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PCDHGA12 Gene

protein-coding   GIFtS: 42
GCID: GC05P141379

Protocadherin Gamma Subfamily A, 12

(Previous name: cadherin 21)
(Previous symbol: CDH21)
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(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
Protocadherin Gamma Subfamily A, 121 2     PCDH-GAMMA-A122
CDH211 2 3     cadherin-212
Cadherin 211 2     Protocadherin Gamma-A122
Fibroblast Cadherin FIB31 2     Cadherin-213
Fibroblast Cadherin-32 3     KIAA05883
FIB32 3     PCDH-gamma-A123

External Ids:    HGNC: 86991   Entrez Gene: 260252   Ensembl: ENSG000002531597   OMIM: 6030595   UniProtKB: O603303   

Export aliases for PCDHGA12 gene to outside databases

Previous GC identifers: GC05P140597 GC05P141318 GC05P140721 GC05P140780 GC05P140800 GC05P140740 GC05P140815 GC05P140838 GC05P140927 GC05P140949 GC05P140970 GC05P140992 GC05P141022 GC05P141052 GC05P141080 GC05P135955 GC05P141119 GC05P141144 GC05P141182 GC05P141213 GC05P141252 GC05P141298


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PCDHGA12 Gene:
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on
chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism
may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3
subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more
distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed
by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes
the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region
exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a
critical role in the establishment and function of specific cell-cell connections in the brain. Alternative
splicing has been described for the gamma cluster genes. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHGA12 Gene:
PCDHGA12 (protocadherin gamma subfamily A, 12) is a protein-coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB16.

UniProtKB/Swiss-Prot: PCDGC_HUMAN, O60330
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain

Gene Wiki entry for PCDHGA12 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 PCDHGA12 gene promoter:
         Oct-B1   AhR   oct-B2   Arnt   c-Ets-1   CREB   HOXA5   COMP1   deltaCREB   Sox9   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHGA12 promoter sequence
   Search Chromatin IP Primers for PCDHGA12

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHGA12


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

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31

PCDHGA12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHGA12 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P141379:  view genomic region     (about GC identifiers)

Start:
140,810,158 bp from pter      End:
140,892,546 bp from pter
Size:
82,389 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: PCDGC_HUMAN, O60330 (See protein sequence)
Recommended Name: Protocadherin gamma-A12 precursor  
Size: 932 amino acids; 100955 Da
Sequence caution: Sequence=BAA25514.2; Type=Erroneous initiation;
Secondary accessions: O15100 Q6UW70 Q9Y5D7
Alternative splicing: 3 isoforms:  O60330-1   O60330-2   O60330-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PCDHGA12: NX_O60330

Explore proteomics data for PCDHGA12 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn265, Asn419, Asn545
  • Modification sites at PhosphoSitePlus

  • See PCDHGA12 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_003726.1  NP_115265.1  

    ENSEMBL proteins: 
     ENSP00000252085  

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    antibodies-online proteins for PCDHGA12 (5 products) 

     
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    antibodies-online antibodies for PCDHGA12 (20 products) 

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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:
    PCDHC: Cadherins / Protocadherins : Clustered

    4 InterPro protein domains:
     IPR015919 Cadherin-like
     IPR013164 Cadherin_N
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry O60330

    ProtoNet protein and cluster: O60330

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDGC_HUMAN, O60330
    Similarity: Contains 6 cadherin domains


    Find genes that share domains with PCDHGA12           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: PCDGC_HUMAN, O60330
    Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
    of specific neuronal connections in the brain

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    Find genes that share ontologies with PCDHGA12           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for PCDHGA12

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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
    PCDGC_HUMAN, O60330: Cell membrane; Single-pass type I membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular2
    cytosol1
    endoplasmic reticulum1
    peroxisome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

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

    Find genes that share ontologies with PCDHGA12           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 PCDHGA12
    Interactions:

        Search GeneGlobe Interaction Network for PCDHGA12

    Gene Ontology (GO): 1 biological process term:    About this table

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

    Find genes that share ontologies with PCDHGA12           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
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PCDHGA12 (PCDGC)

    1 HMDB Compound for PCDHGA12    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--



    (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,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PCDHGA12 gene (2 alternative transcripts): 
    NM_003735.2  NM_032094.1  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000252085(uc003lkt.2)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate PCDHGA12 (see all 29):
    hsa-miR-1226 hsa-miR-448 hsa-miR-4272 hsa-miR-765 hsa-miR-624* hsa-miR-650 hsa-miR-3150a-3p hsa-miR-548a-3p
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      QuantiFast Probe-based Assays in human, mouse, rat PCDHGA12

    Selected AceView cDNA sequences (see all 737):

