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Aliases for PCDHAC2 Gene

Aliases for PCDHAC2 Gene

  • Protocadherin Alpha Subfamily C, 2 2 3 5
  • PCDH-ALPHA-C2 3 4
  • Protocadherin Alpha-C2 3

External Ids for PCDHAC2 Gene

Previous GeneCards Identifiers for PCDHAC2 Gene

  • GC05P140079
  • GC05P140761
  • GC05P140215
  • GC05P140222
  • GC05P140177
  • GC05P140179
  • GC05P140326
  • GC05P140345
  • GC05P135490
  • GC05P141438
  • GC05P141573
  • GC05P141675
  • GC05P141776
  • GC05P141877
  • GC05P141985
  • GC05P142086

Summaries for PCDHAC2 Gene

Entrez Gene Summary for PCDHAC2 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 PCDHAC2 Gene

PCDHAC2 (Protocadherin Alpha Subfamily C, 2) is a Protein Coding gene. Diseases associated with PCDHAC2 include Protocadherin-Alpha Gene Cluster and Spherocytosis, Type 5. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHAC1.

UniProtKB/Swiss-Prot for PCDHAC2 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 PCDHAC2 Gene

Additional gene information for PCDHAC2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHAC2 Gene

Genomics for PCDHAC2 Gene

GeneHancer (GH) Regulatory Elements for PCDHAC2 Gene

Promoters and enhancers for PCDHAC2 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
GH05I140965 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 +0.4 354 1.3 SIN3A ZNF335 GLIS2 ZNF366 ZNF143 SP3 ZNF398 REST ZFP69B ZNF217 ENSG00000279028 PCDHAC2 PCDHA11 PCDHA13 PCDHACT PCDHAC1 PCDHA12 PCDHA10 PCDHA8 PCDHA9
GH05I141084 Enhancer 1.2 FANTOM5 Ensembl ENCODE 20.4 +118.6 118583 1.4 CTCF SAP130 RAD21 YY1 ZNF335 E2F1 ZNF23 GATA3 POLR2A ZNF143 PCDHAC2 PCDHB17P PCDHB1 MALINC1 IGIP PCDHGC4 PCDHB3 PCDHB10 PCDHAC1 PCDHA12
GH05I140717 Promoter/Enhancer 1.6 Ensembl ENCODE 10.8 -247.0 -247026 2.7 MLX IRF4 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GLIS1 GC05P142207 VTRNA1-2 PURA PCDHB18P PCDHB19P PCDHB15 PCDHB12 PCDHB3 PCDHB9 PCDHB13
GH05I140710 Promoter/Enhancer 1.6 Ensembl ENCODE 10.8 -255.2 -255178 1.9 CLOCK FEZF1 IRF4 YY1 ZNF213 ZNF143 SP3 SSRP1 ZNF610 GLIS1 GC05P142198 LOC105378198 VTRNA1-1 HARS2 PCDHB18P PURA WDR55 LOC102723915 HDAC3 PCDHGA6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHAC2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHAC2 gene promoter:

Genomic Locations for PCDHAC2 Gene

Genomic Locations for PCDHAC2 Gene
46,183 bases
Plus strand

Genomic View for PCDHAC2 Gene

Genes around PCDHAC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHAC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHAC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHAC2 Gene

Proteins for PCDHAC2 Gene

  • Protein details for PCDHAC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin alpha-C2
    Protein Accession:
    Secondary Accessions:
    • Q2M3V1
    • Q9Y5F4

    Protein attributes for PCDHAC2 Gene

    1007 amino acids
    Molecular mass:
    109450 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHAC2 Gene


neXtProt entry for PCDHAC2 Gene

Post-translational modifications for PCDHAC2 Gene

  • Glycosylation at Asn280, isoforms=2436, Asn586, and Asn657

Other Protein References for PCDHAC2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHAC2 Gene

Domains & Families for PCDHAC2 Gene

Gene Families for PCDHAC2 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PCDHAC2 Gene

Suggested Antigen Peptide Sequences for PCDHAC2 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHAC2: view

