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Aliases for PCDHGA1 Gene

Aliases for PCDHGA1 Gene

  • Protocadherin Gamma Subfamily A, 1 2 3 5
  • PCDH-GAMMA-A1 3 4
  • Protocadherin Gamma-A1 3

External Ids for PCDHGA1 Gene

Previous GeneCards Identifiers for PCDHGA1 Gene

  • GC05P140526
  • GC05P141293
  • GC05P140693
  • GC05P140738
  • GC05P140690
  • GC05P141047
  • GC05P135855
  • GC05P141240
  • GC05P141288
  • GC05P141367
  • GC05P141440
  • GC05P141515
  • GC05P141622
  • GC05P141724
  • GC05P141823
  • GC05P141922
  • GC05P142030

Summaries for PCDHGA1 Gene

Entrez Gene Summary for PCDHGA1 Gene

  • This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHGA1 Gene

PCDHGA1 (Protocadherin Gamma Subfamily A, 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB3.

UniProtKB/Swiss-Prot for PCDHGA1 Gene

  • Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Additional gene information for PCDHGA1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGA1 Gene

Genomics for PCDHGA1 Gene

GeneHancer (GH) Regulatory Elements for PCDHGA1 Gene

Promoters and enhancers for PCDHGA1 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
GH05I141331 Promoter 1.3 EPDnew Ensembl 550.8 -0.1 -71 0.2 ZNF335 CTCF ZNF654 TEAD1 ZNF143 ZNF384 RAD21 PCDHG@ PCDHGA1 GC05M141306
GH05I141330 Promoter 0.7 EPDnew 550.8 +0.2 189 0.1 ZNF335 CTCF PCDHG@ PCDHGA1 PCDHGA2
GH05I141332 Enhancer 0.3 Ensembl 560.9 +0.3 330 0.2 CTCF PCDHGA1 PCDHG@ PCDHGA2
GH05I141319 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 14.4 -9.9 -9921 1.9 PKNOX1 SMAD1 ARNT ARID4B SIN3A ZNF2 YY1 SLC30A9 POLR2B ZNF213 TAF7 PCDHB15 ANKHD1 ENSG00000272108 WDR55 PCDHB9 LOC102723915 FCHSD1 PCDHB18P PCDHB6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHGA1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHGA1 gene promoter:

Genomic Locations for PCDHGA1 Gene

Genomic Locations for PCDHGA1 Gene
182,411 bases
Plus strand

Genomic View for PCDHGA1 Gene

Genes around PCDHGA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGA1 Gene

Proteins for PCDHGA1 Gene

  • Protein details for PCDHGA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin gamma-A1
    Protein Accession:
    Secondary Accessions:
    • Q2M273
    • Q9Y5D6

    Protein attributes for PCDHGA1 Gene

    931 amino acids
    Molecular mass:
    101226 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGA1 Gene


neXtProt entry for PCDHGA1 Gene

Post-translational modifications for PCDHGA1 Gene

  • Glycosylation at Asn265, Asn419, isoforms=2545, and Asn685

Other Protein References for PCDHGA1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGA1 Gene

Domains & Families for PCDHGA1 Gene

Gene Families for PCDHGA1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for PCDHGA1 Gene

Suggested Antigen Peptide Sequences for PCDHGA1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGA1: view

No data available for UniProtKB/Swiss-Prot for PCDHGA1 Gene

Function for PCDHGA1 Gene

Molecular function for PCDHGA1 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 PCDHGA1 Gene

Gene Ontology (GO) - Molecular Function for PCDHGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGA1: view
genes like me logo Genes that share phenotypes with PCDHGA1: view

Animal Models for PCDHGA1 Gene

MGI Knock Outs for PCDHGA1:

miRNA for PCDHGA1 Gene

miRTarBase miRNAs that target PCDHGA1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PCDHGA1 Gene

Localization for PCDHGA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGA1 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 PCDHGA1 gene
Compartment Confidence
plasma membrane 5
extracellular 2
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for PCDHGA1 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 PCDHGA1: view

Pathways & Interactions for PCDHGA1 Gene

SuperPathways for PCDHGA1 Gene

No Data Available

Interacting Proteins for PCDHGA1 Gene

Gene Ontology (GO) - Biological Process for PCDHGA1 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 PCDHGA1: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGA1 Gene

