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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

External Ids for PCDHGA1 Gene

Previous GeneCards Identifiers for PCDHGA1 Gene

  • GC05P140526
  • GC05P141293
  • GC05P140693
  • GC05P140738
  • GC05P140690
  • GC05P141047
  • GC05P135855
  • GC05P141240
  • GC05P141288
  • GC05P141367
  • GC05P141440
  • GC05P141515

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. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA11.

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.

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

Genomics for PCDHGA1 Gene

Regulatory Elements for PCDHGA1 Gene

Enhancers for PCDHGA1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PCDHGA1 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHGA1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PCDHGA1 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHGA1 Gene

141,330,571 bp from pter
141,512,981 bp from pter
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

Proteomics data for PCDHGA1 Gene at MOPED

Post-translational modifications for PCDHGA1 Gene

  • Glycosylation at Asn 265, Asn 419, Asn 545, and Asn 685
  • Modification sites at PhosphoSitePlus

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

Protein Domains for PCDHGA1 Gene

Suggested Antigen Peptide Sequences for PCDHGA1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 6 cadherin domains.
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHGA1: view

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.
genes like me logo Genes that share phenotypes with PCDHGA1: view

Animal Models for PCDHGA1 Gene

MGI Knock Outs for PCDHGA1:

Animal Model Products

CRISPR Products

miRNA for PCDHGA1 Gene

miRTarBase miRNAs that target PCDHGA1

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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

Jensen Localization Image for PCDHGA1 Gene COMPARTMENTS Subcellular localization image for PCDHGA1 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytosol 1
endoplasmic reticulum 1
lysosome 1
peroxisome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for PCDHGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
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


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 Nutra 0
genes like me logo Genes that share compounds with PCDHGA1: view

Transcripts for PCDHGA1 Gene

mRNA/cDNA for PCDHGA1 Gene

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 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

genes like me logo Genes that share expression patterns with PCDHGA1: view

Protein tissue co-expression partners for PCDHGA1 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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
(Mus musculus)
Mammalia Pcdhga1 35
  • 81.66 (n)
  • 82.97 (a)
Pcdhga1 16
(Pan troglodytes)
Mammalia PCDHGA1 35
  • 98.62 (n)
  • 97.71 (a)
(Rattus norvegicus)
Mammalia Pcdhga1 35
  • 82.42 (n)
  • 84.17 (a)
(Canis familiaris)
Mammalia PCDHGA1 36
  • 80 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 63 (a)
-- 36
  • 63 (a)
-- 36
  • 66 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 65 (a)
-- 36
  • 64 (a)
-- 36
  • 64 (a)
-- 36
  • 67 (a)
-- 36
  • 57 (a)
-- 36
  • 65 (a)
(Gallus gallus)
Aves -- 36
  • 49 (a)
-- 36
  • 50 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 54 (a)
-- 36
  • 53 (a)
-- 36
  • 53 (a)
-- 36
  • 53 (a)
-- 36
  • 54 (a)
-- 36
  • 54 (a)
-- 36
  • 51 (a)
-- 36
  • 52 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.11957 35
African clawed frog
(Xenopus laevis)
Amphibia LOC398725 35
Species with no ortholog for PCDHGA1:
  • 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 Sequence Context AA Info Type
rs2472647 - 141,331,138(-) TGAGA(C/T)TCTGG reference, missense
rs17097185 - 141,331,530(+) TTTCA(C/G)AATGT reference, missense
rs12522664 -- 141,334,459(+) gtagt(C/T)ccagc intron-variant
rs33947955 -- 141,329,597(+) CCTCA(-/TCTT/TCTTA)ACTGG upstream-variant-2KB
rs4912604 -- 141,329,636(+) CTTCT(C/T)TTGGA upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
dgv1857e1 CNV Complex 17122850
dgv6351n71 CNV Loss 21882294
dgv6352n71 CNV Loss 21882294
dgv6353n71 CNV Loss 21882294
nsv882987 CNV Gain 21882294
nsv882990 CNV Loss 21882294
nsv823279 CNV Gain 20364138
nsv823280 CNV Loss 20364138
nsv519627 CNV Loss 19592680
esv267823 CNV Insertion 20981092
nsv518799 CNV Loss 19592680
nsv327707 CNV Loss 16902084
esv2730847 CNV Deletion 23290073
nsv462470 CNV Loss 19166990
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)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for PCDHGA1 Gene

Disorders for PCDHGA1 Gene

Relevant External Links for PCDHGA1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 67
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3
  4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 3
  5. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PMID: 10716726) Wu Q. … Maniatis T. (Proc. Natl. Acad. Sci. U.S.A. 2000) 3

Products for PCDHGA1 Gene

Sources for PCDHGA1 Gene