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Aliases for PCDHA2 Gene

Aliases for PCDHA2 Gene

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

External Ids for PCDHA2 Gene

Previous GeneCards Identifiers for PCDHA2 Gene

  • GC05P139991
  • GC05P140749
  • GC05P140151
  • GC05P140206
  • GC05P140199
  • GC05P140160
  • GC05P135319
  • GC05P141233
  • GC05P141477
  • GC05P141587
  • GC05P141690
  • GC05P141792
  • GC05P141885
  • GC05P141994

Summaries for PCDHA2 Gene

Entrez Gene Summary for PCDHA2 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 PCDHA2 Gene

PCDHA2 (Protocadherin Alpha 2) is a Protein Coding gene. Diseases associated with PCDHA2 include Protocadherin-Alpha Gene Cluster. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHA1.

UniProtKB/Swiss-Prot for PCDHA2 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 PCDHA2 Gene

Additional gene information for PCDHA2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA2 Gene

Genomics for PCDHA2 Gene

GeneHancer (GH) Regulatory Elements for PCDHA2 Gene

Promoters and enhancers for PCDHA2 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
GH05I140794 Promoter 0.6 EPDnew 550.8 +0.1 83 0.1 CTCF PCDHA2 PCDHA1 PCDHA3 PCDHA@ ENSG00000279726
GH05I140795 Promoter 0.6 EPDnew 550.8 0.0 -19 0.1 CTCF PCDHA2 PCDHA1 PCDHA@ ENSG00000279726
GH05I140036 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 21 -754.4 -754366 7 SIN3A ZNF2 IRF4 GLIS2 ZNF207 ZNF143 ATF7 KLF7 FOS RUNX3 NRG2 PCDHA2 PCDHA3 PCDHA7 PURA PCDHA6 PCDHA10 DNAJC18 PFDN1 MATR3
GH05I140291 Enhancer 1.4 Ensembl ENCODE dbSUPER 21.7 -499.2 -499223 7.9 PKNOX1 SMAD1 FEZF1 ZNF2 NCOA2 ZNF213 KLF7 FOS ATF7 ZNF214 PCDHB18P PURA ENSG00000272108 PCDHB19P PCDHB9 PCDHB6 PCDHB5 PCDHB10 PCDHB17P PCDHB15
GH05I140637 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 13.8 -155.8 -155846 2.8 HDGF PKNOX1 SMAD1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 TMCO6 HARS2 ANKHD1 WDR55 HDAC3 LOC102723915 SRA1 PURA MALINC1 CD14
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHA2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHA2 gene promoter:

Genomic Locations for PCDHA2 Gene

Genomic Locations for PCDHA2 Gene
217,493 bases
Plus strand

Genomic View for PCDHA2 Gene

Genes around PCDHA2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHA2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHA2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA2 Gene

Proteins for PCDHA2 Gene

  • Protein details for PCDHA2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin alpha-2
    Protein Accession:
    Secondary Accessions:
    • O75287
    • Q9BTV3

    Protein attributes for PCDHA2 Gene

    948 amino acids
    Molecular mass:
    102063 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHA2 Gene


neXtProt entry for PCDHA2 Gene

Post-translational modifications for PCDHA2 Gene

  • Glycosylation at isoforms=2, 3257, Asn265, Asn362, and Asn548

Other Protein References for PCDHA2 Gene

No data available for DME Specific Peptides for PCDHA2 Gene

Domains & Families for PCDHA2 Gene

Gene Families for PCDHA2 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PCDHA2 Gene

Suggested Antigen Peptide Sequences for PCDHA2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHA2: view

No data available for UniProtKB/Swiss-Prot for PCDHA2 Gene

Function for PCDHA2 Gene

Molecular function for PCDHA2 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 PCDHA2 Gene

Gene Ontology (GO) - Molecular Function for PCDHA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHA2: view
genes like me logo Genes that share phenotypes with PCDHA2: view

miRNA for PCDHA2 Gene

miRTarBase miRNAs that target PCDHA2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHA2 Gene

