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 ... See more...

Aliases for PCDHA12 Gene

Aliases for PCDHA12 Gene

  • Protocadherin Alpha 12 2 3 5
  • Protocadherin Alpha-12 3 4
  • KIAA0345-Like 2 2 3
  • PCDH-Alpha-12 3 4
  • PCDH-ALPHA12 2 3
  • PCDHA12 5

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
  • GC05P142510
  • GC05P142620
  • GC05P142744
  • GC05P142942
  • GC05P141672
  • GC05P141773
  • GC05P141873
  • GC05P141982
  • GC05P142082
  • GC05P142187
  • GC05P142283
  • GC05P142401
  • GC05P143150
  • GC05P143419

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 Hirschsprung Disease 1. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHA10.

UniProtKB/Swiss-Prot Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDHA12 Gene

Genomics for PCDHA12 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCDHA12 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
GH05J140874 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 250.7 +0.2 198 1.8 POLR2A CTCF SIN3A ELF1 RAD21 SMC3 TOE1 ZNF143 USF2 USF1 ENSG00000278915 LOC112267934 PCDHA12 PCDHA11 PCDHA9 IK PCDHA13 PCDHA10 PCDHA8 PCDHA7
GH05J140878 Promoter 0.3 EPDnew 250.7 +1.9 1877 0.1 ENSG00000278915 LOC112267934 PCDHA12 PCDHA13 PCDHA11 PCDHA10 PCDHA9 PCDHA8 PCDHA7 PCDHA6
GH05J140875 Enhancer 0.2 Ensembl 250.7 -1.4 -1401 0.2 LOC112267934 PCDHA12 ENSG00000279726 PCDHA11 PCDHA10 PCDHA9 PCDHA8 PCDHA7 PCDHA6 PCDHA5
GH05J141832 Enhancer 1 Ensembl ENCODE dbSUPER 11.1 +957.5 957501 1.6 NFIC CEBPB EP300 ELF1 CUX1 STAT3 TCF7L2 ETV1 NFIB GATA2 HSALNG0045454 HSALNG0045455 PCDH1 PCDHAC2 PCDHA12 ARAP3 PCDHAC1 PCDHB17P DELE1 ENSG00000272108
GH05J141777 Enhancer 0.9 Ensembl dbSUPER 11.1 +904.2 904199 3.4 ZNF600 JUND ZIC2 BHLHE40 MNT SIN3A SP2 ZNF316 ZBTB48 REST PCDHAC2 PCDHA12 PCDHAC1 PCDHB17P PCDHA2 ENSG00000272108 PCDHA10 HSALNG0045445 HSALNG0045443 ENSG00000286736
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHA12 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDHA12

Top Transcription factor binding sites by QIAGEN in the PCDHA12 gene promoter:
  • AP-4
  • C/EBPalpha
  • CHOP-10
  • FOXD3
  • FOXO1
  • FOXO1a
  • FOXO4
  • HFH-1
  • p300
  • Sox9

Genomic Locations for PCDHA12 Gene

Latest Assembly
chr5:140,875,302-141,012,347
(GRCh38/hg38)
Size:
137,046 bases
Orientation:
Plus strand

Previous Assembly
chr5:140,254,893-140,391,932
(GRCh37/hg19 by Entrez Gene)
Size:
137,040 bases
Orientation:
Plus strand

chr5:140,255,058-140,391,929
(GRCh37/hg19 by Ensembl)
Size:
136,872 bases
Orientation:
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:
    Q9UN75-PCDAC_HUMAN
    Recommended name:
    Protocadherin alpha-12
    Protein Accession:
    Q9UN75
    Secondary Accessions:
    • O75278
    • Q2M1N8

    Protein attributes for PCDHA12 Gene

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

    Alternative splice isoforms for PCDHA12 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHA12 Gene

Post-translational modifications for PCDHA12 Gene

  • Glycosylation at Asn257, Asn265, and Asn548
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PCDAC_HUMAN (1675)

Other Protein References for PCDHA12 Gene

Antibodies for research

  • Abcam antibodies for PCDHA12
  • Boster Bio Antibodies for PCDHA12

No data available for DME Specific Peptides for PCDHA12 Gene

Domains & Families for PCDHA12 Gene

Gene Families for PCDHA12 Gene

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

Protein Domains for PCDHA12 Gene

Suggested Antigen Peptide Sequences for PCDHA12 Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin alpha-12 (PCDAC_HUMAN)
genes like me logo Genes that share domains with PCDHA12: view

No data available for Graphical View of Domain Structure and 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.

