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PKD2L1 polycystin 2 like 1, transient receptor potential cation channel [ Homo sapiens (human) ]

Gene ID: 9033, updated on 14-Aug-2021

Summary

Official Symbol
PKD2L1provided by HGNC
Official Full Name
polycystin 2 like 1, transient receptor potential cation channelprovided by HGNC
Primary source
HGNC:HGNC:9011
See related
Ensembl:ENSG00000107593 MIM:604532
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
PCL; PKDL; PKD2L; TRPP3
Summary
This gene encodes a member of the polycystin protein family. The encoded protein contains multiple transmembrane domains, and cytoplasmic N- and C-termini. The protein may be an integral membrane protein involved in cell-cell/matrix interactions. This protein functions as a calcium-regulated nonselective cation channel. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
Expression
Biased expression in spleen (RPKM 1.0), testis (RPKM 0.9) and 7 other tissues See more
Orthologs
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Genomic context

See PKD2L1 in Genome Data Viewer
Location:
10q24.31
Exon count:
20
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (100288145..100347030, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (102047906..102089985, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene CWF19 like cell cycle control factor 1 Neighboring gene RNA, U6 small nuclear 422, pseudogene Neighboring gene biogenesis of lysosomal organelles complex 1 subunit 2 Neighboring gene stearoyl-CoA desaturase Neighboring gene oligodendrocyte maturation-associated long intergenic non-coding RNA

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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
An atlas of genetic influences on human blood metabolites.
GeneReviews: Not available
Genetic determinants influencing human serum metabolome among African Americans.
GeneReviews: Not available
Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
GeneReviews: Not available
Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
GeneReviews: Not available
Human metabolic individuality in biomedical and pharmaceutical research.
GeneReviews: Not available
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables alpha-actinin binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables calcium activated cation channel activity IDA
Inferred from Direct Assay
more info
PubMed 
enables calcium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables calcium channel activity IDA
Inferred from Direct Assay
more info
PubMed 
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
enables calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables calcium-activated potassium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables calcium-activated potassium channel activity IDA
Inferred from Direct Assay
more info
PubMed 
enables cation channel activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to cation transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables cytoskeletal protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables identical protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables muscle alpha-actinin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables muscle alpha-actinin binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables sodium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables sodium channel activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to sour taste receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
involved_in calcium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
involved_in cation transport ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cellular response to acidic pH ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in detection of chemical stimulus involved in sensory perception of sour taste ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in detection of chemical stimulus involved in sensory perception of taste ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in detection of mechanical stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in inorganic cation transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in potassium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in potassium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in protein homotetramerization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to water IEA
Inferred from Electronic Annotation
more info
 
involved_in sensory perception of sour taste IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in sodium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
part_of calcium channel complex IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with cell surface ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in ciliary membrane IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
 
located_in endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
located_in integral component of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in non-motile cilium IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
part_of receptor complex ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
polycystic kidney disease 2-like 1 protein
Names
polycystin-2 homolog
polycystin-2L1
polycystin-L
polycystin-L1
transient receptor potential cation channel, subfamily P, member 3

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

  1. NG_047099.1 RefSeqGene

    Range
    21297..63376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001253837.2NP_001240766.1  polycystic kidney disease 2-like 1 protein isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice junction at the 5' end of coding exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AF073481, BC025665, DQ084244
    UniProtKB/Swiss-Prot
    Q9P0L9
    UniProtKB/TrEMBL
    Q1L4F0
    Conserved Domains (1) summary
    pfam08016
    Location:99520
    PKD_channel; Polycystin cation channel
  2. NM_016112.3NP_057196.2  polycystic kidney disease 2-like 1 protein isoform 1

    See identical proteins and their annotated locations for NP_057196.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL139819
    Consensus CDS
    CCDS7492.1
    UniProtKB/Swiss-Prot
    Q9P0L9
    Related
    ENSP00000325296.3, ENST00000318222.4
    Conserved Domains (2) summary
    pfam08016
    Location:147567
    PKD_channel; Polycystin cation channel
    pfam18109
    Location:702735
    Fer4_24; Ferredoxin I 4Fe-4S cluster domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    100288145..100347030 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017016875.2XP_016872364.1  polycystic kidney disease 2-like 1 protein isoform X1

    Conserved Domains (1) summary
    pfam08016
    Location:49470
    PKD_channel; Polycystin cation channel
  2. XM_011540323.3XP_011538625.1  polycystic kidney disease 2-like 1 protein isoform X1

    See identical proteins and their annotated locations for XP_011538625.1

    Conserved Domains (1) summary
    pfam08016
    Location:49470
    PKD_channel; Polycystin cation channel
  3. XM_011540325.3XP_011538627.1  polycystic kidney disease 2-like 1 protein isoform X2

    Conserved Domains (1) summary
    pfam08016
    Location:26447
    PKD_channel; Polycystin cation channel
  4. XM_017016876.1XP_016872365.1  polycystic kidney disease 2-like 1 protein isoform X3

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