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

PCDH20 Gene

protein-coding   GIFtS: 49
GCID: GC13M061983

Protocadherin 20

  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
Protocadherin 201 2
PCDH132 3
Protocadherin 132
protocadherin-132
protocadherin-202
Protocadherin-133

External Ids:    HGNC: 142571   Entrez Gene: 648812   Ensembl: ENSG000001979917   OMIM: 6144495   UniProtKB: Q8N6Y13   

Export aliases for PCDH20 gene to outside databases

Previous GC identifers: GC13M059951 GC13M055978 GC13M060920 GC13M059781 GC13M060881 GC13M042676


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

Entrez Gene summary for PCDH20 Gene:
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a
protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing
from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related
neuronal receptor is thought to play a role in the establishment and function of specific cell-cell connections
in the brain. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDH20 Gene: 
PCDH20 (protocadherin 20) is a protein-coding gene. Diseases associated with PCDH20 include lung cancer, and asthma. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH7.

UniProtKB/Swiss-Prot: PCD20_HUMAN, Q8N6Y1
Function: Potential calcium-dependent cell-adhesion protein

Gene Wiki entry for PCDH20 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_000013.10  NC_018924.2  NT_024524.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PCDH20 gene promoter:
         AML1a   GATA-3   CUTL1   GATA-2   GATA-1   MEF-2A   FOXO4   HSF2   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDH20 promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDH20

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDH20


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

Entrez Gene cytogenetic band: 13q21   Ensembl cytogenetic band:  13q21.2   HGNC cytogenetic band: 13q21

PCDH20 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDH20 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M061983:  view genomic region     (about GC identifiers)

Start:
61,983,818 bp from pter      End:
62,002,220 bp from pter
Size:
18,403 bases      Orientation:
minus 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: PCD20_HUMAN, Q8N6Y1 (See protein sequence)
Recommended Name: Protocadherin-20 precursor  
Size: 924 amino acids; 101927 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Sequence caution: Sequence=AAF89690.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=CAD38690.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=CAH73802.3;
Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: B1AQU2 Q8NDN4 Q9NRT9

Explore the universe of human proteins at neXtProt for PCDH20: NX_Q8N6Y1

Explore proteomics data for PCDH20 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8N6Y1

  • PCDH20 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PCDH20 Protein Expression
    REFSEQ proteins: NP_073754.2  
    ENSEMBL proteins: 
     ENSP00000387250   ENSP00000386653  

    Human Recombinant Protein Products for PCDH20: 
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    Cloud-Clone Corp. Proteins for PCDH20 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016020membrane ----
    GO:0016021integral to membrane IEA--

    PCDH20 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: 
    PCDHN: Cadherins / Protocadherins : Non-clustered

    3 InterPro protein domains:
     IPR015919 Cadherin-like
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q8N6Y1

    ProtoNet protein and cluster: Q8N6Y1

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCD20_HUMAN, Q8N6Y1
    Similarity: Contains 6 cadherin domains


    PCDH20 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: PCD20_HUMAN, Q8N6Y1
    Function: Potential calcium-dependent cell-adhesion protein

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    PCDH20 for ontologies           About GeneDecksing


    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidPCDH20 3' UTR sequence
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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 PCDH20

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for PCDH20 (Q8N6Y13 ENSP000003866534) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RYKP349253, ENSP000002960844I2D: score=1 STRING: ENSP00000296084
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--

    PCDH20 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 PCDH20 (PCD20)

    1 HMDB Compound for PCDH20    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDH20 / PCD20

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PCDH20 gene: 
    NM_022843.3  

    Unigene Cluster for PCDH20:

    Protocadherin 20
    Hs.391781  [show with all ESTs]
    Unigene Representative Sequence: AL833830
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000409204(uc001vid.4) ENST00000409186(uc010thj.2) ENST00000472649

    miRNA
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    8/17 QIAGEN miScript miRNA Assays for microRNAs that regulate PCDH20 (see all 17):
    hsa-miR-30c hsa-miR-3607-3p hsa-miR-30d hsa-miR-340 hsa-miR-4267 hsa-miR-649 hsa-miR-30a hsa-miR-4325
    SwitchGear 3'UTR luciferase reporter plasmidPCDH20 3' UTR sequence
    Inhib. RNA
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PCDH20
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PCDH20

    Additional mRNA sequence: 

    AF169693.1 AK025871.1 AK094680.1 AK289924.1 AK314607.1 AL833830.1 BC027907.1 

    3 DOTS entries:

    DT.97768248  DT.99933397  DT.120763635 

    24/36 AceView cDNA sequences (see all 36):

    AK094680 T04933 BU070294 C16499 BI766301 BU608937 BI462451 NM_022843 
    AA453141 BI546525 BQ439228 AI039143 AA040057 AA625076 BC027907 AL833830 
    N34280 Z43057 AF169693 BC038756 AA040043 AI375140 AK025871 CK902366 

    GeneLoc Exon Structure


    (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

    PCDH20 expression in normal human tissues (normalized intensities)      PCDH20 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDH20 Expression
    About this image


    PCDH20 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/10 selected tissues (see all 10) fully expand
     
     Brain (Nervous System)    fully expand to see all 18 entries
             Oligodendrocyte Precursor Cells Forebrain White Matter
             Thalamus
             Septum   
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Zeugopod Epiphyseal End
             HyStem+BMP4-induced MEL2 cells
     
     Spinal Cord (Nervous System)    fully expand to see all 2 entries
             Dorsal Horn   
     
     Nose (Sensory Organs)
             sensory organ/nose/nasal cavity   
     
     Head Mesenchyme (Muscoskeletal System)
             Frontonasal Process

    See PCDH20 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDH20

    SOURCE GeneReport for Unigene cluster: Hs.391781
        SABiosciences Custom PCR Arrays for PCDH20
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    In Situ
    Assay Products:
     

     
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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 chordates.

