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Aliases for PCDHGA12 Gene

Aliases for PCDHGA12 Gene

  • Protocadherin Gamma Subfamily A, 12 2 3 5
  • Fibroblast Cadherin FIB3 2 3
  • Fibroblast Cadherin-3 3 4
  • PCDH-GAMMA-A12 3 4
  • Cadherin 21 2 3
  • CDH21 3 4
  • FIB3 3 4
  • Protocadherin Gamma-A12 3
  • Cadherin-21 4
  • KIAA0588 4

External Ids for PCDHGA12 Gene

Previous HGNC Symbols for PCDHGA12 Gene

  • CDH21

Previous GeneCards Identifiers for PCDHGA12 Gene

  • GC05P140597
  • GC05P141318
  • GC05P140721
  • GC05P140780
  • GC05P140800
  • GC05P140740
  • GC05P140815
  • GC05P140838
  • GC05P140927
  • GC05P140949
  • GC05P140970
  • GC05P140992
  • GC05P141022
  • GC05P141052
  • GC05P141080
  • GC05P135955
  • GC05P141119
  • GC05P141144
  • GC05P141182
  • GC05P141213
  • GC05P141252
  • GC05P141298
  • GC05P141379
  • GC05P141448
  • GC05P141523
  • GC05P141643
  • GC05P141744
  • GC05P141843
  • GC05P141949
  • GC05P142051

Summaries for PCDHGA12 Gene

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. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA11.

UniProtKB/Swiss-Prot for PCDHGA12 Gene

  • 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

Additional gene information for PCDHGA12 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGA12 Gene

Genomics for PCDHGA12 Gene

GeneHancer (GH) Regulatory Elements for PCDHGA12 Gene

Promoters and enhancers for PCDHGA12 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I141429 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 550.8 +0.2 173 1.5 CTCF POLR2A TRIM22 ZNF143 MYC RAD21 PCDHGA12 PCDHGA1 HDAC3 PCDHGA11 PCDHGB9P PCDHGB7 PCDHGA10 PCDHGB6 PCDHGA9 PCDHGB5
GH05I141475 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 0.2 +46.5 46465 3.8 PKNOX1 NFIB SIN3A BATF RAD21 RFX5 YY1 ZNF335 ZNF143 BCLAF1 PCDHGC3 PCDHGA6 ARAP3 PCDHGA2 HDAC3 PCDHGA1 RN7SL68P PCDHGA12 PCDHGA11 PCDHGB7
GH05I141483 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 0.2 +53.9 53945 1.4 SP1 E2F1 POLR2A L3MBTL2 SIN3A RFX5 GC05P142209 PCDHGC4 PIR35622 PCDHGA6 PCDHGA11 IK PCDHGC3 RN7SL68P PCDHGA12 PCDHGB7
GH05I141493 Enhancer 1.1 FANTOM5 Ensembl ENCODE dbSUPER 0.2 +64.6 64566 3.2 POLR2A GLIS1 FOXP2 ZIC2 ENSG00000272070 CD14 PCDHB2 DIAPH1 RELL2 TAF7 PCDHB16 PCDHGC5 PCDHGC4 PCDHGC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHGA12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHGA12 gene promoter:

Genomic Locations for PCDHGA12 Gene

Genomic Locations for PCDHGA12 Gene
82,391 bases
Plus strand

Genomic View for PCDHGA12 Gene

Genes around PCDHGA12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGA12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGA12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGA12 Gene

Proteins for PCDHGA12 Gene

  • Protein details for PCDHGA12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin gamma-A12
    Protein Accession:
    Secondary Accessions:
    • O15100
    • Q6UW70
    • Q9Y5D7

    Protein attributes for PCDHGA12 Gene

    932 amino acids
    Molecular mass:
    100955 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAQ89305.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305}; Sequence=BAA25514.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for PCDHGA12 Gene


neXtProt entry for PCDHGA12 Gene

Post-translational modifications for PCDHGA12 Gene

  • Glycosylation at Asn265, Asn419, and isoforms=2545

Other Protein References for PCDHGA12 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGA12 Gene

Domains & Families for PCDHGA12 Gene

Gene Families for PCDHGA12 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted membrane proteins