Phenotypes From GWAS Catalog for PCDHA12 Gene

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

miRNA for PCDHA12 Gene

miRTarBase miRNAs that target PCDHA12

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHA12

No data available for Enzyme Numbers (IUBMB) , 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

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 PCDHA12 gene
Compartment Confidence
plasma membrane 3

Subcellular locations from the

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

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 21873635
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

PathCards logo

SuperPathways for PCDHA12 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHA12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,IBA 21873635
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
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 Nutra 6959
genes like me logo Genes that share compounds with PCDHA12: view

Transcripts for PCDHA12 Gene

mRNA/cDNA for PCDHA12 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHA12

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

No ASD Table

Relevant External Links for PCDHA12 Gene

GeneLoc Exon Structure for
PCDHA12

Expression for PCDHA12 Gene

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



Protein tissue co-expression partners for PCDHA12 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDHA12

Evidence on tissue expression from TISSUES for PCDHA12 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with PCDHA12: view

Primer products for research

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
Chimpanzee
(Pan troglodytes)
Mammalia PCDHA12 29
  • 99.47 (n)
Rat
(Rattus norvegicus)
Mammalia Pcdha11 29
  • 78.31 (n)
Mouse
(Mus musculus)
Mammalia Pcdha10 29 16
  • 77.97 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 67 (a)
ManyToMany
-- 30
  • 65 (a)
ManyToMany
-- 30
  • 64 (a)
ManyToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 62 (a)
OneToMany
Chicken
(Gallus gallus)
Aves PCDHA11 30
  • 52 (a)
ManyToMany
-- 30
  • 46 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 55 (a)
ManyToMany
-- 30
  • 55 (a)
ManyToMany
-- 30
  • 54 (a)
ManyToMany
-- 30
  • 54 (a)
ManyToMany
-- 30
  • 54 (a)
ManyToMany
-- 30
  • 54 (a)
ManyToMany
-- 30
  • 54 (a)
ManyToMany
-- 30
  • 54 (a)
ManyToMany
-- 30
  • 54 (a)
ManyToMany
-- 30
  • 53 (a)
ManyToMany
-- 30
  • 53 (a)
ManyToMany
-- 30
  • 53 (a)
ManyToMany
-- 30
  • 53 (a)
ManyToMany
-- 30
  • 52 (a)
ManyToMany
-- 30
  • 51 (a)
ManyToMany
-- 30
  • 50 (a)
ManyToMany
Zebrafish
(Danio rerio)
Actinopterygii pcdh2ab1 30
  • 43 (a)
ManyToMany
pcdh2ab3 30
  • 42 (a)
ManyToMany
CT573264.5 30
  • 42 (a)
ManyToMany
pcdh2ab8 30
  • 42 (a)
ManyToMany
pcdh2ab12 30
  • 42 (a)
ManyToMany
pcdh2ab11 30
  • 42 (a)
ManyToMany
CR847851.8 30
  • 41 (a)
ManyToMany
pcdh2ab7 30
  • 41 (a)
ManyToMany
pcdh2ab9 30
  • 41 (a)
ManyToMany
pcdh2ab6 30
  • 41 (a)
ManyToMany
CR847851.6 30
  • 41 (a)
ManyToMany
pcdh1a6 30
  • 41 (a)
ManyToMany
pcdh2ab2 30 30
  • 41 (a)
ManyToMany
pcdh2ab10 30
  • 41 (a)
ManyToMany
CT573264.4 30
  • 41 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 32 (a)
ManyToMany
CSA.7308 30
  • 19 (a)
ManyToMany
Species where no ortholog for PCDHA12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for PCDHA12 (if available)
TreeFam:
Gene Tree for PCDHA12 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDHA12: view image
Alliance of Genome Resources:
Additional Orthologs for PCDHA12

Paralogs for PCDHA12 Gene

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

Variants for PCDHA12 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDHA12 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs150254638 Uncertain Significance: Hirschsprung disease 1 140,978,974(+) G/A
NM_018899.6(PCDHAC2):c.2591G>A (p.Arg864His)
MISSENSE
rs1554262284 Likely Benign: not provided 141,009,697(+) C/T
NM_018904.3(PCDHA13):c.2613C>T (p.Tyr871=)
SYNONYMOUS
rs200585286 Likely Benign: not provided 141,009,754(+) C/A
NM_018906.3(PCDHA3):c.2670C>A (p.Ile890=)
SYNONYMOUS
rs386352346 Uncertain Significance: not provided 140,929,288(+) G/A
NM_018901.4(PCDHA10):c.2389-49661G>A
MISSENSE_VARIANT,INTRON
rs560855761 Likely Benign: not provided 140,978,960(+) C/G
NM_031857.2(PCDHA9):c.2406C>G (p.Pro802=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PCDHA12 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

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

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

Human Gene Mutation Database (HGMD)
PCDHA12
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHA12
Leiden Open Variation Database (LOVD)
PCDHA12

SNP Genotyping and Copy Number Assays for research

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: GCD

Disorder Aliases PubMed IDs
hirschsprung disease 1
  • hirschsprung disease, susceptibility to, 1
- 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
  2. The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J … Rubin EM (Nature 2004) 3 4
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  4. A Genome-Wide CRISPR Screen Identifies Genes Critical for Resistance to FLT3 Inhibitor AC220. (PMID: 28625976) Hou P … Huang J (Cancer research 2017) 3
  5. 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

Products for PCDHA12 Gene

Sources for PCDHA12 Gene