Localization for PCDHA2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA2 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 PCDHA2 gene
Compartment Confidence
plasma membrane 5
nucleus 2
endoplasmic reticulum 2
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PCDHA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane TAS 10380929
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PCDHA2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDHA2 Gene

Pathways & Interactions for PCDHA2 Gene

SuperPathways for PCDHA2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 10380929
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development TAS 10380929
genes like me logo Genes that share ontologies with PCDHA2: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHA2 Gene

Drugs & Compounds for PCDHA2 Gene

(1) Drugs for PCDHA2 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 PCDHA2: view

Transcripts for PCDHA2 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA2 Gene

No ASD Table

Relevant External Links for PCDHA2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHA2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHA2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PCDHA2 Gene

This gene is overexpressed in Brain - Cerebellum (x5.6), Brain - Cerebellar Hemisphere (x4.7), and Pituitary (x4.6).

Protein differential expression in normal tissues from HIPED for PCDHA2 Gene

This gene is overexpressed in Lung (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHA2 Gene

Protein tissue co-expression partners for PCDHA2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHA2 Gene:


Evidence on tissue expression from TISSUES for PCDHA2 Gene

  • Blood(4)
  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHA2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHA2 Gene

Orthologs for PCDHA2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHA2 33
  • 99.33 (n)
(Mus musculus)
Mammalia Pcdha2 33 16
  • 84.74 (n)
(Rattus norvegicus)
Mammalia Pcdha2 33
  • 84.09 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 70 (a)
-- 34
  • 68 (a)
-- 34
  • 66 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 63 (a)
(Gallus gallus)
Aves PCDHA3 33
  • 66.15 (n)
PCDHA11 34
  • 54 (a)
-- 34
  • 48 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 56 (a)
-- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 55 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 53 (a)
-- 34
  • 53 (a)
-- 34
  • 51 (a)
(Danio rerio)
Actinopterygii pcdh2ab1 34
  • 43 (a)
pcdh2ab8 34
  • 43 (a)
CT573264.5 34
  • 42 (a)
pcdh1a6 34
  • 42 (a)
pcdh2ab12 34
  • 42 (a)
pcdh2ab3 34
  • 42 (a)
pcdh2ab6 34
  • 42 (a)
CR847851.6 34
  • 41 (a)
CR847851.8 34
  • 41 (a)
CT573264.4 34
  • 41 (a)
pcdh2ab10 34
  • 41 (a)
pcdh2ab11 34
  • 41 (a)
pcdh2ab2 34 34
  • 41 (a)
pcdh2ab7 34
  • 41 (a)
pcdh2ab9 34
  • 41 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 33 (a)
CSA.7308 34
  • 20 (a)
Species where no ortholog for PCDHA2 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 PCDHA2 Gene

Gene Tree for PCDHA2 (if available)
Gene Tree for PCDHA2 (if available)

Paralogs for PCDHA2 Gene

Variants for PCDHA2 Gene

Sequence variations from dbSNP and Humsavar for PCDHA2 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
rs193920994 uncertain-significance, Malignant tumor of prostate 140,857,214(+) C/T genic_downstream_transcript_variant, intron_variant
rs587776956 uncertain-significance, Variant of unknown significance 140,802,947(+) T/C genic_downstream_transcript_variant, intron_variant
rs139390480 likely-benign, not specified 140,856,945(+) A/T genic_downstream_transcript_variant, intron_variant
rs386352344 uncertain-significance, not provided 140,795,974(+) C/A/T coding_sequence_variant, missense_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for PCDHA2 Gene