Protein Domains for PCDHGA12 Gene

Suggested Antigen Peptide Sequences for PCDHGA12 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGA12: view

No data available for UniProtKB/Swiss-Prot for PCDHGA12 Gene

Function for PCDHGA12 Gene

Molecular function for PCDHGA12 Gene

UniProtKB/Swiss-Prot 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) - Molecular Function for PCDHGA12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGA12: view

Phenotypes for PCDHGA12 Gene

GenomeRNAi human phenotypes for PCDHGA12:
genes like me logo Genes that share phenotypes with PCDHGA12: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGA12 Gene

Localization for PCDHGA12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGA12 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

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 PCDHGA12 gene
Compartment Confidence
plasma membrane 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleus (2)
  • Plasma membrane (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDHGA12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHGA12: view

Pathways & Interactions for PCDHGA12 Gene

SuperPathways for PCDHGA12 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHGA12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IBA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development IBA --
genes like me logo Genes that share ontologies with PCDHGA12: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGA12 Gene

Drugs & Compounds for PCDHGA12 Gene

(1) Drugs for PCDHGA12 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with PCDHGA12: view

Transcripts for PCDHGA12 Gene

mRNA/cDNA for PCDHGA12 Gene

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGA12 Gene

No ASD Table

Relevant External Links for PCDHGA12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHGA12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGA12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDHGA12 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHGA12 Gene

Protein tissue co-expression partners for PCDHGA12 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGA12 Gene:


Evidence on tissue expression from TISSUES for PCDHGA12 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHGA12: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHGA12 Gene

Orthologs for PCDHGA12 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGA12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHGA12 33
  • 99.46 (n)
(Mus musculus)
Mammalia Pcdhga12 33 16
  • 83.93 (n)
(Rattus norvegicus)
Mammalia Pcdhga12 33
  • 83.75 (n)
(Canis familiaris)
Mammalia PCDHGA12 33
  • 83.11 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 70 (a)
-- 34
  • 69 (a)
-- 34
  • 68 (a)
-- 34
  • 67 (a)
-- 34
  • 66 (a)
-- 34
  • 59 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 67 (a)
-- 34
  • 64 (a)
-- 34
  • 62 (a)
(Gallus gallus)
Aves -- 34
  • 52 (a)
-- 34
  • 50 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 53 (a)
-- 34
  • 53 (a)
-- 34
  • 53 (a)
-- 34
  • 52 (a)
-- 34
  • 52 (a)
-- 34
  • 52 (a)
Species where no ortholog for PCDHGA12 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)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PCDHGA12 Gene

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

Paralogs for PCDHGA12 Gene

genes like me logo Genes that share paralogs with PCDHGA12: view

Variants for PCDHGA12 Gene

Sequence variations from dbSNP and Humsavar for PCDHGA12 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs386352347 uncertain-significance, not provided 141,485,635(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000022316 -- 141,472,751(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000136303 -- 141,452,887(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000138324 -- 141,499,091(+) A/C genic_downstream_transcript_variant, intron_variant
rs1000179570 -- 141,485,122(+) G/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGA12 Gene

Variant ID Type Subtype PubMed ID
nsv599923 CNV loss 21841781
nsv462470 CNV loss 19166990
nsv1125852 CNV tandem duplication 24896259
nsv1123990 CNV deletion 24896259
esv2759382 CNV gain 17122850
esv2730847 CNV deletion 23290073
esv25744 CNV gain 19812545

Variation tolerance for PCDHGA12 Gene

Residual Variation Intolerance Score: 56.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.85; 58.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHGA12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGA12 Gene

Disorders for PCDHGA12 Gene

Additional Disease Information for PCDHGA12

No disorders were found for PCDHGA12 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGA12 Gene

Publications for PCDHGA12 Gene

  1. A striking organization of a large family of human neural cadherin-like cell adhesion genes. (PMID: 10380929) Wu Q … Maniatis T (Cell 1999) 2 3 4 58
  2. Multiple cadherins are expressed in human fibroblasts. (PMID: 9199196) Matsuyoshi N … Imamura S (Biochemical and biophysical research communications 1997) 3 4 22 58
  3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 58
  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. (PMID: 9628581) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for PCDHGA12 Gene

Sources for PCDHGA12 Gene

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