Drugs & Compounds for PCDHGA1 Gene

(1) Drugs for PCDHGA1 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 PCDHGA1: view

Transcripts for PCDHGA1 Gene

mRNA/cDNA for PCDHGA1 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGA1 Gene

No ASD Table

Relevant External Links for PCDHGA1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHGA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGA1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDHGA1 Gene

This gene is overexpressed in Heart (38.8) and Peripheral blood mononuclear cells (30.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHGA1 Gene

Protein tissue co-expression partners for PCDHGA1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGA1 Gene:


Evidence on tissue expression from TISSUES for PCDHGA1 Gene

  • Lung(4)
  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHGA1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHGA1 Gene

Orthologs for PCDHGA1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGA1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHGA1 33
  • 98.62 (n)
(Rattus norvegicus)
Mammalia Pcdhga1 33
  • 82.42 (n)
(Mus musculus)
Mammalia Pcdhga1 33 16
  • 81.66 (n)
(Canis familiaris)
Mammalia PCDHGA1 34
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 67 (a)
-- 34
  • 65 (a)
-- 34
  • 65 (a)
-- 34
  • 64 (a)
-- 34
  • 64 (a)
-- 34
  • 57 (a)
(Monodelphis domestica)
Mammalia -- 34
  • 66 (a)
-- 34
  • 63 (a)
-- 34
  • 63 (a)
(Gallus gallus)
Aves -- 34
  • 50 (a)
-- 34
  • 49 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 54 (a)
-- 34
  • 53 (a)
-- 34
  • 53 (a)
-- 34
  • 53 (a)
-- 34
  • 52 (a)
-- 34
  • 51 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.11957 33
African clawed frog
(Xenopus laevis)
Amphibia LOC398725 33
Species where no ortholog for PCDHGA1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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)
  • zebrafish (Danio rerio)

Evolution for PCDHGA1 Gene

Gene Tree for PCDHGA1 (if available)
Gene Tree for PCDHGA1 (if available)

Paralogs for PCDHGA1 Gene

genes like me logo Genes that share paralogs with PCDHGA1: view

Variants for PCDHGA1 Gene

Sequence variations from dbSNP and Humsavar for PCDHGA1 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs386352347 uncertain-significance, not provided 141,485,635(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000014772 -- 141,409,727(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000022316 -- 141,472,751(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000098905 -- 141,353,769(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000136303 -- 141,452,887(+) C/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGA1 Gene

Variant ID Type Subtype PubMed ID
nsv980740 CNV duplication 23825009
nsv980739 CNV duplication 23825009
nsv968259 CNV duplication 23825009
nsv968258 CNV duplication 23825009
nsv964962 CNV duplication 23825009
nsv823280 CNV loss 20364138
nsv823279 CNV gain 20364138
nsv599923 CNV loss 21841781
nsv599922 CNV loss 21841781
nsv599921 CNV loss 21841781
nsv519627 CNV loss 19592680
nsv518799 CNV loss 19592680
nsv462470 CNV loss 19166990
nsv327707 CNV deletion 16902084
nsv1125852 CNV tandem duplication 24896259
nsv1123990 CNV deletion 24896259
esv3606987 CNV gain 21293372
esv3606985 CNV gain 21293372
esv3606984 CNV loss 21293372
esv3606983 CNV gain 21293372
esv3606982 CNV loss 21293372
esv3606981 CNV gain 21293372
esv3606980 CNV loss 21293372
esv3570470 CNV loss 25503493
esv3422812 CNV insertion 20981092
esv2759382 CNV gain 17122850
esv2730847 CNV deletion 23290073
esv25744 CNV gain 19812545

Variation tolerance for PCDHGA1 Gene

Residual Variation Intolerance Score: 48.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.73; 66.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHGA1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGA1 Gene

Disorders for PCDHGA1 Gene

Additional Disease Information for PCDHGA1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PCDHGA1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGA1 Gene

Publications for PCDHGA1 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. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 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) 4 58
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 58
  5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q … Maniatis T (Genome research 2001) 3 58

Products for PCDHGA1 Gene

Sources for PCDHGA1 Gene

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