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, sub... See more...

Aliases for PCDHGA1 Gene

Aliases for PCDHGA1 Gene

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

External Ids for PCDHGA1 Gene

Previous GeneCards Identifiers for PCDHGA1 Gene

  • GC05P140526
  • GC05P141293
  • GC05P140693
  • GC05P140738
  • GC05P140690
  • GC05P141047
  • GC05P135855
  • GC05P141240
  • GC05P141288
  • GC05P141367
  • GC05P141440
  • GC05P141515
  • GC05P142442
  • GC05P142546
  • GC05P142657
  • GC05P141622
  • GC05P141724
  • GC05P141823
  • GC05P141922
  • GC05P142030
  • GC05P142138
  • GC05P142236
  • GC05P142338

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 PCDHGA3.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification 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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J141331 Promoter 1 EPDnew Ensembl 510.8 +0.2 229 0.8 CTCF TRIM22 TEAD1 ZNF384 RAD21 ZNF335 ZNF654 MBD1 ZNF143 PCDHGA1 PCDHG@ PCDHGA2
GH05J141318 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 14.3 -10.6 -10570 4.4 ZBTB40 EP300 CTCF NRF1 TCF12 POLR2G SP1 GTF2E2 PHF8 ZFX ENSG00000288095 TAF7 lnc-SLC25A2-1 PCDHB15 PCDHGB4 ENSG00000272108 PCDHB9 PCDHB18P PCDHB6 PCDHGA3
GH05J142222 Enhancer 1.1 ENCODE dbSUPER 25.5 +892.8 892750 2 ZNF300 JUND ZNF639 ZIC2 RELA KLF7 ZNF662 CTBP1 JUN TRIM22 PCDHB18P PCDHB15 PCDHGA7 PCDHGA6 PCDHGB4 PCDHGB3 PCDHB19P PCDHGA8 PCDHGA5 PCDHGA2
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 13 +639.0 638996 3 EP300 HNRNPK ZBTB40 ZNF217 CTCF ZSCAN5C SIN3A NRF1 TCF12 USF1 RNF14 PCDH12 lnc-GNPDA1-2 PCDHB18P PCDHGA6 PCDHGA7 PCDHGA5 DELE1 PCDHB12 PCDHB19P
GH05J140717 Promoter/Enhancer 1.4 Ensembl ENCODE 13.9 -611.3 -611277 3 FOXK2 ZBTB40 ZNF217 CTCF ZSCAN5C TCF12 NCOR1 JUND PHB2 FOS VTRNA1-2 PURA PCDHB18P PCDHB19P PCDHB15 PCDHB12 PCDHB3 PCDHB9 PCDHB13 PCDHB7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHGA1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDHGA1

Top Transcription factor binding sites by QIAGEN in the PCDHGA1 gene promoter:
  • AP-1
  • AREB6
  • ATF-2
  • c-Jun
  • Sp1

Genomic Locations for PCDHGA1 Gene

Genomic Locations for PCDHGA1 Gene
chr5:141,330,571-141,512,981
(GRCh38/hg38)
Size:
182,411 bases
Orientation:
Plus strand
chr5:140,710,252-140,892,546
(GRCh37/hg19)
Size:
182,295 bases
Orientation:
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:
    Q9Y5H4-PCDG1_HUMAN
    Recommended name:
    Protocadherin gamma-A1
    Protein Accession:
    Q9Y5H4
    Secondary Accessions:
    • Q2M273
    • Q9Y5D6

    Protein attributes for PCDHGA1 Gene

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

    Alternative splice isoforms for PCDHGA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGA1 Gene

Post-translational modifications for PCDHGA1 Gene

  • Glycosylation at Asn265, Asn419, Asn545, and Asn685
  • 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

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

Protein Domains for PCDHGA1 Gene

Suggested Antigen Peptide Sequences for PCDHGA1 Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin gamma-A1 (PCDG1_HUMAN)
  • Protocadherin gamma subfamily A, 1, isoform 2 (Q2M273_HUMAN)
genes like me logo Genes that share domains with PCDHGA1: view

No data available for Graphical View of Domain Structure and 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:

Animal Model Products

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

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 PCDHGA1 gene
Compartment Confidence
plasma membrane 4
extracellular 2
peroxisome 1
endoplasmic reticulum 0
cytosol 0
lysosome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
  • Vesicles (2)
  • Cytosol (1)
  • Nucleoplasm (1)
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 21873635
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

PathCards logo

SuperPathways for PCDHGA1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IBA 21873635
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
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 7884
genes like me logo Genes that share compounds with PCDHGA1: view

Transcripts for PCDHGA1 Gene

mRNA/cDNA for PCDHGA1 Gene

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

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
PCDHGA1

Expression for PCDHGA1 Gene

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



Protein tissue co-expression partners for PCDHGA1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDHGA1

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
chimpanzee
(Pan troglodytes)
Mammalia PCDHGA1 30
  • 98.62 (n)
rat
(Rattus norvegicus)
Mammalia Pcdhga1 30
  • 82.42 (n)
mouse
(Mus musculus)
Mammalia Pcdhga1 17 30
  • 81.66 (n)
dog
(Canis familiaris)
Mammalia PCDHGA1 31
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 67 (a)
ManyToMany
-- 31
  • 65 (a)
ManyToMany
-- 31
  • 65 (a)
ManyToMany
-- 31
  • 64 (a)
ManyToMany
-- 31
  • 64 (a)
ManyToMany
-- 31
  • 57 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 66 (a)
ManyToMany
-- 31
  • 63 (a)
ManyToMany
-- 31
  • 63 (a)
ManyToMany
chicken
(Gallus gallus)
Aves -- 31
  • 50 (a)
ManyToMany
-- 31
  • 49 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 54 (a)
ManyToMany
-- 31
  • 54 (a)
ManyToMany
-- 31
  • 54 (a)
ManyToMany
-- 31
  • 53 (a)
ManyToMany
-- 31
  • 53 (a)
ManyToMany
-- 31
  • 53 (a)
ManyToMany
-- 31
  • 52 (a)
ManyToMany
-- 31
  • 51 (a)
ManyToMany
African clawed frog
(Xenopus laevis)
Amphibia LOC398725 30
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.11957 30
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

ENSEMBL:
Gene Tree for PCDHGA1 (if available)
TreeFam:
Gene Tree for PCDHGA1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDHGA1: view image

Paralogs for PCDHGA1 Gene

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

Variants for PCDHGA1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDHGA1 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs17097185 - p.His282Gln
rs2472647 - p.Val152Ile

Additional dbSNP identifiers (rs#s) for PCDHGA1 Gene

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

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

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
PCDHGA1

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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 54
  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 41 54
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 54
  4. 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 54
  5. 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 54

Products for PCDHGA1 Gene

Sources for PCDHGA1 Gene