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PKD2L2 Gene

protein-coding   GIFtS: 50
GCID: GC05P137225

Polycystic Kidney Disease 2-Like 2

  See PKD2L2-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)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 channel activity and 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   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
   Search Chromatin IP Primers for PKD2L2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PK2L2_HUMAN, Q9NZM6 (See protein sequence)
Recommended Name: Polycystic kidney disease 2-like 2 protein  
Size: 624 amino acids; 73790 Da
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: 

  • Glycosylation2 at Asn115, Asn138
  • Modification sites at PhosphoSitePlus

  • See PKD2L2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    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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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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


    Find genes that share domains with PKD2L2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    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:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005262calcium channel activity IBA--
    GO:0005509calcium ion binding IEA--
         
    Find genes that share ontologies with PKD2L2           About GenesLikeMe


    Phenotypes:
         1 MGI mutant phenotype (inferred from 2 alleles(MGI details for Pkd2l2):
     behavior/neurological 

    Find genes that share phenotypes with PKD2L2           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PKD2L2

    miRNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PK2L2_HUMAN, Q9NZM6: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    cytosol1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane ----
    GO:0016021integral component of membrane TAS10602361

    Find genes that share ontologies with PKD2L2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PKD2L2
    Interactions:

        Search GeneGlobe Interaction Network for PKD2L2

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    5 Interacting proteins for PKD2L2 (ENSP000002904314) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HERPUD1ENSP000003003024STRING: ENSP00000300302
    PSMD7ENSP000002193134STRING: ENSP00000219313
    VCPENSP000003517774STRING: ENSP00000351777
    CSNK2A1ENSP000002172444STRING: ENSP00000217244
    CSNK2A2ENSP000002625064STRING: ENSP00000262506
    About this table

    Gene Ontology (GO): 5 biological process terms:    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--

    Find genes that share ontologies with PKD2L2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for 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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
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    REFSEQ mRNAs for PKD2L2 gene (3 alternative transcripts): 
    NM_001258448.1  NM_001258449.1  NM_014386.3  

    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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    18 AceView cDNA sequences:

    AF182034 NM_014386 BC044581 BX281986 AF118125 BG719682 BG721989 CD359324 
    BG772786 BI463953 BC038714 BC034619 AW593268 BG772072 BP369099 BI550278 
    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PKD2L2 expression in normal human tissues (normalized intensities)
    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
     selected tissues (see all 3) fully expand
     
     Ovary (Reproductive System)
             Primary Oocyte Primordial Follicle
     
     Gonad
             Primary Oocyte Primordial Follicle
     
     Testis (Reproductive System)
    PKD2L2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PKD2L2 Protein Expression

    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)
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    This gene was present in the common ancestor of animals.

    Orthologs for PKD2L2 gene from Selected 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 80.82(n)1
    81.94(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 61.57(n)
    54.79(a)
      416298  XM_414617.4  XP_414617.4 
    lizard
    (Anolis carolinensis)
    Reptilia PKD2L26
    polycystic kidney disease 2-like 2
    54(a)
    1 ↔ 1
    2(142147917-142274542)
    zebrafish
    (Danio rerio)
    Actinopterygii pkd1l36
    polycystic kidney disease 1 like 3

    many ↔ many
    7(57751665-57779964) ENSDARG00000091803
    fruit fly
    (Drosophila melanogaster)
    Insecta Pkd23   -- 38(a)   33E3   --
    worm
    (Caenorhabditis elegans)
    Secernentea pkd-26
    Protein PKD-2 (pkd-2) mRNA, complete cds
    28(a)
    1 → many
    IV(15227883-15237238) WBGene00004035


    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)
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    Paralogs for PKD2L2 gene
    PKD22  PKDREJ2  PKD12  PKD1L22  PKD2L12  PKD1L12  
    4 SIMAP similar genes for PKD2L2 using alignment to 3 protein entries:     PK2L2_HUMAN (see all proteins):
    PKD2L1    PKD2    FLJ00078    PKD1L2

    Find genes that share paralogs with PKD2L2           About GenesLikeMe



    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PKD2L2 (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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 604669    OMIM disorders: --

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


    Find genes that share disorders with PKD2L2           About GenesLikeMe


    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)
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    PubMed articles for PKD2L2 gene integrated from 10 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. (Eur. J. Hum. Genet. 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. (Genomics 2000)
    3. Polycystin channels and kidney disease. (PubMed id 11698076)1, 2 Stayner C. and Zhou J. (Trends Pharmacol. Sci. 2001)
    4. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    5. 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. (Genome Res. 2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (Nature 2004)
    8. 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. (FEBS Lett. 2002)
    9. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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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, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    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

    GeneCards and IP:
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