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Aliases for PCDHA12 Gene

Aliases for PCDHA12 Gene

  • Protocadherin Alpha 12 2 3 5
  • KIAA0345-Like 2 2 3
  • PCDH-Alpha-12 3 4
  • Protocadherin Alpha-12 3
  • PCDH-ALPHA12 3

External Ids for PCDHA12 Gene

Previous GeneCards Identifiers for PCDHA12 Gene

  • GC05P140071
  • GC05P140759
  • GC05P140204
  • GC05P140197
  • GC05P140168
  • GC05P140240
  • GC05P140249
  • GC05P140258
  • GC05P140267
  • GC05P140277
  • GC05P140287
  • GC05P140298
  • GC05P140307
  • GC05P140319
  • GC05P140328
  • GC05P140340
  • GC05P135399
  • GC05P140360
  • GC05P140380
  • GC05P140390
  • GC05P140403
  • GC05P140420
  • GC05P140437
  • GC05P140451
  • GC05P141435
  • GC05P141570
  • GC05P141672
  • GC05P141773
  • GC05P141873
  • GC05P141982
  • GC05P142082

Summaries for PCDHA12 Gene

Entrez Gene Summary for PCDHA12 Gene

  • This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHA12 Gene

PCDHA12 (Protocadherin Alpha 12) is a Protein Coding gene. Diseases associated with PCDHA12 include Protocadherin-Alpha Gene Cluster. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHA10.

UniProtKB/Swiss-Prot for PCDHA12 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 PCDHA12 Gene

Additional gene information for PCDHA12 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA12 Gene

Genomics for PCDHA12 Gene

GeneHancer (GH) Regulatory Elements for PCDHA12 Gene

Promoters and enhancers for PCDHA12 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
GH05I140874 Promoter/Enhancer 1.1 EPDnew ENCODE 550.8 -0.2 -159 0.9 CTCF USF1 USF2 SIN3A ELF1 RAD21 MITF POLR2A SMC3 ENSG00000278915 PCDHA12 PCDHA9 IK ENSG00000278946 PCDHA11 PCDHA10 PCDHA8 PCDHA7 PCDHA6
GH05I141084 Enhancer 1.2 FANTOM5 Ensembl ENCODE 11.2 +209.4 209443 1.4 CTCF SAP130 RAD21 YY1 ZNF335 E2F1 ZNF23 GATA3 POLR2A ZNF143 PCDHAC2 PCDHB17P PCDHB1 MALINC1 IGIP PCDHGC4 PCDHB3 PCDHB10 PCDHAC1 PCDHA12
GH05I141832 Enhancer 0.9 ENCODE dbSUPER 11.1 +957.6 957572 1.5 ZNF449 NFIB ETV1 ZNF23 GATA3 PRDM10 RCOR1 TCF7L2 STAT1 CBFA2T3 PCDH1 PCDHAC2 PCDHA12 ARAP3 PCDHAC1 PCDHB17P KIAA0141 ENSG00000272108 PCDHA10 ENSG00000278925
GH05I140868 Promoter/Enhancer 1.2 EPDnew ENCODE 0.4 -6.1 -6071 0.8 CTCF PKNOX1 ESRRA ZBTB6 SIN3A CEBPG ZNF2 RAD21 ZNF335 CTBP1 PCDHA11 ENSG00000278946 PCDHA12 PCDHA10 PCDHA9 PCDHA8 PCDHA7 PCDHA6 PCDHA5 PCDHA4
GH05I140926 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 0.2 +51.3 51298 0.8 KLF17 SIN3A ZNF2 RAD21 ZEB1 ZNF335 GLIS2 ZNF143 KLF7 SP3 PCDHAC1 PCDHA11 PCDHA10 PIR58635 PCDHA13 PCDHA12 PCDHA9 PCDHA8 PCDHA7 PCDHA6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHA12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHA12 gene promoter:

Genomic Locations for PCDHA12 Gene

Genomic Locations for PCDHA12 Gene
137,043 bases
Plus strand

Genomic View for PCDHA12 Gene

Genes around PCDHA12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHA12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHA12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA12 Gene

Proteins for PCDHA12 Gene

  • Protein details for PCDHA12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin alpha-12
    Protein Accession:
    Secondary Accessions:
    • O75278
    • Q2M1N8

    Protein attributes for PCDHA12 Gene

    941 amino acids
    Molecular mass:
    101652 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHA12 Gene


neXtProt entry for PCDHA12 Gene

Post-translational modifications for PCDHA12 Gene

  • Glycosylation at Asn257, Asn265, and Asn548

Other Protein References for PCDHA12 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHA12 Gene

Domains & Families for PCDHA12 Gene

Gene Families for PCDHA12 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PCDHA12 Gene

Suggested Antigen Peptide Sequences for PCDHA12 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHA12: view

