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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PKD2L2 Gene

protein-coding   GIFtS: 51
GCID: GC05P137225

Polycystic Kidney Disease 2-Like 2

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Polycystic Kidney Disease 2-Like 21 2     polycystin-L22
TRPP52     Polycystin-2L23
Polycystic Kidney Disease 2-Like 2 Protein2     Polycystin-L23
polycystin-2L22     

External Ids:    HGNC: 90121   Entrez Gene: 270392   Ensembl: ENSG000000787957   OMIM: 6046695   UniProtKB: Q9NZM63   

Export aliases for PKD2L2 gene to outside databases

Previous GC identifers: GC05P137100 GC05P137898 GC05P137256 GC05P137301 GC05P137253 GC05P132416


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for PKD2L2 Gene: 
PKD2L2 (polycystic kidney disease 2-like 2) is a protein-coding gene. Diseases associated with PKD2L2 include kidney disease, and polycystic kidney disease. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PKD2.

UniProtKB/Swiss-Prot: PK2L2_HUMAN, Q9NZM6
Function: May function as a subunit of a cation channel and play a role in fertilization

Gene Wiki entry for PKD2L2 (TRPP3) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NT_034772.6  NC_018916.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PKD2L2 gene promoter:
         Max1   MEF-2   CUTL1   MEF-2A   POU2F1   Zic1   POU2F1a   aMEF-2   RSRFC4   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPKD2L2 promoter sequence
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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PKD2L2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.2   HGNC cytogenetic band: 5q31

PKD2L2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PKD2L2 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P137225:  view genomic region     (about GC identifiers)

Start:
137,223,657 bp from pter      End:
137,278,436 bp from pter
Size:
54,780 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PK2L2_HUMAN, Q9NZM6 (See protein sequence)
Recommended Name: Polycystic kidney disease 2-like 2 protein  
Size: 624 amino acids; 73790 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
Sequence caution: Sequence=AAD46478.1; Type=Frameshift; Positions=595;
Secondary accessions: A6NK98 B4DXD2 E9PC91 E9PDG4 Q86YB4 Q9UNJ0
Alternative splicing: 7 isoforms:  Q9NZM6-1   Q9NZM6-2   Q9NZM6-3   Q9NZM6-4   Q9NZM6-5   Q9NZM6-6   Q9NZM6-7   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PKD2L2: NX_Q9NZM6

Explore proteomics data for PKD2L2 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9NZM6

  • PKD2L2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PKD2L2 Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001245377.1  NP_001245378.1  NP_055201.2  

    ENSEMBL proteins: 
     ENSP00000424885   ENSP00000423382   ENSP00000388060   ENSP00000425513   ENSP00000424725  
     ENSP00000290431   ENSP00000423926   ENSP00000344177  

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    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane ----
    GO:0016021integral to membrane TAS10602361

    PKD2L2 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    TRP: Voltage-gated ion channels / Transient receptor potential cation channels

    IUPHAR Guide to PHARMACOLOGY protein family classification: TRPP3 
    Transient Receptor Potential channels

    2 InterPro protein domains:
     IPR003915 PKD_2
     IPR013122 PKD1_2_channel

    Graphical View of Domain Structure for InterPro Entry Q9NZM6

    ProtoNet protein and cluster: Q9NZM6

    UniProtKB/Swiss-Prot: PK2L2_HUMAN, Q9NZM6
    Similarity: Belongs to the polycystin family


    PKD2L2 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PK2L2_HUMAN, Q9NZM6
    Function: May function as a subunit of a cation channel and play a role in fertilization

         Genatlas biochemistry entry for PKD2L2:
    polycystic kidney disease 2(polycystin)-like 2,restrictively expressed in testis

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005262calcium channel activity IBA--
    GO:0005509calcium ion binding IEA--
         
    PKD2L2 for ontologies           About GeneDecksing


    Phenotypes:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Pkd2l2):
     behavior/neurological 

    PKD2L2 for phenotypes           About GeneDecksing

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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section




    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PKD2L2

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006811ion transport ----
    GO:0008150biological_process ND--
    GO:0050982detection of mechanical stimulus IBA--
    GO:0055085transmembrane transport ----
    GO:0070588calcium ion transmembrane transport IBA--

    PKD2L2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PKD2L2 (PK2L2)

    Search CenterWatch for drugs/clinical trials and news about PKD2L2 / PK2L2

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    About This Section

    REFSEQ mRNAs for PKD2L2 gene (3 alternative transcripts): 
    NM_001258448.1  NM_001258449.1  NM_014386.3  

    Unigene Cluster for PKD2L2:

    Polycystic kidney disease 2-like 2
    Hs.716884  [show with all ESTs]
    Unigene Representative Sequence: BC044581
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000503015 ENST00000508638(uc010jep.1 uc003lbx.3) ENST00000414094
    ENST00000502810(uc011cyi.1) ENST00000508883(uc003lby.3) ENST00000290431(uc003lbw.1)
    ENST00000511176 ENST00000350250
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    Additional mRNA sequence: 

    AF118125.1 AF182034.1 AK301924.1 BC034619.1 BC038714.1 BC044581.1 

    7 DOTS entries:

    DT.95190872  DT.100689736  DT.92020931  DT.91665933  DT.95208964  DT.86859752  DT.95211987 

    18 AceView cDNA sequences:

    NM_014386 AF118125 AF182034 BC044581 BX281986 BC034619 BI463953 BG719682 
    CD359324 BG772786 BC038714 BG721989 BP369099 BG772072 BI550278 AW593268 
    BF799765 BU852497 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for PKD2L2    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14
    SP1:                                                                                                                  
    SP2:        -     -                                                                                                   
    SP3:        -                                                                                                         
    SP4:                                                                                                                  


