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Aliases for PKD2L1 Gene

Aliases for PKD2L1 Gene

  • Polycystin 2 Like 1, Transient Receptor Potential Cation Channel 2 3 5
  • Transient Receptor Potential Cation Channel, Subfamily P, Member 3 2 3
  • Polycystin-2 Homolog 3 4
  • Polycystin-2L1 3 4
  • Polycystin-L1 3 4
  • Polycystin-L 3 4
  • PKD2L 3 4
  • TRPP3 3 4
  • PKDL 3 4
  • Polycystic Kidney Disease 2-Like 1 Protein 3
  • Polycystic Kidney Disease 2-Like 1 2
  • PCL 3

External Ids for PKD2L1 Gene

Previous HGNC Symbols for PKD2L1 Gene

  • PKD2L
  • PKDL

Previous GeneCards Identifiers for PKD2L1 Gene

  • GC10M100941
  • GC10M101281
  • GC10M102179
  • GC10M101712
  • GC10M102037
  • GC10M095676
  • GC10M102047

Summaries for PKD2L1 Gene

Entrez Gene Summary for PKD2L1 Gene

  • 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]

GeneCards Summary for PKD2L1 Gene

PKD2L1 (Polycystin 2 Like 1, Transient Receptor Potential Cation Channel) is a Protein Coding gene. Diseases associated with PKD2L1 include Polycystic Kidney Disease and Polycystic Kidney Disease 2. Among its related pathways are Taste transduction. GO annotations related to this gene include calcium ion binding and ion channel activity. An important paralog of this gene is PKD2.

UniProtKB/Swiss-Prot for PKD2L1 Gene

  • Pore-forming subunit of a ciliary calcium channel that controls calcium concentration within primary cilia without affecting cytoplasmic calcium concentration. Forms a heterodimer with PKD1L1 in primary cilia and forms a calcium-permeant ciliary channel that regulates sonic hedgehog/SHH signaling and GLI2 transcription. May act as a sour taste receptor by forming a calcium channel with PKD1L3 in gustatory cells; however, its contribution to sour taste perception is unclear in vivo and may be indirect.

Gene Wiki entry for PKD2L1 Gene

Additional gene information for PKD2L1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PKD2L1 Gene

Genomics for PKD2L1 Gene

Regulatory Elements for PKD2L1 Gene

Enhancers for PKD2L1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10H100341 1.5 Ensembl ENCODE dbSUPER 24.7 +4.5 4503 2 HDGF FOXA2 ARID4B DMAP1 ZNF2 YY1 ZNF143 DEK REST PPARG PKD2L1 WNT8B CWF19L1 RNU6-422P ENSG00000231188 BLOC1S2
GH10H100345 1.4 ENCODE dbSUPER 23.8 -2.0 -1990 6 MLX ARID4B SIN3A DMAP1 YY1 FOS PAF1 SP3 SP5 ZHX2 PKD2L1 SEC31B LOC101927300 SCD OLMALINC
GH10H100339 1.2 Ensembl ENCODE dbSUPER 24.8 +7.2 7246 0 CTCF FOXA2 RAD21 CC2D1A FOXK2 EED ZNF143 RUNX3 IKZF2 GATAD2A PKD2L1 SEC31B HIF1AN NDUFB8 ENSG00000255339 ENSG00000231188 BLOC1S2
GH10H100333 0.7 dbSUPER 23.2 +12.2 12160 2 GTF2F1 TBP JUN MAX RAD21 ZFHX2 PRDM10 EGR2 TCF7L2 HLF PKD2L1 SEC31B ENSG00000231188 BLOC1S2
GH10H100356 0.8 ENCODE dbSUPER 19.3 -10.8 -10795 1 PAF1 PRDM6 POLR2A ZNF366 PRDM1 SUPT5H PKD2L1 SCD OLMALINC
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PKD2L1 on UCSC Golden Path with GeneCards custom track

Genomic Location for PKD2L1 Gene

Chromosome:
10
Start:
100,288,145 bp from pter
End:
100,346,524 bp from pter
Size:
58,380 bases
Orientation:
Minus strand

