like
56436 - C-type lectin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1B4R - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P98161
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005262 calcium channel activity
GO:0005515 protein binding
GO:0019901 protein kinase binding
GO:0019904 protein domain specific binding
GO:0030246 carbohydrate binding
GO:0044325 ion channel binding

Biological Process:
GO:0001502 cartilage condensation
GO:0001568 blood vessel development
GO:0001701 in utero embryonic development
GO:0001822 kidney development
GO:0001889 liver development
GO:0001892 embryonic placenta development
GO:0006611 protein export from nucleus
GO:0006807 nitrogen compound metabolic process
GO:0006816 calcium ion transport
GO:0007050 cell cycle arrest
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007160 cell-matrix adhesion
GO:0007161 calcium-independent cell-matrix adhesion
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007259 JAK-STAT cascade
GO:0007507 heart development
GO:0009653 anatomical structure morphogenesis
GO:0018105 peptidyl-serine phosphorylation
GO:0021510 spinal cord development
GO:0021915 neural tube development
GO:0030010 establishment of cell polarity
GO:0030155 regulation of cell adhesion
GO:0031659 positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle
GO:0032092 positive regulation of protein binding
GO:0034405 response to fluid shear stress
GO:0036303 lymph vessel morphogenesis
GO:0042994 cytoplasmic sequestering of transcription factor
GO:0043588 skin development
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048565 digestive tract development
GO:0048754 branching morphogenesis of an epithelial tube
GO:0048806 genitalia development
GO:0050982 detection of mechanical stimulus
GO:0051216 cartilage development
GO:0060236 regulation of mitotic spindle organization
GO:0060428 lung epithelium development
GO:0060674 placenta blood vessel development
GO:0061136 regulation of proteasomal protein catabolic process
GO:0070588 calcium ion transmembrane transport
GO:0072001 renal system development
GO:0072164 mesonephric tubule development
GO:0072177 mesonephric duct development
GO:0072205 metanephric collecting duct development
GO:0072218 metanephric ascending thin limb development
GO:0072237 metanephric proximal tubule development
GO:0072287 metanephric distal tubule morphogenesis
GO:0098609 cell-cell adhesion