No data available for UniProtKB/Swiss-Prot for PCDHAC2 Gene

Function for PCDHAC2 Gene

Molecular function for PCDHAC2 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 PCDHAC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHAC2: view

Phenotypes for PCDHAC2 Gene

genes like me logo Genes that share phenotypes with PCDHAC2: view

Animal Models for PCDHAC2 Gene

MGI Knock Outs for PCDHAC2:

Animal Model Products

CRISPR Products

miRNA for PCDHAC2 Gene

miRTarBase miRNAs that target PCDHAC2

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PCDHAC2 Gene

Localization for PCDHAC2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHAC2 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 PCDHAC2 gene
Compartment Confidence
plasma membrane 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDHAC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane TAS 10380929
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHAC2: view

Pathways & Interactions for PCDHAC2 Gene

SuperPathways for PCDHAC2 Gene

No Data Available

Interacting Proteins for PCDHAC2 Gene

Gene Ontology (GO) - Biological Process for PCDHAC2 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,IBA --
genes like me logo Genes that share ontologies with PCDHAC2: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHAC2 Gene

Drugs & Compounds for PCDHAC2 Gene

(1) Drugs for PCDHAC2 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 PCDHAC2: view

Transcripts for PCDHAC2 Gene

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHAC2 Gene

No ASD Table

Relevant External Links for PCDHAC2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHAC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHAC2 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHAC2 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x6.7), Brain - Frontal Cortex (BA9) (x6.0), and Brain - Anterior cingulate cortex (BA24) (x5.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHAC2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHAC2 Gene:


Evidence on tissue expression from TISSUES for PCDHAC2 Gene

  • Nervous system(5)
genes like me logo Genes that share expression patterns with PCDHAC2: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHAC2 Gene

Orthologs for PCDHAC2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHAC2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHA2 34
  • 100 (a)
  • 99.74 (n)
(Canis familiaris)
Mammalia PCDHAC2 34
  • 94 (a)
(Mus musculus)
Mammalia Pcdha2 34
  • 93 (a)
Pcdhac2 33 16
  • 89.3 (n)
(Rattus norvegicus)
Mammalia Pcdhac2 33
  • 89.13 (n)
(Bos Taurus)
Mammalia PCDHGC3 34
  • 40 (a)
(Monodelphis domestica)
Mammalia PCDHAC2 34
  • 40 (a)
(Gallus gallus)
Aves PCDHAC2 33
  • 70.98 (n)
  • 41 (a)
(Anolis carolinensis)
Reptilia PCDHAC2 34
  • 42 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdhac2 33
  • 63.96 (n)
(Danio rerio)
Actinopterygii pcdh2ac 33
  • 57.5 (n)
  • 44 (a)
Species where no ortholog for PCDHAC2 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)
  • 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 PCDHAC2 Gene

Gene Tree for PCDHAC2 (if available)
Gene Tree for PCDHAC2 (if available)

Paralogs for PCDHAC2 Gene

Variants for PCDHAC2 Gene

Sequence variations from dbSNP and Humsavar for PCDHAC2 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
rs1000122176 -- 140,965,777(+) C/T upstream_transcript_variant
rs1000356638 -- 140,999,029(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000598682 -- 140,966,096(+) G/A upstream_transcript_variant
rs1000754704 -- 141,007,303(+) C/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHAC2 Gene

Variant ID Type Subtype PubMed ID
esv2759382 CNV gain 17122850
nsv1031849 CNV loss 25217958

Variation tolerance for PCDHAC2 Gene

Residual Variation Intolerance Score: 15.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.33; 26.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHAC2 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 PCDHAC2 Gene

Disorders for PCDHAC2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PCDHAC2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
protocadherin-alpha gene cluster
  • pcdha@
spherocytosis, type 5
  • sph5
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHAC2

genes like me logo Genes that share disorders with PCDHAC2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHAC2 Gene

Publications for PCDHAC2 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. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  3. 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
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 58
  5. 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) 4 58

Products for PCDHAC2 Gene

Sources for PCDHAC2 Gene

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