PKD1 polycystin 1, transient receptor potential channel interacting [Homo sapiens (human)] - Gene

Summary

Official Symbol: PKD1provided by HGNC
Official Full Name: polycystin 1, transient receptor potential channel interactingprovided by HGNC
Primary source: HGNC:HGNC:9008
See related: Ensembl:ENSG00000008710 MIM:601313; AllianceGenome:HGNC:9008
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: PBP; PC1; Pc-1; TRPP1
Summary: This gene encodes a member of the polycystin protein family. The encoded glycoprotein contains a large N-terminal extracellular region, multiple transmembrane domains and a cytoplasmic C-tail. It is an integral membrane protein that functions as a regulator of calcium permeable cation channels and intracellular calcium homoeostasis. It is also involved in cell-cell/matrix interactions and may modulate G-protein-coupled signal-transduction pathways. It plays a role in renal tubular development, and mutations in this gene cause autosomal dominant polycystic kidney disease type 1 (ADPKD1). ADPKD1 is characterized by the growth of fluid-filled cysts that replace normal renal tissue and result in end-stage renal failure. Splice variants encoding different isoforms have been noted for this gene. Also, six pseudogenes, closely linked in a known duplicated region on chromosome 16p, have been described. [provided by RefSeq, Oct 2008]
Annotation information: Annotation category: suggests misassembly
Expression: Ubiquitous expression in endometrium (RPKM 11.1), fat (RPKM 9.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p13.3

Exon count:: 51

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (2088708..2135898, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (2108809..2158372, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (2138709..2185899, complement)

Chromosome 16 - NC_000016.10 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 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?

PKD1 Truncating Mutations Accelerate eGFR Decline in Autosomal Dominant Polycystic Kidney Disease Patients.
Title: PKD1 Truncating Mutations Accelerate eGFR Decline in Autosomal Dominant Polycystic Kidney Disease Patients.
Comprehensive Analysis of PKD1 and PKD2 by Long-Read Sequencing in Autosomal Dominant Polycystic Kidney Disease.
Title: Comprehensive Analysis of PKD1 and PKD2 by Long-Read Sequencing in Autosomal Dominant Polycystic Kidney Disease.
Mutation Analysis of PKD1 and PKD2 Genes in a Large Italian Cohort Reveals Novel Pathogenic Variants Including a Novel Complex Rearrangement.
Title: Mutation Analysis of PKD1 and PKD2 Genes in a Large Italian Cohort Reveals Novel Pathogenic Variants Including a Novel Complex Rearrangement.
A de novo PKD1 mutation in a Chinese family with autosomal dominant polycystic kidney disease.
Title: A de novo PKD1 mutation in a Chinese family with autosomal dominant polycystic kidney disease.
Prenatal diagnosis of polycystic kidney caused by biallelic hypomorphic variants in the PKD1 gene.
Title: Prenatal diagnosis of polycystic kidney caused by biallelic hypomorphic variants in the PKD1 gene.
circSSPO boosts growth of esophageal squamous cell carcinoma through upregulation of micrRNA-6820-5p-mediated KLK8 and PKD1 expression.
Title: circSSPO boosts growth of esophageal squamous cell carcinoma through upregulation of micrRNA-6820-5p-mediated KLK8 and PKD1 expression.
Polycystin-1 Interacting Protein-1 (CU062) Interacts with the Ectodomain of Polycystin-1 (PC1).
Title: Polycystin-1 Interacting Protein-1 (CU062) Interacts with the Ectodomain of Polycystin-1 (PC1).
A novel heterozygous PKD1 variant causing alternative splicing in a Chinese family with autosomal dominant polycystic kidney disease.
Title: A novel heterozygous PKD1 variant causing alternative splicing in a Chinese family with autosomal dominant polycystic kidney disease.
Targeted Next Generation Sequencing Revealed Novel Variants in the PKD1 and PKD2 Genes of Iranian Patients with Autosomal Dominant Polycystic Kidney Disease.
Title: Targeted Next Generation Sequencing Revealed Novel Variants in the PKD1 and PKD2 Genes of Iranian Patients with Autosomal Dominant Polycystic Kidney Disease.
PKD1 Mutation Is a Biomarker for Autosomal Dominant Polycystic Kidney Disease.
Title: PKD1 Mutation Is a Biomarker for Autosomal Dominant Polycystic Kidney Disease.