Variant ID Type Subtype PubMed ID
dgv724n27 CNV loss 19166990
dgv970n67 CNV gain 20364138
dgv971n67 CNV loss 20364138
dgv972n67 CNV gain 20364138
esv21596 CNV gain 19812545
esv2421858 CNV deletion 20811451
esv2505753 CNV deletion 19546169
esv26168 CNV gain 19812545
esv2657537 CNV deletion 23128226
esv2659321 CNV deletion 23128226
esv27071 CNV loss 19812545
esv2730838 CNV deletion 23290073
esv2730839 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv2861013 CNV duplication 24192839
esv29977 CNV gain 17803354
esv3606955 CNV loss 21293372
esv3606956 CNV loss 21293372
esv3606957 CNV gain 21293372
esv3606958 CNV loss 21293372
esv3606959 CNV gain 21293372
esv3890744 CNV loss 25118596
esv8310 CNV loss 19470904
nsv1024237 CNV loss 25217958
nsv1031849 CNV loss 25217958
nsv10752 CNV gain+loss 18304495
nsv10753 CNV gain 18304495
nsv10754 CNV gain 18304495
nsv1133616 CNV deletion 24896259
nsv1135376 CNV deletion 24896259
nsv1161301 OTHER complex 26073780
nsv330045 CNV deletion 16902084
nsv436885 CNV insertion 17901297
nsv437955 CNV loss 16468122
nsv442962 CNV loss 18776908
nsv514324 CNV loss 21397061
nsv515909 CNV loss 19592680
nsv964954 CNV duplication 23825009
nsv964955 CNV duplication 23825009
nsv964956 CNV duplication 23825009
nsv968251 CNV duplication 23825009
nsv968252 CNV duplication 23825009
nsv968992 CNV duplication 23825009
nsv980734 CNV duplication 23825009
esv3566721 CNV deletion 23714750
esv33939 CNV gain+loss 17666407
dgv3182n106 CNV deletion 24896259
dgv1653e212 CNV loss 25503493
dgv1652e212 CNV loss 25503493
dgv1651e212 CNV loss 25503493
dgv138e203 CNV loss 21179565
dgv1044e199 CNV deletion 23128226
dgv1043e199 CNV deletion 23128226
dgv10105n54 CNV loss 21841781
dgv10104n54 CNV loss 21841781
dgv10103n54 CNV loss 21841781
dgv10102n54 CNV loss 21841781
dgv10101n54 CNV loss 21841781
dgv10100n54 CNV loss 21841781
dgv10099n54 CNV loss 21841781
dgv10098n54 CNV loss 21841781
dgv10097n54 CNV loss 21841781
dgv10096n54 CNV loss 21841781
dgv10095n54 CNV loss 21841781
dgv10094n54 CNV loss 21841781
dgv10093n54 CNV loss 21841781
dgv10092n54 CNV loss 21841781
nsv964953 CNV duplication 23825009
nsv964951 CNV duplication 23825009
nsv964950 CNV duplication 23825009
nsv964949 CNV duplication 23825009
nsv964948 CNV duplication 23825009
nsv964947 CNV duplication 23825009
nsv950415 CNV duplication 24416366
nsv830508 CNV loss 17160897
nsv823264 CNV gain 20364138
nsv823263 CNV gain 20364138
nsv823262 CNV gain 20364138
nsv823251 CNV gain 20364138
nsv820841 CNV deletion 20802225
nsv819207 CNV gain 19587683
nsv599904 CNV loss 21841781
nsv599903 CNV loss 21841781
nsv599902 CNV loss 21841781
nsv599894 CNV loss 21841781
nsv599870 CNV loss 21841781
nsv599864 CNV loss 21841781
nsv599859 CNV loss 21841781
nsv599842 CNV loss 21841781
nsv599841 CNV loss 21841781
nsv599839 CNV gain 21841781

Variation tolerance for PCDHA2 Gene

Residual Variation Intolerance Score: 39.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.97; 49.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHA2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHA2 Gene

Disorders for PCDHA2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDHA2 Gene - From: GeneCards

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

Additional Disease Information for PCDHA2

genes like me logo Genes that share disorders with PCDHA2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHA2 Gene

Publications for PCDHA2 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. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. (PMID: 12665801) Gevaert K … Vandekerckhove J (Nature biotechnology 2003) 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 PCDHA2 Gene

Sources for PCDHA2 Gene

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