    Orthologs for PCDH20 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdh201 , 5 protocadherin 201, 5 87.24(n)1
    92.53(a)1
      14 (44.43 cM)5
    2192571  NM_178685.51  NP_848800.31 
     884647475 
    chicken
    (Gallus gallus)
    Aves PCDH201 protocadherin 20 75.13(n)
    80.89(a)
      428063  XM_425621.3  XP_425621.2 
    lizard
    (Anolis carolinensis)
    Reptilia PCDH206
    Uncharacterized protein
    75(a)
    1 ↔ 1
    3(76240477-76250370)
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh201 protocadherin 20 60.51(n)
    59.23(a)
      100007362  XM_001345807.2  XP_001345843.2 


    ENSEMBL Gene Tree for PCDH20 (if available)
    TreeFam Gene Tree for PCDH20 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDH20 gene
    PCDH72  PCDH12  PCDHA122  PCDH11Y2  PCDH122  PCDHA112  PCDHA12  PCDH182  
    PCDH92  PCDH192  PCDH82  PCDH172  PCDHGB32  PCDHA72  PCDHGB62  PCDH11X2  
    PCDHA62  PCDH102  PCDHA102  PCDHA132  PCDHA92  PCDHA32  PCDHA42  
    5 SIMAP similar genes for PCDH20 using alignment to 2 protein entries:     PCD20_HUMAN (see all proteins):
    PCDH9    PCDH11X    PCDH11Y    PCDH1    PCDH7

    PCDH20 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

    10/225 SNPs in PCDH20 are shown (see all 225)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0361114
    A breast cancer sample4--see VAR_0361112 V M mis40--------
    rs1831546401,2
    --61983477(+) CATTGC/TTGCCT 1 -- int10--------
    rs79905361,2
    C,F,A,H--61983572(+) CTTGGT/CTGTTT 1 -- int18Minor allele frequency- C:0.35NA WA EA 504
    rs1878038161,2
    --61983649(+) TAACAA/GAGGAT 1 -- int10--------
    rs1388719131,2
    --61984000(+) GAAAAC/TATATA 1 -- ut310--------
    rs1179045451,2
    C,F--61984060(+) ATGCCA/GAAAAG 1 -- ut311Minor allele frequency- G:0.02NA 120
    rs1924268091,2
    C--61984098(+) TTCCTG/TGTTTA 1 -- ut310--------
    rs1427384431,2
    --61984130(+) TCTCAC/TATAAA 1 -- ut310--------
    rs412934381,2
    C,F--61984275(+) TTTAAT/CCCAAA 1 -- ut311Minor allele frequency- C:0.02NA 120
    rs1849555901,2
    --61984320(+) AACCTA/GAACAA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for PCDH20 (61983818 - 62002220 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for PCDH20:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv900245CNV Loss21882294
    nsv832628CNV Loss17160897
    nsv510587CNV Loss20534489

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing PCDH20
    DNA2.0 Custom Variant and Variant Library Synthesis for PCDH20

    (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: 614449    OMIM disorders: --

    3 diseases for PCDH20:    About MalaCards
    lung cancer    asthma    neuronitis


    PCDH20 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDH20

    Export disorders for PCDH20 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 PCDH20 gene, integrated from 9 sources (see all 21):
    (articles sorted by number of sources associating them with PCDH20)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. Genome-wide association study identifies novel loci as sociated with circulating phospho- and sphingolipid concentrations. (PubMed id 22359512)1 Demirkan A....Schmitz G. (2012)
    3. Genome-wide association study of clinical dimensions o f schizophrenia: polygenic effect on disorganized symptoms. (PubMed id 23212062)1 Fanous A.H....Levinson D.F. (2012)
    4. Identification of IL6R and chromosome 11q13.5 as risk loci for asthma. (PubMed id 21907864)1 Ferreira M.A....Thompson P.J. (2011)
    5. Mindbomb 1, an E3 ubiquitin ligase, forms a complex w ith RYK to activate Wnt/I^-catenin signaling. (PubMed id 21875946)1 Berndt J.D....Moon R.T. (2011)
    6. Joint influence of small-effect genetic variants on h uman longevity. (PubMed id 20834067)1 Yashin A.I....Ukraintseva S.V. (2010)
    7. Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study. (PubMed id 17903306)4 Newton-Cheh C....Larson M.G. (2007)
    8. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (2007)
    9. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    10. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (2006)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 64881 HGNC: 14257 AceView: PCDH20 Ensembl:ENSG00000197991 euGenes: HUgn64881
    ECgene: PCDH20 H-InvDB: PCDH20

    (According to HUGE)
    About This Section
      --

    (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 PCDH20 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PCDH20 gene:
    Search GeneIP for patents involving PCDH20

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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