Submit: New GeneRIF Correction See all GeneRIFs (262)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Polycystic kidney disease, adult type MedGen: C3149841 OMIM: 173900 GeneReviews: Polycystic Kidney Disease, Autosomal Dominant	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-06-10) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-06-10) ClinGen Genome Curation PagePubMed

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of polycystic kidney disease 1, autosomal dominant (PKD1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D16S3252 (e-PCR)
- UniSTS:473411

RH68414 (e-PCR)
- UniSTS:51785

SHGC-30026 (e-PCR)
- UniSTS:72026

STS-U24497 (e-PCR)
- UniSTS:25178

GDB:641995 (e-PCR)
- UniSTS:158554

PMC356914P1 (e-PCR)
- UniSTS:273266

PMC356914P2 (e-PCR)
- UniSTS:273267

GDB:378419 (e-PCR)
- UniSTS:157074

STS-L48546 (e-PCR)
- UniSTS:34465

D10Bir17 (e-PCR), detects polymorphism
- UniSTS:141482

GDB:626063 (e-PCR)
- UniSTS:158382

D16S3394 (e-PCR)
- UniSTS:12991

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables Wnt receptor activity	IDA Inferred from Direct Assay more info	PubMed
contributes_to calcium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables calcium channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
contributes_to monoatomic cation channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription regulator inhibitor activity	ISS Inferred from Sequence or Structural Similarity more info
enables transmembrane transporter binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in anatomical structure morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in branching morphogenesis of an epithelial tube	IDA Inferred from Direct Assay more info	PubMed
involved_in calcium ion transmembrane transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in calcium ion transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in calcium-independent cell-matrix adhesion	TAS Traceable Author Statement more info	PubMed
involved_in cartilage condensation	IEA Inferred from Electronic Annotation more info
involved_in cartilage development	IEP Inferred from Expression Pattern more info	PubMed
involved_in cell surface receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in cell surface receptor signaling pathway via JAK-STAT	ISO Inferred from Sequence Orthology more info
involved_in cell surface receptor signaling pathway via JAK-STAT	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-matrix adhesion	TAS Traceable Author Statement more info	PubMed
involved_in detection of mechanical stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in digestive tract development	IEP Inferred from Expression Pattern more info	PubMed
involved_in embryonic placenta development	ISS Inferred from Sequence or Structural Similarity more info
involved_in establishment of epithelial cell polarity	IEA Inferred from Electronic Annotation more info
involved_in genitalia development	IEP Inferred from Expression Pattern more info	PubMed
involved_in heart development	IEP Inferred from Expression Pattern more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	TAS Traceable Author Statement more info	PubMed
involved_in in utero embryonic development	ISS Inferred from Sequence or Structural Similarity more info
involved_in kidney development	ISS Inferred from Sequence or Structural Similarity more info
involved_in liver development	IEA Inferred from Electronic Annotation more info
involved_in lung epithelium development	IEP Inferred from Expression Pattern more info	PubMed
involved_in lymph vessel morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in mesonephric duct development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mesonephric tubule development	IEP Inferred from Expression Pattern more info	PubMed
involved_in metanephric ascending thin limb development	IEP Inferred from Expression Pattern more info	PubMed
involved_in metanephric collecting duct development	IEP Inferred from Expression Pattern more info	PubMed
involved_in metanephric distal tubule morphogenesis	IEP Inferred from Expression Pattern more info	PubMed
involved_in metanephric proximal tubule development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mitocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in neural tube development	IEP Inferred from Expression Pattern more info	PubMed
involved_in nitrogen cycle metabolic process	IEA Inferred from Electronic Annotation more info
involved_in peptidyl-serine phosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in placenta blood vessel development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytosolic calcium ion concentration	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein export from nucleus	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein heterotetramerization	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of regulation of G1/S transition of mitotic cell cycle	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mitotic spindle organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of proteasomal protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in response to fluid shear stress	IEA Inferred from Electronic Annotation more info
involved_in skin development	IEP Inferred from Expression Pattern more info	PubMed
involved_in spinal cord development	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in Golgi membrane	TAS Traceable Author Statement more info
located_in Golgi-associated vesicle membrane	TAS Traceable Author Statement more info
located_in basolateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
part_of calcium channel complex	IDA Inferred from Direct Assay more info	PubMed
part_of cation channel complex	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in ciliary membrane	TAS Traceable Author Statement more info
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular exosome	IDA Inferred from Direct Assay more info	PubMed
located_in lateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in migrasome	IDA Inferred from Direct Assay more info	PubMed
located_in motile cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
part_of polycystin complex	IPI Inferred from Physical Interaction more info	PubMed
part_of polycystin complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: polycystin-1

Names: autosomal dominant polycystic kidney disease 1 protein; polycystic kidney disease 1 (autosomal dominant); polycystic kidney disease-associated protein; transient receptor potential cation channel, subfamily P, member 1

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_008617.1 RefSeqGene

Range

5001..54511

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000296.4 → NP_000287.4 polycystin-1 isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate acceptor splice site, 3 nt downstream of that used by transcript variant 1, at the junction of one of the coding exons. This results in an isoform (2) that is 1 aa shorter than isoform 1.

