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Aliases for PCDHGA6 Gene

Aliases for PCDHGA6 Gene

  • Protocadherin Gamma Subfamily A, 6 2 3 5
  • PCDH-GAMMA-A6 3 4
  • Protocadherin Gamma-A6 3

External Ids for PCDHGA6 Gene

Previous GeneCards Identifiers for PCDHGA6 Gene

  • GC05P140570
  • GC05P141308
  • GC05P140705
  • GC05P140764
  • GC05P140784
  • GC05P140723
  • GC05P140817
  • GC05P140825
  • GC05P140841
  • GC05P140866
  • GC05P140892
  • GC05P140914
  • GC05P140926
  • GC05P140948
  • GC05P140969
  • GC05P140991
  • GC05P141010
  • GC05P141039
  • GC05P141067
  • GC05P135898
  • GC05P141105
  • GC05P141146
  • GC05P141184
  • GC05P141215
  • GC05P141255
  • GC05P141299
  • GC05P141382
  • GC05P141450
  • GC05P141526
  • GC05P141630
  • GC05P141732
  • GC05P141831
  • GC05P141934
  • GC05P142038

Summaries for PCDHGA6 Gene

Entrez Gene Summary for PCDHGA6 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 PCDHGA6 Gene

PCDHGA6 (Protocadherin Gamma Subfamily A, 6) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA7.

UniProtKB/Swiss-Prot for PCDHGA6 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 PCDHGA6 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGA6 Gene

Genomics for PCDHGA6 Gene

GeneHancer (GH) Regulatory Elements for PCDHGA6 Gene

Promoters and enhancers for PCDHGA6 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
GH05I141373 Promoter 0.8 EPDnew 559 0.0 -42 0.1 CTCF ZNF654 SMC3 ZNF2 RAD21 PCDHGA6 PCDHGB3 PCDHGA5 PCDHGB2 PCDHGA4 PCDHGB1 PCDHGA3 PCDHGA2 PCDHG@ PCDHGA1
GH05I141374 Promoter 0.7 EPDnew 550.8 +0.2 152 0.1 CTCF ZNF2 PCDHGA6 GC05P142215 GC05P142216 PCDHGB3 PCDHGA5 PCDHGB2 PCDHGA4 PCDHGB1 PCDHGA3 PCDHGA2
GH05I140399 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 29.9 -971.9 -971885 4.7 CLOCK ZFP64 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 ANKHD1 ANKHD1-EIF4EBP3 ENSG00000249637 PURA HARS2 PCDHB18P PCDHGA6 IK APBB3 PCDHGA7
GH05I142221 Enhancer 1.4 Ensembl ENCODE dbSUPER 42.9 +848.7 848740 3.3 FOXA2 SMAD1 FEZF1 ZNF2 ZNF213 ZNF143 FOS SP3 JUNB REST PCDHB18P PCDHB15 PCDHGA7 PCDHGA6 PCDHGB4 PCDHGB3 PCDHB19P PCDHGA8 PCDHGA5 PCDHGA2
GH05I141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 27.1 +595.7 595653 3 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B RNF14 PCDH12 PCDHB18P PCDHGA6 PCDHGA7 LOC102723915 HDAC3 KIAA0141 PCDHGA5 PCDHB12
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHGA6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHGA6 gene promoter:

Genomic Locations for PCDHGA6 Gene

Genomic Locations for PCDHGA6 Gene
chr5:141,373,914-141,512,979
(GRCh38/hg38)
Size:
139,066 bases
Orientation:
Plus strand
chr5:140,753,651-140,892,546
(GRCh37/hg19)

Genomic View for PCDHGA6 Gene

Genes around PCDHGA6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGA6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGA6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGA6 Gene

Proteins for PCDHGA6 Gene

  • Protein details for PCDHGA6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5G7-PCDG6_HUMAN
    Recommended name:
    Protocadherin gamma-A6
    Protein Accession:
    Q9Y5G7
    Secondary Accessions:
    • A6H8K7
    • B2RN55
    • Q9Y5D1

    Protein attributes for PCDHGA6 Gene

    Size:
    932 amino acids
    Molecular mass:
    100871 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGA6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGA6 Gene

Post-translational modifications for PCDHGA6 Gene

  • Glycosylation at Asn81, Asn419, isoforms=2545, and Asn685
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGA6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGA6 Gene