    ECgene alternative splicing isoforms for PKD2L2

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PKD2L2 expression in normal human tissues (normalized intensities)      PKD2L2 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTTTTATAA
    PKD2L2 Expression
    About this image


    PKD2L2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/3 selected tissues (see all 3) fully expand
     
     Ovary (Reproductive System)
             Primary Oocyte Primordial Follicle
     
     Gonad
             Primary Oocyte Primordial Follicle
     
     Testis (Reproductive System)

    See PKD2L2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PKD2L2

    SOURCE GeneReport for Unigene cluster: Hs.716884

    UniProtKB/Swiss-Prot: PK2L2_HUMAN, Q9NZM6
    Tissue specificity: According to PubMed:10602361, expressed only in testis. According to PubMed:10756092,
    expressed also in brain and kidney. Isoform 2 is found only in transformed lymphoblasts. Isoform 3 is found in
    all tissues tested

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for PKD2L2 gene from 5/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pkd2l21 , 5 polycystic kidney disease 2-like 21, 5 80.58(n)1
    81.65(a)1
      18 (18.62 cM)5
    538711  NM_001163004.11  NP_001156476.11 
     344094235 
    chicken
    (Gallus gallus)
    Aves PKD2L21 polycystic kidney disease 2-like 2 63.84(n)
    58.49(a)
      416298  XM_414617.3  XP_414617.3 
    lizard
    (Anolis carolinensis)
    Reptilia PKD2L26
    Uncharacterized protein
    54(a)
    1 ↔ 1
    2(142147917-142274542)
    fruit fly
    (Drosophila melanogaster)
    Insecta Pkd21 , 3 Polycystic kidney disease gene-21 38(a)3
    49.56(n)1
    39.23(a)1
      33E33
    346511  NM_135717.21  NP_609561.21 
    worm
    (Caenorhabditis elegans)
    Secernentea pkd-26
    Polycystin-2
    27(a)
    1 → many
    IV(15227883-15237238)


    ENSEMBL Gene Tree for PKD2L2 (if available)
    TreeFam Gene Tree for PKD2L2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PKD2L2 gene
    PKD22  PKDREJ2  PKD12  PKD2L12  PKD1L22  PKD1L12  
    4 SIMAP similar genes for PKD2L2 using alignment to 3 protein entries:     PK2L2_HUMAN (see all proteins):
    PKD2L1    PKD2    FLJ00078    PKD1L2

    PKD2L2 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/899 SNPs in PKD2L2 are shown (see all 899)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs77037951,2
    C,A,H--137224052(+) TCAGAT/CAATCT 3 -- us2k15Minor allele frequency- C:0.00NS EA NA 416
    rs1387834181,2
    --137224091(+) CAGCTC/GAGAGT 3 -- us2k10--------
    rs792161031,2
    --137224122(+) ATCCTA/TTTGTT 3 -- us2k10--------
    rs1474767941,2
    --137224128(+) TTGTTA/GAAACT 3 -- us2k10--------
    rs787082071,2
    C,F--137224203(+) TCCTGT/CTCCTC 3 -- us2k13Minor allele frequency- C:0.08NA WA 240
    rs801934421,2
    C--137224215(+) CATCGA/CTGGTA 3 -- us2k10--------
    rs1863067831,2
    --137224380(+) CCTGGC/GGCCTT 3 -- us2k10--------
    rs77220881,2
    A,H--137224440(+) CTGGTC/GTTACA 3 -- us2k14Minor allele frequency- G:0.00NS EA 418
    rs1889092061,2
    --137224597(+) ACATAA/TTCACT 3 -- us2k10--------
    rs1821743241,2
    --137224602(+) ATCACC/TGCAGA 3 -- us2k10--------

    HapMap Linkage Disequilibrium report for PKD2L2 (137223657 - 137278436 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for PKD2L2:    About this table     
    Variant IDTypeSubtypePubMed ID
    dgv6339n71CNV Loss21882294
    nsv882936CNV Loss21882294
    nsv830501CNV Gain17160897
    nsv830502CNV Gain17160897

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 604669    OMIM disorders: --

    2 diseases for PKD2L2:    About MalaCards
    kidney disease    polycystic kidney disease


    PKD2L2 for disorders           About GeneDecksing


    Export disorders for PKD2L2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for PKD2L2 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PKD2L2)
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    1. Genes homologous to the autosomal dominant polycystic kidney disease genes (PKD1 and PKD2). (PubMed id 10602361)1, 2, 3 Veldhuisen B.... Peters D.J.M. (1999)
    2. Identification and characterization of a novel polycystin family member, polycystin-L2, in mouse and human: sequence, expression, alternative splicing, and chromosomal localization. (PubMed id 10756092)1, 2, 9 Guo L.... Zhou J. (2000)
    3. Polycystin channels and kidney disease. (PubMed id 11698076)1, 2 Stayner C. and Zhou J. (2001)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    6. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (2004)
    7. The calcium-binding EF-hand in polycystin-L is not a domain for channel activation and ensuing inactivation. (PubMed id 11959145)1 Li Q....Chen X.Z. (2002)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 27039 HGNC: 9012 AceView: PKD2L2 Ensembl:ENSG00000078795 euGenes: HUgn27039
    ECgene: PKD2L2 H-InvDB: PKD2L2

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PKD2L2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PKD2L2 gene:
    Search GeneIP for patents involving PKD2L2

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