No data available for UniProtKB/Swiss-Prot for PCDHA12 Gene

Function for PCDHA12 Gene

Molecular function for PCDHA12 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 PCDHA12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHA12: view
genes like me logo Genes that share phenotypes with PCDHA12: view

Animal Model Products

miRNA for PCDHA12 Gene

miRTarBase miRNAs that target PCDHA12

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHA12 Gene

Localization for PCDHA12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA12 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 PCDHA12 gene
Compartment Confidence
plasma membrane 3

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PCDHA12 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 PCDHA12: view

Pathways & Interactions for PCDHA12 Gene

SuperPathways for PCDHA12 Gene

No Data Available

Interacting Proteins for PCDHA12 Gene

Gene Ontology (GO) - Biological Process for PCDHA12 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 PCDHA12: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHA12 Gene

Drugs & Compounds for PCDHA12 Gene

(1) Drugs for PCDHA12 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 PCDHA12: view

Transcripts for PCDHA12 Gene

mRNA/cDNA for PCDHA12 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA12 Gene

No ASD Table

Relevant External Links for PCDHA12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHA12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHA12 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHA12 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x8.2), Brain - Cerebellum (x5.0), and Testis (x4.2).

Protein differential expression in normal tissues from HIPED for PCDHA12 Gene

This gene is overexpressed in Cerebrospinal fluid (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHA12 Gene

Protein tissue co-expression partners for PCDHA12 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHA12 Gene:


Evidence on tissue expression from TISSUES for PCDHA12 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHA12: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHA12 Gene

Orthologs for PCDHA12 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHA12 33
  • 99.47 (n)
(Rattus norvegicus)
Mammalia Pcdha11 33
  • 78.31 (n)
(Mus musculus)
Mammalia Pcdha10 33 16
  • 77.97 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 67 (a)
-- 34
  • 65 (a)
-- 34
  • 64 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 62 (a)
(Gallus gallus)
Aves PCDHA11 34
  • 52 (a)
-- 34
  • 46 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 53 (a)
-- 34
  • 53 (a)
-- 34
  • 53 (a)
-- 34
  • 53 (a)
-- 34
  • 52 (a)
-- 34
  • 51 (a)
-- 34
  • 50 (a)
(Danio rerio)
Actinopterygii pcdh2ab1 34
  • 43 (a)
CT573264.5 34
  • 42 (a)
pcdh2ab11 34
  • 42 (a)
pcdh2ab12 34
  • 42 (a)
pcdh2ab3 34
  • 42 (a)
pcdh2ab8 34
  • 42 (a)
CR847851.6 34
  • 41 (a)
CR847851.8 34
  • 41 (a)
CT573264.4 34
  • 41 (a)
pcdh1a6 34
  • 41 (a)
pcdh2ab10 34
  • 41 (a)
pcdh2ab2 34 34
  • 41 (a)
pcdh2ab6 34
  • 41 (a)
pcdh2ab7 34
  • 41 (a)
pcdh2ab9 34
  • 41 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 32 (a)
CSA.7308 34
  • 19 (a)
Species where no ortholog for PCDHA12 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)
  • dog (Canis familiaris)
  • 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 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)

Evolution for PCDHA12 Gene

Gene Tree for PCDHA12 (if available)
Gene Tree for PCDHA12 (if available)

Paralogs for PCDHA12 Gene

Variants for PCDHA12 Gene

Sequence variations from dbSNP and Humsavar for PCDHA12 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs150254638 uncertain-significance, Hirschsprung disease 1 140,978,974(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs386352346 uncertain-significance, not provided 140,929,288(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000122176 -- 140,965,777(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000158608 -- 140,908,533(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000222500 -- 140,957,863(+) T/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHA12 Gene

Variant ID Type Subtype PubMed ID
nsv968992 CNV duplication 23825009
nsv968252 CNV duplication 23825009
nsv964956 CNV duplication 23825009
nsv823264 CNV gain 20364138
nsv599904 CNV loss 21841781
nsv10754 CNV gain 18304495
nsv1031849 CNV loss 25217958
esv3606959 CNV gain 21293372
esv2759382 CNV gain 17122850
esv2505753 CNV deletion 19546169

Variation tolerance for PCDHA12 Gene

Residual Variation Intolerance Score: 83.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.67; 57.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHA12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHA12 Gene

Disorders for PCDHA12 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDHA12 Gene - From: GeneCards

Disorder Aliases PubMed IDs
protocadherin-alpha gene cluster
  • pcdha@
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHA12

genes like me logo Genes that share disorders with PCDHA12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHA12 Gene

Publications for PCDHA12 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. The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J … Rubin EM (Nature 2004) 3 4 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PMID: 22589738) Fox CS … Borecki IB (PLoS genetics 2012) 3 58
  5. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. (PMID: 17474147) Wu C … Li SS (Proteomics 2007) 3 58

Products for PCDHA12 Gene

Sources for PCDHA12 Gene

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