Domains & Families for PCDHGA6 Gene

Gene Families for PCDHGA6 Gene

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

Protein Domains for PCDHGA6 Gene

Suggested Antigen Peptide Sequences for PCDHGA6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGA6: view

No data available for UniProtKB/Swiss-Prot for PCDHGA6 Gene

Function for PCDHGA6 Gene

Molecular function for PCDHGA6 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 PCDHGA6 Gene

Gene Ontology (GO) - Molecular Function for PCDHGA6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGA6: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGA6 Gene

Localization for PCDHGA6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGA6 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 PCDHGA6 gene
Compartment Confidence
plasma membrane 3

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 PCDHGA6 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 PCDHGA6: view

Pathways & Interactions for PCDHGA6 Gene

SuperPathways for PCDHGA6 Gene

No Data Available

Interacting Proteins for PCDHGA6 Gene

Gene Ontology (GO) - Biological Process for PCDHGA6 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 PCDHGA6: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGA6 Gene

Drugs & Compounds for PCDHGA6 Gene

(1) Drugs for PCDHGA6 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 PCDHGA6: view

Transcripts for PCDHGA6 Gene

mRNA/cDNA for PCDHGA6 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGA6 Gene

No ASD Table

Relevant External Links for PCDHGA6 Gene

GeneLoc Exon Structure for
PCDHGA6
ECgene alternative splicing isoforms for
PCDHGA6

Expression for PCDHGA6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGA6 Gene

Protein differential expression in normal tissues from HIPED for PCDHGA6 Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCDHGA6 Gene



Protein tissue co-expression partners for PCDHGA6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGA6 Gene:

PCDHGA6

Evidence on tissue expression from TISSUES for PCDHGA6 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHGA6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHGA6 Gene

Orthologs for PCDHGA6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGA6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHGA6 33
  • 99.57 (n)
cow
(Bos Taurus)
Mammalia PCDHGA6 33
  • 83.5 (n)
dog
(Canis familiaris)
Mammalia PCDHGB3 33
  • 81.2 (n)
mouse
(Mus musculus)
Mammalia Pcdhga6 33 16
  • 81.13 (n)
rat
(Rattus norvegicus)
Mammalia LOC102552796 33
  • 80.68 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 69 (a)
ManyToMany
-- 34
  • 66 (a)
ManyToMany
-- 34
  • 66 (a)
ManyToMany
-- 34
  • 66 (a)
ManyToMany
-- 34
  • 64 (a)
ManyToMany
-- 34
  • 58 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 65 (a)
ManyToMany
-- 34
  • 64 (a)
ManyToMany
-- 34
  • 64 (a)
ManyToMany
chicken
(Gallus gallus)
Aves -- 34
  • 50 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 57 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
-- 34
  • 55 (a)
ManyToMany
-- 34
  • 54 (a)
ManyToMany
-- 34
  • 54 (a)
ManyToMany
-- 34
  • 54 (a)
ManyToMany
-- 34
  • 53 (a)
ManyToMany
-- 34
  • 52 (a)
ManyToMany
Species where no ortholog for PCDHGA6 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)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PCDHGA6 Gene

ENSEMBL:
Gene Tree for PCDHGA6 (if available)
TreeFam:
Gene Tree for PCDHGA6 (if available)

Paralogs for PCDHGA6 Gene

genes like me logo Genes that share paralogs with PCDHGA6: view

Variants for PCDHGA6 Gene

Sequence variations from dbSNP and Humsavar for PCDHGA6 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
rs1000136303 -- 141,452,887(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000138324 -- 141,499,091(+) A/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGA6 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
esv2730847 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv3422812 CNV insertion 20981092
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
nsv599922 CNV loss 21841781
nsv599923 CNV loss 21841781
nsv823279 CNV gain 20364138
nsv823280 CNV loss 20364138
nsv968259 CNV duplication 23825009
nsv980740 CNV duplication 23825009

Variation tolerance for PCDHGA6 Gene

Residual Variation Intolerance Score: 36.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.90; 59.22% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHGA6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGA6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGA6 Gene

Disorders for PCDHGA6 Gene

Additional Disease Information for PCDHGA6

No disorders were found for PCDHGA6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGA6 Gene

Publications for PCDHGA6 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. A catalogue of putative HIV-1 protease host cell substrates. (PMID: 22944692) Impens F … Gevaert K (Biological chemistry 2012) 3 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 PCDHGA6 Gene

Sources for PCDHGA6 Gene

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