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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, Seizures, Spasticity, And Brain Calcifications and Microcephaly With Spastic Quadriplegia. 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 (By similarity). Acts as a regulator of cell migration, probably via increasing cell-cell adhesion (PubMed:21402705). Promotes homotypic calcium-dependent aggregation and adhesion and clusters at intercellular junctions (By similarity). 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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.2 174 3 CLOCK DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC GLIS1 RNF14 PCDH12 LOC102723915 HDAC3 PCDHB18P PCDHGA6 PCDHGA7 DELE1 PCDHGA5 ENSG00000271871
GH05J141957 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 650.4 +10.4 10381 4.5 HDGF ARNT ARID4B ZNF2 ETS1 ZNF766 E2F8 ELK1 ARID2 ZNF143 RNF14 GC05M141957 PCDH12 LOC102723915 HDAC3 DELE1 FCHSD1 ARAP3 ENSG00000271871 PCDH1
GH05J141679 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 10.5 +287.9 287930 4.7 HDGF ARNT SIN3A ZNF2 YY1 CBX5 ZNF213 FOS SP3 REST ARAP3 PCDHB19P HARS2 DELE1 PCDHB18P PCDHGA7 PCDH1 PCDH12 RNF14 HDAC3
GH05J141691 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 DELE1 GNPDA1 ARAP3 ENSG00000278925
GH05J141882 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 11.1 +87.5 87480 1.9 PKNOX1 KLF1 RFX1 EBF1 BMI1 GLIS2 POLR2A RFX3 CTBP2 ZNF143 GC05P142293 DELE1 RNF14 PCDH12 ARAP3 PCDHGC4 PCDHGA9 PCDHGC5 NDFIP1 PCDH1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDH12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDH12 gene promoter:
  • FOXL1
  • RelA
  • NF-kappaB1
  • NF-kappaB
  • ITF-2
  • Tal-1beta
  • HFH-1
  • Zic1
  • AREB6
  • Evi-1

Genomic Locations for PCDH12 Gene

Genomic Locations for PCDH12 Gene
chr5:141,943,585-141,969,741
(GRCh38/hg38)
Size:
26,157 bases
Orientation:
Minus strand
chr5:141,323,150-141,349,304
(GRCh37/hg19)
Size:
26,155 bases
Orientation:
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:
    Q9NPG4-PCD12_HUMAN
    Recommended name:
    Protocadherin-12
    Protein Accession:
    Q9NPG4
    Secondary Accessions:
    • Q6UXB6
    • Q96KB8
    • Q9H7Y6
    • Q9H8E0

    Protein attributes for PCDH12 Gene

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

neXtProt entry for PCDH12 Gene

Post-translational modifications for PCDH12 Gene

  • Protocadherin-12: Cleaved by ADAM10 close to the transmembrane domain to release the Protocadherin-12, secreted form in the serum. Cleavage results in reduced cellular adhesion in a cell migration assay.
  • Glycosylation at isoforms=662, isoforms=659, isoforms=582, and isoforms=415
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDH12 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • R&D Systems Antibodies for PCDH12 (Protocadherin-12)
  • Abcam antibodies for PCDH12
  • Boster Bio Antibodies for PCDH12

No data available for DME Specific Peptides for PCDH12 Gene

Domains & Families for PCDH12 Gene

Gene Families for PCDH12 Gene

HGNC:
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 (By similarity). Acts as a regulator of cell migration, probably via increasing cell-cell adhesion (PubMed:21402705). Promotes homotypic calcium-dependent aggregation and adhesion and clusters at intercellular junctions (By similarity). 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

Human Phenotype Ontology for PCDH12 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PCDH12 Gene

MGI Knock Outs for PCDH12:

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDH12

Clone Products

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

Localization for PCDH12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH12 Gene

Protocadherin-12: Cell membrane; Single-pass type I membrane protein. Cell junction.
Protocadherin-12, secreted form: Secreted. Note=The secreted form is produced following cleavage by ADAM10. {ECO:0000269 PubMed:21402705}.

Subcellular locations from

COMPARTMENTS
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
SP1:
SP2:

Relevant External Links for PCDH12 Gene

GeneLoc Exon Structure for
PCDH12
ECgene alternative splicing isoforms for
PCDH12

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 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:

PCDH12

SOURCE GeneReport for Unigene cluster for PCDH12 Gene:

Hs.439474

mRNA Expression by UniProt/SwissProt for PCDH12 Gene:

Q9NPG4-PCD12_HUMAN
Tissue specificity: Expressed in highly vascularized tissues including the heart and placenta, but most tissues contain a low level of expression (PubMed:11063261). Prominent expression in the spleen (PubMed:11063261). Present in villous and extravillous trophoblast (at protein level) (PubMed:21402705).

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
chimpanzee
(Pan troglodytes)
Mammalia PCDH12 34 33
  • 99.32 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PCDH12 34 33
  • 87.31 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PCDH12 34 33
  • 86.82 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pcdh12 16 34 33
  • 82.73 (n)
rat
(Rattus norvegicus)
Mammalia Pcdh12 33
  • 82.29 (n)
oppossum
(Monodelphis domestica)
Mammalia PCDH12 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves PCDH12 34 33
  • 62.04 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh12 33
  • 57.49 (n)
zebrafish
(Danio rerio)
Actinopterygii pcdh12 33
  • 53.6 (n)
PCDH12 34
  • 42 (a)
OneToOne
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

ENSEMBL:
Gene Tree for PCDH12 (if available)
TreeFam:
Gene Tree for PCDH12 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDH12: view image

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
VAR_080386 Microcephaly, seizures, spasticity, and brain calcifications (MISSBC) [MIM:251280] p.Ser147Ile
VAR_080387 Microcephaly, seizures, spasticity, and brain calcifications (MISSBC) [MIM:251280] p.Ile332Asn
VAR_080389 Microcephaly, seizures, spasticity, and brain calcifications (MISSBC) [MIM:251280] p.Gly1091Ser
rs1000035838 -- 141,958,479(-) C/T 5_prime_UTR_variant

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

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

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)
PCDH12
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDH12

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

Disorders for PCDH12 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PCDH12 Gene - From: HGMD, OMIM, ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
microcephaly, seizures, spasticity, and brain calcifications
  • missbc
microcephaly with spastic quadriplegia
  • recessive microcephaly with spastic quadriplegia
dyskinetic cerebral palsy
  • athetoid dyskinetic cerebral palsy
spasticity
microcephaly
  • microcephalus
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PCD12_HUMAN
  • Microcephaly, seizures, spasticity, and brain calcifications (MISSBC) [MIM:251280]: An autosomal recessive syndrome characterized by congenital microcephaly, hypothalamic midbrain dysplasia, epilepsy, and severe global developmental delay with profound intellectual disability, spasticity or dystonia. Brain imaging shows intracerebral calcifications. {ECO:0000269 PubMed:27164683, ECO:0000269 PubMed:28804758}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PCDH12

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

No data available for 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. Loss of function of PCDH12 underlies recessive microcephaly mimicking intrauterine infection. (PMID: 27164683) Aran A … Levy-Lahad E (Neurology 2016) 3 4 58
  5. Protocadherin-12 cleavage is a regulated process mediated by ADAM10 protein: evidence of shedding up-regulation in pre-eclampsia. (PMID: 21402705) Bouillot S … Huber P (The Journal of biological chemistry 2011) 3 4 58

Products for PCDH12 Gene

Sources for PCDH12 Gene

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