    AA364655 AL583555 BU620424 CA392030 AA331816 BQ318895 AF152324 AF152519 
    AF152336 AI911632 AF152522 BQ055812 BX346373 AF152512 AW002439 AF152332 
    NM_018920 F04936 NM_032090 AI363503 BC027451 AF152329 AI184539 AF152321 

    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™, 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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    PCDHGA12 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHGA12 Expression
    About this image


    PCDHGA12 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 4 entries
             Zeugopod Long Bone
     
     Cartilage (Muscoskeletal System)
             Meckel's Cartilage
    PCDHGA12 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDHGA12 Protein Expression
        Custom PCR Arrays for PCDHGA12
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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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for PCDHGA12 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhga121 , 5 protocadherin gamma subfamily A, 121, 5 83.93(n)1
    85.71(a)1
      18 (19.63 cM)5
    937241  NM_033595.41  NP_291073.11 
     377655805 
    chicken
    (Gallus gallus)
    Aves --
    --
    Uncharacterized protein
    52(a)
    50(a)
    many ↔ many
    many ↔ many
    13(1193472-1213360)
    13(1131593-1134055)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 8)
    Uncharacterized protein
    (see all 8)
    55(a)
    55(a)
    (see all 8)
    many ↔ many
    many ↔ many
    (see all 8)
    4(76884496-76886922)
    4(76897250-76899667)


    ENSEMBL Gene Tree for PCDHGA12 (if available)
    TreeFam Gene Tree for PCDHGA12 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHGA12 gene
    PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGB22  PCDHGA92  
    PCDHGA82  PCDHGB32  PCDHGB62  PCDHGA52  PCDHB52  PCDHB132  PCDHGA42  PCDHGA72  
    PCDHB42  PCDHB112  ENSG000002556222  PCDHB142  PCDHB122  PCDHB82  PCDHGB12  PCDHGB42  
    PCDHGA22  PCDHGA62  PCDHB32  PCDHGA112  PCDHB62  PCDHGC42  PCDHGC52  PCDHGA12  
    PCDHB102  PCDHB12  PCDHGA32  PCDHGB72  
    Selected SIMAP similar genes for PCDHGA12 using alignment to 1 protein entry:     PCDGC_HUMAN(see all similar genes):
    PCDHGA11    PCDHGA10    PCDHGA2    PCDHGA5    PCDHGA6    PCDHGA7
    PCDHGA8    PCDHGA9    PCDHGA4    PCDHGA1    PCDHGA3    PCDHGB7
    PCDHGB2    PCDHGB6    PCDHGB3    PCDHGB5    PCDHGB4    PCDHGB1

    Find genes that share paralogs with PCDHGA12           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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    4 SNPs for PCDHGA12    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1165348671,2
    F--135958480(+) AAAAAA/CAAAAA 1 -- ds50012Minor allele frequency- C:0.03WA NA 238
    rs561912081,2
    ----135958487(+) AAAAA-/ACTTTA 1 -- ds50010--------
    rs794044171,2
    ----135958468(+) TATCTC/AAAAAA 1 -- ds50011Minor allele frequency- A:0.50NA 2
    rs792032011,2
    ----135958470(+) TCTCAC/AAAAAA 1 -- ds50011Minor allele frequency- A:0.50NA 2

    HapMap Linkage Disequilibrium report for PCDHGA12 (140810158 - 140892546 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for PCDHGA12:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2730847CNV Deletion23290073
    nsv462470CNV Loss19166990
    dgv6352n71CNV Loss21882294
    esv25744CNV Gain19812545
    dgv1857e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing PCDHGA12
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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: 603059    OMIM disorders: --


    Find genes that share disorders with PCDHGA12           About GenesLikeMe

    Genetic Association Database (GAD): PCDHGA12

    Export disorders for PCDHGA12 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 PCDHGA12 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with PCDHGA12)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)1, 2, 3 Wu Q. and Maniatis T. (Cell 1999)
    2. Multiple cadherins are expressed in human fibroblasts. (PubMed id 9199196)1, 2, 9 Matsuyoshi N. and Imamura S. (Biochem. Biophys. Res. Commun. 1997)
    3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    4. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PubMed id 9628581)1, 2 Nagase T....Ohara O. (DNA Res. 1998)
    5. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
    6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    7. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (Genome Res. 2001)
    8. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PubMed id 10835267)1 Nollet F....van Roy F. (J. Mol. Biol. 2000)
    9. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (Proc. Natl. Acad. Sci. U.S.A. 2000)
    10. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (amp 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
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      Query String
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    OMIM
    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: 26025 HGNC: 8699 AceView: PCDHGC3 Ensembl:ENSG00000253159 euGenes: HUgn26025
    ECgene: PCDHGA12 H-InvDB: PCDHGA12

    (According to HUGE)
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    HUGE: KIAA0588

    (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 PCDHGA12 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 PCDHGA12 gene:
    Search GeneIP for patents involving PCDHGA12

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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