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Aliases for PCDH12 Gene

Aliases for PCDH12 Gene

  • Protocadherin 12 2 3 5
  • Vascular Cadherin-2 3 4
  • VE-Cadherin-2 3 4
  • VE-Cad-2 3 4
  • Vascular Endothelial Cadherin 2 3
  • Vascular Endothelial Cadherin-2 4
  • Protocadherin-12 3
  • VE-Cadherin 2 3
  • VECAD2 3

External Ids for PCDH12 Gene

Previous GeneCards Identifiers for PCDH12 Gene

  • GC05M141146
  • GC05M141907
  • GC05M141307
  • GC05M141353
  • GC05M141305
  • GC05M136467

Summaries for PCDH12 Gene

Entrez Gene Summary for PCDH12 Gene

  • This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 6 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of the classical cadherins. The gene localizes to the region on chromosome 5 where the protocadherin gene clusters reside. The exon organization of this transcript is similar to that of the gene cluster transcripts, notably the first large exon, but no significant sequence homology exists. The function of this cellular adhesion protein is undetermined but mouse protocadherin 12 does not bind catenins and appears to have no affect on cell migration or growth. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDH12 Gene

PCDH12 (Protocadherin 12) is a Protein Coding gene. Diseases associated with PCDH12 include Microcephaly With Spastic Quadriplegia and Microcephaly, Seizures, Spasticity, And Brain Calcifications. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH18.

UniProtKB/Swiss-Prot for PCDH12 Gene

  • Cellular adhesion molecule that may play an important role in cell-cell interactions at interendothelial junctions. Promotes homotypic calcium-dependent aggregation and adhesion and clusters at intercellular junctions. Unable to bind to catenins, weakly associates with the cytoskeleton (By similarity).

Gene Wiki entry for PCDH12 Gene

Additional gene information for PCDH12 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH12 Gene

Genomics for PCDH12 Gene

GeneHancer (GH) Regulatory Elements for PCDH12 Gene

Promoters and enhancers for PCDH12 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
GH05I141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.2 174 3 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B RNF14 PCDH12 PCDHB18P PCDHGA6 PCDHGA7 LOC102723915 HDAC3 KIAA0141 PCDHGA5 PCDHB12
GH05I141957 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 550.4 +10.4 10381 4.5 HDGF ARNT ARID4B ZNF2 ETS1 ZNF766 E2F8 ELK1 ARID2 ZNF143 RNF14 GC05M141957 PCDH12 LOC102723915 HDAC3 KIAA0141 FCHSD1 ARAP3 ENSG00000271871 PCDH1
GH05I141679 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 10.5 +287.9 287930 4.7 HDGF ARNT SIN3A ZNF2 CBX5 ZNF213 FOS SP3 REST ZNF592 ARAP3 PCDHB19P HARS2 KIAA0141 PCDHB18P PCDHGA7 PCDH1 PCDH12 RNF14 HDAC3
GH05I141882 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 11.1 +87.5 87480 1.9 PKNOX1 KLF1 RFX1 ZNF449 EBF1 REST BMI1 GLIS2 POLR2A RFX3 GC05P142196 KIAA0141 RNF14 PCDH12 ARAP3 PCDHGC4 PCDHGA9 PCDHGC5 PCDH1 NDFIP1
GH05I141691 Enhancer 1.2 Ensembl ENCODE 11.7 +277.7 277723 1.6 ARNT ARID4B SIN3A ZNF2 IRF4 ZNF766 ZNF213 ZNF207 ZNF143 KLF13 RNF14 PCDH12 PCDH1 FCHSD1 HDAC3 RELL2 KIAA0141 GNPDA1 ARAP3 ENSG00000278925
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDH12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDH12 gene promoter:

Genomic Locations for PCDH12 Gene

Genomic Locations for PCDH12 Gene
26,157 bases
Minus strand

Genomic View for PCDH12 Gene

Genes around PCDH12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDH12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDH12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH12 Gene

Proteins for PCDH12 Gene

  • Protein details for PCDH12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q6UXB6
    • Q96KB8
    • Q9H7Y6
    • Q9H8E0

    Protein attributes for PCDH12 Gene

    1184 amino acids
    Molecular mass:
    128995 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDH12 Gene

Post-translational modifications for PCDH12 Gene

  • Glycosylation at Asn415, Asn582, isoforms=659, and isoforms=662

Other Protein References for PCDH12 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDH12 Gene

Domains & Families for PCDH12 Gene

Gene Families for PCDH12 Gene

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

Protein Domains for PCDH12 Gene

Suggested Antigen Peptide Sequences for PCDH12 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDH12: view

No data available for UniProtKB/Swiss-Prot for PCDH12 Gene

Function for PCDH12 Gene

Molecular function for PCDH12 Gene

UniProtKB/Swiss-Prot Function:
Cellular adhesion molecule that may play an important role in cell-cell interactions at interendothelial junctions. Promotes homotypic calcium-dependent aggregation and adhesion and clusters at intercellular junctions. Unable to bind to catenins, weakly associates with the cytoskeleton (By similarity).