Source sequence(s)

AC009065, AC093513

Consensus CDS

CCDS45385.1

UniProtKB/TrEMBL

Q15142

Related

ENSP00000399501.1, ENST00000423118.5

Conserved Domains (6) summary

TIGR00864
Location:97 → 2728

PCC; polycystin cation channel protein

smart00303
Location:3011 → 3060

GPS; G-protein-coupled receptor proteolytic site domain

COG4886
Location:50 → 126

LRR; Leucine-rich repeat (LRR) protein [Transcription]

cd01752
Location:3118 → 3237

PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...

sd00031
Location:70 → 92

LRR_1; leucine-rich repeat [structural motif]

pfam08016
Location:3712 → 4112

PKD_channel; Polycystin cation channel
NM_001009944.3 → NP_001009944.3 polycystin-1 isoform 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC009065, AC093513

Consensus CDS

CCDS32369.1

UniProtKB/Swiss-Prot

P98161, Q15140, Q15141

UniProtKB/TrEMBL

Q15142

Related

ENSP00000262304.4, ENST00000262304.9

Conserved Domains (6) summary

TIGR00864
Location:97 → 2728

PCC; polycystin cation channel protein

smart00303
Location:3011 → 3060

GPS; G-protein-coupled receptor proteolytic site domain

COG4886
Location:50 → 126

LRR; Leucine-rich repeat (LRR) protein [Transcription]

cd01752
Location:3118 → 3237

PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...

sd00031
Location:70 → 92

LRR_1; leucine-rich repeat [structural motif]

pfam08016
Location:3713 → 4113

PKD_channel; Polycystin cation channel

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

2088708..2135898 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047434209.1 → XP_047290165.1 polycystin-1 isoform X2
XM_047434208.1 → XP_047290164.1 polycystin-1 isoform X1
XM_047434211.1 → XP_047290167.1 polycystin-1 isoform X6
XM_011522529.3 → XP_011520831.1 polycystin-1 isoform X4

UniProtKB/TrEMBL

Q15142

Conserved Domains (11) summary

TIGR00864
Location:115 → 2746

PCC; polycystin cation channel protein

smart00303
Location:3029 → 3078

GPS; G-protein-coupled receptor proteolytic site domain

smart00034
Location:424 → 549

CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)

smart00082
Location:143 → 195

LRRCT; Leucine rich repeat C-terminal domain

smart00089
Location:1146 → 1227

PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins

smart00321
Location:195 → 289

WSC; present in yeast cell wall integrity and stress response component proteins

cd01752
Location:3136 → 3255

PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...

sd00031
Location:111 → 134

LRR_1; leucine-rich repeat [structural motif]

pfam00801
Location:1741 → 1810

PKD; PKD domain

pfam04479
Location:3892 → 3974

RTA1; RTA1 like protein

pfam08016
Location:3728 → 4130

PKD_channel; Polycystin cation channel
XM_011522528.4 → XP_011520830.1 polycystin-1 isoform X3

UniProtKB/TrEMBL

Q15142

Conserved Domains (11) summary

TIGR00864
Location:115 → 2746

PCC; polycystin cation channel protein

smart00303
Location:3029 → 3078

GPS; G-protein-coupled receptor proteolytic site domain

smart00034
Location:424 → 549

CLECT; C-type lectin (CTL) or carbohydrate-recognition domain (CRD)

smart00082
Location:143 → 195

LRRCT; Leucine rich repeat C-terminal domain

smart00089
Location:1146 → 1227

PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins

smart00321
Location:195 → 289

WSC; present in yeast cell wall integrity and stress response component proteins

cd01752
Location:3136 → 3255

PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...

sd00031
Location:111 → 134

LRR_1; leucine-rich repeat [structural motif]

pfam00801
Location:1741 → 1810

PKD; PKD domain

pfam04479
Location:3893 → 3975

RTA1; RTA1 like protein

pfam08016
Location:3729 → 4131

PKD_channel; Polycystin cation channel
XM_047434210.1 → XP_047290166.1 polycystin-1 isoform X5
XM_047434212.1 → XP_047290168.1 polycystin-1 isoform X7
XM_047434213.1 → XP_047290169.1 polycystin-1 isoform X9
XM_011522537.2 → XP_011520839.1 polycystin-1 isoform X8

UniProtKB/TrEMBL

Q15142

Conserved Domains (8) summary

smart00303
Location:2037 → 2086

GPS; G-protein-coupled receptor proteolytic site domain

smart00089
Location:154 → 235

PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins

COG3291
Location:81 → 307

COG3291; PKD repeat [Function unknown]

cd01752
Location:2144 → 2263

PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...

pfam00801
Location:749 → 818

PKD; PKD domain

pfam02010
Location:1197 → 1640

REJ; REJ domain

pfam04479
Location:2901 → 2983

RTA1; RTA1 like protein

pfam08016
Location:2737 → 3139

PKD_channel; Polycystin cation channel
XM_005255370.4 → XP_005255427.1 polycystin-1 isoform X10

Conserved Domains (8) summary

smart00303
Location:1996 → 2045

GPS; G-protein-coupled receptor proteolytic site domain

smart00089
Location:113 → 194

PKD; Repeats in polycystic kidney disease 1 (PKD1) and other proteins

COG3291
Location:40 → 266

COG3291; PKD repeat [Function unknown]

cd01752
Location:2103 → 2222

PLAT_polycystin; PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological ...

pfam00801
Location:708 → 777

PKD; PKD domain

pfam02010
Location:1156 → 1599

REJ; REJ domain

pfam04479
Location:2860 → 2942

RTA1; RTA1 like protein

pfam08016
Location:2696 → 3098

PKD_channel; Polycystin cation channel