Genomic View for PKD2L1 Gene

Genes around PKD2L1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PKD2L1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PKD2L1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PKD2L1 Gene

Proteins for PKD2L1 Gene

  • Protein details for PKD2L1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P0L9-PK2L1_HUMAN
    Recommended name:
    Polycystic kidney disease 2-like 1 protein
    Protein Accession:
    Q9P0L9
    Secondary Accessions:
    • O75972
    • Q5W039
    • Q9UP35
    • Q9UPA2

    Protein attributes for PKD2L1 Gene

    Size:
    805 amino acids
    Molecular mass:
    91982 Da
    Quaternary structure:
    • Homotrimer; trimerization is independent of calcium-binding. Calcium channels are probably composed of 3 subunit of PKD2L1 and 1 subunit of some PKD1 protein (PKD1, PKD1L1, PKD1L2 or PKDL3). Interacts with PKD1. Interacts with PKD1L1; to form ciliary calcium channel. Interacts with PKD1L3, to form putative sour taste receptor. Interacts with RACK1; inhibits the channel activity possibly by impairing localization to the cell membrane.

    Three dimensional structures from OCA and Proteopedia for PKD2L1 Gene

    Alternative splice isoforms for PKD2L1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PKD2L1 Gene

Post-translational modifications for PKD2L1 Gene

  • Glycosylation at Asn177, Asn207, Asn241, and posLast=505505
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PKD2L1 Gene

Domains & Families for PKD2L1 Gene

Gene Families for PKD2L1 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters
  • Voltage-gated ion channels

Protein Domains for PKD2L1 Gene

Suggested Antigen Peptide Sequences for PKD2L1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9P0L9

UniProtKB/Swiss-Prot:

PK2L1_HUMAN :
  • The EF-hand domain probably mediates calcium-binding. It is not required for channel activation (PubMed:11959145).
  • Belongs to the polycystin family.
Domain:
  • The EF-hand domain probably mediates calcium-binding. It is not required for channel activation (PubMed:11959145).
Family:
  • Belongs to the polycystin family.
genes like me logo Genes that share domains with PKD2L1: view

Function for PKD2L1 Gene

Molecular function for PKD2L1 Gene

GENATLAS Biochemistry:
polycystic kidney disease 2 (polycystin)-like 1,expressed at high level in fetal tissues,including kidney and liver,down-regulated in adult,deleted in mice with kidney and retinal defects,calcium modulated non selective cation channel permeable to Na+,K+,Ca++ ions,highly homolog to PKD2
UniProtKB/Swiss-Prot EnzymeRegulation:
The calcium channel is gated following an off-response property by acid: gated open after the removal of acid stimulus, but not during acid application.
UniProtKB/Swiss-Prot Function:
Pore-forming subunit of a ciliary calcium channel that controls calcium concentration within primary cilia without affecting cytoplasmic calcium concentration. Forms a heterodimer with PKD1L1 in primary cilia and forms a calcium-permeant ciliary channel that regulates sonic hedgehog/SHH signaling and GLI2 transcription. May act as a sour taste receptor by forming a calcium channel with PKD1L3 in gustatory cells; however, its contribution to sour taste perception is unclear in vivo and may be indirect.

Phenotypes From GWAS Catalog for PKD2L1 Gene

Gene Ontology (GO) - Molecular Function for PKD2L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005227 calcium activated cation channel activity IDA 10517637
GO:0005261 cation channel activity IDA,IEA 17944866
GO:0005262 calcium channel activity IEA,IDA 24336289
GO:0005272 sodium channel activity IDA 10517637
GO:0005509 calcium ion binding ISS --
genes like me logo Genes that share ontologies with PKD2L1: view
genes like me logo Genes that share phenotypes with PKD2L1: view

Animal Models for PKD2L1 Gene

MGI Knock Outs for PKD2L1:

Animal Model Products

CRISPR Products

miRNA for PKD2L1 Gene

miRTarBase miRNAs that target PKD2L1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PKD2L1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PKD2L1 Gene

Localization for PKD2L1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PKD2L1 Gene