Cellular Component:
GO:0000139 Golgi membrane
GO:0002133 polycystin complex
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005929 cilium
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016323 basolateral plasma membrane
GO:0016328 lateral plasma membrane
GO:0030660 Golgi-associated vesicle membrane
GO:0031514 motile cilium
GO:0042995 cell projection
GO:0060170 ciliary membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  U24497 - Human autosomal dominant polycystic kidney disease protein 1 (PKD1) mRNA, complete cds.
L33243 - Homo sapiens polycystic kidney disease 1 protein (PKD1) mRNA, complete cds.
JD068037 - Sequence 49061 from Patent EP1572962.
JD451378 - Sequence 432402 from Patent EP1572962.
JD152060 - Sequence 133084 from Patent EP1572962.
JD135204 - Sequence 116228 from Patent EP1572962.
JD112664 - Sequence 93688 from Patent EP1572962.
JD076091 - Sequence 57115 from Patent EP1572962.
JD388661 - Sequence 369685 from Patent EP1572962.
JD431626 - Sequence 412650 from Patent EP1572962.
JD492917 - Sequence 473941 from Patent EP1572962.
JD451074 - Sequence 432098 from Patent EP1572962.
JD409635 - Sequence 390659 from Patent EP1572962.
JD387045 - Sequence 368069 from Patent EP1572962.
JD149780 - Sequence 130804 from Patent EP1572962.
JD481824 - Sequence 462848 from Patent EP1572962.
JD561185 - Sequence 542209 from Patent EP1572962.
JD035037 - Sequence 16061 from Patent EP1572962.
JD219594 - Sequence 200618 from Patent EP1572962.
JD122088 - Sequence 103112 from Patent EP1572962.
JD161997 - Sequence 143021 from Patent EP1572962.
JD527805 - Sequence 508829 from Patent EP1572962.
JD086674 - Sequence 67698 from Patent EP1572962.
JD483534 - Sequence 464558 from Patent EP1572962.
JD361986 - Sequence 343010 from Patent EP1572962.
JD429696 - Sequence 410720 from Patent EP1572962.
JD368413 - Sequence 349437 from Patent EP1572962.
AK309422 - Homo sapiens cDNA, FLJ99463.
AB209025 - Homo sapiens mRNA for Polycystin 1 precursor variant protein.
AB209675 - Homo sapiens mRNA for polycystin 1 isoform 2 precursor variant protein.
LP986459 - Sequence 97 from Patent EP3201339.
MA014119 - JP 2017536338-A/97: TARGETED AUGMENTATION OF NUCLEAR GENE OUTPUT.
LP986457 - Sequence 95 from Patent EP3201339.
MA014117 - JP 2017536338-A/95: TARGETED AUGMENTATION OF NUCLEAR GENE OUTPUT.
LP986455 - Sequence 93 from Patent EP3201339.
MA014115 - JP 2017536338-A/93: TARGETED AUGMENTATION OF NUCLEAR GENE OUTPUT.
LP986454 - Sequence 92 from Patent EP3201339.
MA014114 - JP 2017536338-A/92: TARGETED AUGMENTATION OF NUCLEAR GENE OUTPUT.
LP986452 - Sequence 90 from Patent EP3201339.
MA014112 - JP 2017536338-A/90: TARGETED AUGMENTATION OF NUCLEAR GENE OUTPUT.
LP986450 - Sequence 88 from Patent EP3201339.
MA014110 - JP 2017536338-A/88: TARGETED AUGMENTATION OF NUCLEAR GENE OUTPUT.
JD317694 - Sequence 298718 from Patent EP1572962.
JD520817 - Sequence 501841 from Patent EP1572962.
JD137644 - Sequence 118668 from Patent EP1572962.
JD290135 - Sequence 271159 from Patent EP1572962.
JD423344 - Sequence 404368 from Patent EP1572962.
JD128355 - Sequence 109379 from Patent EP1572962.
JD054738 - Sequence 35762 from Patent EP1572962.
JD448244 - Sequence 429268 from Patent EP1572962.
JD141849 - Sequence 122873 from Patent EP1572962.
JD394760 - Sequence 375784 from Patent EP1572962.
JD483504 - Sequence 464528 from Patent EP1572962.
DQ600103 - Homo sapiens piRNA piR-38169, complete sequence.
JD124684 - Sequence 105708 from Patent EP1572962.
JD476391 - Sequence 457415 from Patent EP1572962.
JD144195 - Sequence 125219 from Patent EP1572962.
JD150029 - Sequence 131053 from Patent EP1572962.
JD380353 - Sequence 361377 from Patent EP1572962.
JD131263 - Sequence 112287 from Patent EP1572962.
JD074668 - Sequence 55692 from Patent EP1572962.
JD083851 - Sequence 64875 from Patent EP1572962.
JD216773 - Sequence 197797 from Patent EP1572962.
JD289087 - Sequence 270111 from Patent EP1572962.
JD364016 - Sequence 345040 from Patent EP1572962.
JD496431 - Sequence 477455 from Patent EP1572962.
JD124998 - Sequence 106022 from Patent EP1572962.
JD220747 - Sequence 201771 from Patent EP1572962.
JD231211 - Sequence 212235 from Patent EP1572962.
JD399588 - Sequence 380612 from Patent EP1572962.
JD394732 - Sequence 375756 from Patent EP1572962.
JD535946 - Sequence 516970 from Patent EP1572962.
JD108599 - Sequence 89623 from Patent EP1572962.
JD142272 - Sequence 123296 from Patent EP1572962.
JD041963 - Sequence 22987 from Patent EP1572962.
JD148743 - Sequence 129767 from Patent EP1572962.
JD546498 - Sequence 527522 from Patent EP1572962.
JD057103 - Sequence 38127 from Patent EP1572962.
JD081332 - Sequence 62356 from Patent EP1572962.
JD131925 - Sequence 112949 from Patent EP1572962.
JD458624 - Sequence 439648 from Patent EP1572962.
JD200570 - Sequence 181594 from Patent EP1572962.
JD108978 - Sequence 90002 from Patent EP1572962.
JD142690 - Sequence 123714 from Patent EP1572962.
JD407148 - Sequence 388172 from Patent EP1572962.
JD185626 - Sequence 166650 from Patent EP1572962.
JD185188 - Sequence 166212 from Patent EP1572962.
JD257328 - Sequence 238352 from Patent EP1572962.
JD172744 - Sequence 153768 from Patent EP1572962.
JD389746 - Sequence 370770 from Patent EP1572962.
JD059954 - Sequence 40978 from Patent EP1572962.
JD227440 - Sequence 208464 from Patent EP1572962.
JD498004 - Sequence 479028 from Patent EP1572962.
JD051791 - Sequence 32815 from Patent EP1572962.
JD431945 - Sequence 412969 from Patent EP1572962.
JD133140 - Sequence 114164 from Patent EP1572962.
JD192880 - Sequence 173904 from Patent EP1572962.
JD462095 - Sequence 443119 from Patent EP1572962.
JD129333 - Sequence 110357 from Patent EP1572962.
DL489985 - Novel nucleic acids.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P98161 (Reactome details) participates in the following event(s):

R-HSA-5620914 ARF4:GTP binds VxPx-motifs of membrane proteins
R-HSA-5620918 ASAP1 dimer binds membrane proteins
R-HSA-5623519 RAB3IP and RAB8A bind to the ciliary targeting complex
R-HSA-5623513 ASAP1 stimulates GTPase activity of ARF4
R-HSA-5620921 ASAP1 recruits RAB11FIP3 and RAB11 to the ciliary targeting complex
R-HSA-5623521 RAB3IP stimulates nucleotide exchange on RAB8A
R-HSA-5623524 The exocyst complex binds to RAB3IP in the ciliary targeting complex
R-HSA-5620916 VxPx cargo-targeting to cilium
R-HSA-5620920 Cargo trafficking to the periciliary membrane
R-HSA-5617833 Cilium Assembly
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000262304.1, ENST00000262304.2, ENST00000262304.3, ENST00000262304.4, ENST00000262304.5, ENST00000262304.6, ENST00000262304.7, ENST00000262304.8, NM_001009944, P98161, PKD1 , PKD1_HUMAN, Q15140, Q15141, uc317gyv.1, uc317gyv.2
UCSC ID: ENST00000262304.9_11
RefSeq Accession: NM_001009944.3
Protein: P98161 (aka PKD1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PKD1:
pkd-ad (Polycystic Kidney Disease, Autosomal Dominant)
taa (Heritable Thoracic Aortic Disease Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.