Phenotypes From GWAS Catalog for PCDH12 Gene

Gene Ontology (GO) - Molecular Function for PCDH12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDH12: view
genes like me logo Genes that share phenotypes with PCDH12: view

Animal Models for PCDH12 Gene

MGI Knock Outs for PCDH12:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for PCDH12 Gene

Localization for PCDH12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH12 Gene

Cell membrane; Single-pass type I membrane protein. Cell junction.

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 PCDH12 gene
Compartment Confidence
plasma membrane 5
extracellular 5

Gene Ontology (GO) - Cellular Components for PCDH12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS 10380929
GO:0005887 integral component of plasma membrane TAS 10716726
GO:0005911 cell-cell junction IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDH12: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDH12 Gene

Pathways & Interactions for PCDH12 Gene

SuperPathways for PCDH12 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDH12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005977 glycogen metabolic process IEA --
GO:0007155 cell adhesion IBA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0008038 neuron recognition TAS 10380929
genes like me logo Genes that share ontologies with PCDH12: view

No data available for Pathways by source and SIGNOR curated interactions for PCDH12 Gene

Drugs & Compounds for PCDH12 Gene

(1) Drugs for PCDH12 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 PCDH12: view

Transcripts for PCDH12 Gene

mRNA/cDNA for PCDH12 Gene

Unigene Clusters for PCDH12 Gene

Protocadherin 12:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH12 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5

Relevant External Links for PCDH12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDH12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDH12 Gene

mRNA differential expression in normal tissues according to GTEx for PCDH12 Gene

This gene is overexpressed in Spleen (x5.9).

Protein differential expression in normal tissues from HIPED for PCDH12 Gene

This gene is overexpressed in Serum (51.3) and Plasma (17.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDH12 Gene

Protein tissue co-expression partners for PCDH12 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDH12 Gene:


SOURCE GeneReport for Unigene cluster for PCDH12 Gene:


mRNA Expression by UniProt/SwissProt for PCDH12 Gene:

Tissue specificity: Expressed in highly vascularized tissues including the heart and placenta, but most tissues contain a low level of expression. Prominent expression in the spleen.

Evidence on tissue expression from TISSUES for PCDH12 Gene

  • Liver(4.1)
genes like me logo Genes that share expression patterns with PCDH12: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDH12 Gene

Orthologs for PCDH12 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDH12 33 34
  • 99.32 (n)
(Bos Taurus)
Mammalia PCDH12 33 34
  • 87.31 (n)
(Canis familiaris)
Mammalia PCDH12 33 34
  • 86.82 (n)
(Mus musculus)
Mammalia Pcdh12 33 16 34
  • 82.73 (n)
(Rattus norvegicus)
Mammalia Pcdh12 33
  • 82.29 (n)
(Monodelphis domestica)
Mammalia PCDH12 34
  • 71 (a)
(Gallus gallus)
Aves PCDH12 33 34
  • 62.04 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh12 33
  • 57.49 (n)
(Danio rerio)
Actinopterygii pcdh12 33
  • 53.6 (n)
PCDH12 34
  • 42 (a)
Species where no ortholog for PCDH12 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)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PCDH12 Gene

Gene Tree for PCDH12 (if available)
Gene Tree for PCDH12 (if available)

Paralogs for PCDH12 Gene

Variants for PCDH12 Gene

Sequence variations from dbSNP and Humsavar for PCDH12 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs375346212 pathogenic, Microcephaly with spastic quadriplegia 141,955,337(-) G/A/T coding_sequence_variant, stop_gained, synonymous_variant
rs1000035838 -- 141,958,479(-) C/T 5_prime_UTR_variant
rs1000041136 -- 141,943,922(-) C/G 3_prime_UTR_variant
rs1000195098 -- 141,950,448(-) T/A intron_variant
rs1000242762 -- 141,950,696(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDH12 Gene

Variant ID Type Subtype PubMed ID
nsv599924 CNV gain 21841781
nsv526702 CNV loss 19592680
nsv1154058 CNV deletion 26484159

Variation tolerance for PCDH12 Gene

Residual Variation Intolerance Score: 75.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.75; 66.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDH12 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDH12 Gene

Disorders for PCDH12 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PCDH12 Gene - From: HGMD, ClinVar, and DISEASES

Disorder Aliases PubMed IDs
microcephaly with spastic quadriplegia
  • recessive microcephaly with spastic quadriplegia
microcephaly, seizures, spasticity, and brain calcifications
  • missbc
aicardi-goutieres syndrome
  • cree encephalitis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDH12

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PCDH12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDH12 Gene

Publications for PCDH12 Gene

  1. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PMID: 10716726) Wu Q … Maniatis T (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4 22 58
  2. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. (PMID: 19054571) Gregório SP … Dias-Neto E (Psychiatry research 2009) 3 22 44 58
  3. cDNA cloning, chromosomal mapping, and expression analysis of human VE-Cadherin-2. (PMID: 11063261) Ludwig D … Pytowski B (Mammalian genome : official journal of the International Mammalian Genome Society 2000) 3 4 22 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. 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

Products for PCDH12 Gene

Sources for PCDH12 Gene

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