Cell projection, cilium membrane; Multi-pass membrane protein. Cell membrane; Multi-pass membrane protein. Endoplasmic reticulum. Note=Interaction with PKD1 or PKD1L3 is required for localization to the cell membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PKD2L1 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 3
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for PKD2L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum ISS --
GO:0005886 plasma membrane IMP 17944866
GO:0005929 cilium IEA --
GO:0009986 colocalizes_with cell surface IEA,ISS --
GO:0016020 membrane IDA,IEA 19812697
genes like me logo Genes that share ontologies with PKD2L1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PKD2L1 Gene

Pathways & Interactions for PKD2L1 Gene

SuperPathways for PKD2L1 Gene

SuperPathway Contained pathways
1 Taste transduction
genes like me logo Genes that share pathways with PKD2L1: view

Pathways by source for PKD2L1 Gene

1 KEGG pathway for PKD2L1 Gene

Gene Ontology (GO) - Biological Process for PKD2L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001581 detection of chemical stimulus involved in sensory perception of sour taste ISS --
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006812 cation transport IEA,ISS --
GO:0006816 calcium ion transport IEA --
genes like me logo Genes that share ontologies with PKD2L1: view

No data available for SIGNOR curated interactions for PKD2L1 Gene

Drugs & Compounds for PKD2L1 Gene

(16) Drugs for PKD2L1 Gene - From: DrugBank, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Amiloride Approved Pharma Channel blocker, blocker 55
Calcium Citrate Approved Pharma Transporter, substrate 0
Calcium Phosphate Approved Pharma Transporter, substrate 0
Flufenamic Acid Experimental Pharma Channel blocker 1
malic acid Investigational Pharma Agonist, Activator 0

(2) Additional Compounds for PKD2L1 Gene - From: IUPHAR

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Ca<sub>i</sub><sup>2+</sup>
Activator
Ca<sub>o</sub><sup>2+</sup>
Agonist, Activator
genes like me logo Genes that share compounds with PKD2L1: view

Transcripts for PKD2L1 Gene

mRNA/cDNA for PKD2L1 Gene

Unigene Clusters for PKD2L1 Gene

Polycystic kidney disease 2-like 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PKD2L1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for PKD2L1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16
SP1:
SP2: -

Relevant External Links for PKD2L1 Gene

GeneLoc Exon Structure for
PKD2L1
ECgene alternative splicing isoforms for
PKD2L1

Expression for PKD2L1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PKD2L1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PKD2L1 Gene

This gene is overexpressed in Brain - Cortex (x9.3), Brain - Frontal Cortex (BA9) (x8.9), Spleen (x8.1), and Testis (x5.3).

Protein differential expression in normal tissues from HIPED for PKD2L1 Gene

This gene is overexpressed in Plasma (44.1) and Colon (24.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PKD2L1 Gene



Protein tissue co-expression partners for PKD2L1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PKD2L1 Gene:

PKD2L1

SOURCE GeneReport for Unigene cluster for PKD2L1 Gene:

Hs.159241

mRNA Expression by UniProt/SwissProt for PKD2L1 Gene:

Q9P0L9-PK2L1_HUMAN
Tissue specificity: Expressed in adult heart, skeletal muscle, brain, spleen, testis, retina and liver. According to PubMed:9748274, expressed at high levels in fetal tissues, including kidney and liver, and down-regulated in adult tissues. According to PubMed:10602361, expressed in fetal brain, but not expressed in fetal lung, liver or kidney. Isoform 4 appears to be expressed only in transformed lymphoblasts.

Evidence on tissue expression from TISSUES for PKD2L1 Gene

  • Nervous system(4.3)
  • Eye(4.2)
genes like me logo Genes that share expression patterns with PKD2L1: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PKD2L1 Gene

Orthologs for PKD2L1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PKD2L1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PKD2L1 33 34
  • 99.54 (n)
dog
(Canis familiaris)
Mammalia PKD2L1 33 34
  • 89.96 (n)
cow
(Bos Taurus)
Mammalia PKD2L1 33 34
  • 89.29 (n)
mouse
(Mus musculus)
Mammalia Pkd2l1 33 16 34
  • 86.53 (n)
rat
(Rattus norvegicus)
Mammalia Pkd2l1 33
  • 85.57 (n)
oppossum
(Monodelphis domestica)
Mammalia PKD2L1 34
  • 77 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PKD2L1 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves PKD2L1 33 34
  • 72.01 (n)
lizard
(Anolis carolinensis)
Reptilia PKD2L1 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pkd2l1 33
  • 67.95 (n)
zebrafish
(Danio rerio)
Actinopterygii pkd2l1 33 34
  • 63.59 (n)
fruit fly
(Drosophila melanogaster)
Insecta Pkd2 35 34
  • 39 (a)
worm
(Caenorhabditis elegans)
Secernentea pkd-2 35 34
  • 37 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 51 (a)
OneToOne
Species where no ortholog for PKD2L1 was found in the sources mined by GeneCards:
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)
  • 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)

Evolution for PKD2L1 Gene

ENSEMBL:
Gene Tree for PKD2L1 (if available)
TreeFam:
Gene Tree for PKD2L1 (if available)

Paralogs for PKD2L1 Gene

Paralogs for PKD2L1 Gene

(2) SIMAP similar genes for PKD2L1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with PKD2L1: view

Variants for PKD2L1 Gene

Sequence variations from dbSNP and Humsavar for PKD2L1 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs193920845 Uncertain significance 100,330,034(-) ACCCC(A/G)CCTAC intron-variant, reference, missense, utr-variant-5-prime
rs1000023638 -- 100,339,933(+) AAAGA(A/G)TGATG intron-variant, upstream-variant-2KB
rs1000054519 -- 100,339,691(+) GCACC(A/G)GGCCC intron-variant, upstream-variant-2KB
rs1000107175 -- 100,298,056(+) ATCAG(C/G)CTCCT intron-variant
rs1000142091 -- 100,341,178(+) CTACG(C/T)TGGCT intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for PKD2L1 Gene

Variant ID Type Subtype PubMed ID
esv2740073 CNV deletion 23290073
esv2740084 CNV deletion 23290073
esv2761622 CNV loss 21179565
nsv1043825 CNV loss 25217958
nsv831961 CNV loss 17160897

Variation tolerance for PKD2L1 Gene

Residual Variation Intolerance Score: 91.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.36; 92.69% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PKD2L1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PKD2L1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PKD2L1 Gene

Disorders for PKD2L1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for PKD2L1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
polycystic kidney disease
  • pkd
polycystic kidney disease 2
  • apkd2
kidney disease
  • nephropathy
autosomal dominant polycystic kidney disease
  • polycystic kidney and hepatic disease 1
polycystic kidney disease 1
  • apkd1
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for PKD2L1

Genetic Association Database (GAD)
PKD2L1
Human Genome Epidemiology (HuGE) Navigator
PKD2L1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PKD2L1
genes like me logo Genes that share disorders with PKD2L1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PKD2L1 Gene

Publications for PKD2L1 Gene

  1. Identification of PKDL, a novel polycystic kidney disease 2-like gene whose murine homologue is deleted in mice with kidney and retinal defects. (PMID: 9748274) Nomura H … Zhou J (The Journal of biological chemistry 1998) 2 3 4 22 60
  2. The calcium-binding EF-hand in polycystin-L is not a domain for channel activation and ensuing inactivation. (PMID: 11959145) Li Q … Chen XZ (FEBS letters 2002) 3 4 22 60
  3. The human polycystic kidney disease 2-like (PKDL) gene: exon/intron structure and evidence for a novel splicing mechanism. (PMID: 10602992) Guo L … Zhou J (Mammalian genome : official journal of the International Mammalian Genome Society 2000) 3 4 22 60
  4. Genes homologous to the autosomal dominant polycystic kidney disease genes (PKD1 and PKD2). (PMID: 10602361) Veldhuisen B … Peters DJ (European journal of human genetics : EJHG 1999) 3 4 22 60
  5. Identification of PKD2L, a human PKD2-related gene: tissue-specific expression and mapping to chromosome 10q25. (PMID: 9878261) Wu G … Somlo S (Genomics 1998) 2 3 4 60

Products for PKD2L1 Gene

Sources for PKD2L1 Gene

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