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Aliases for PCDHGC4 Gene

Aliases for PCDHGC4 Gene

  • Protocadherin Gamma Subfamily C, 4 2 3 5
  • PCDH-GAMMA-C4 3 4
  • Protocadherin Gamma-C4 3

External Ids for PCDHGC4 Gene

Previous GeneCards Identifiers for PCDHGC4 Gene

  • GC05P140592
  • GC05P141320
  • GC05P140717
  • GC05P140775
  • GC05P140796
  • GC05P140735
  • GC05P140744
  • GC05P140819
  • GC05P140844
  • GC05P140861
  • GC05P140887
  • GC05P140909
  • GC05P140919
  • GC05P140941
  • GC05P140962
  • GC05P140984
  • GC05P141056
  • GC05P141077
  • GC05P136009
  • GC05P141125
  • GC05P141138
  • GC05P141190
  • GC05P141223
  • GC05P141263
  • GC05P141341
  • GC05P141397

Summaries for PCDHGC4 Gene

Entrez Gene Summary for PCDHGC4 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 PCDHGC4 Gene

PCDHGC4 (Protocadherin Gamma Subfamily C, 4) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGC5.

UniProtKB/Swiss-Prot for PCDHGC4 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 PCDHGC4 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGC4 Gene

Genomics for PCDHGC4 Gene

GeneHancer (GH) Regulatory Elements for PCDHGC4 Gene

Promoters and enhancers for PCDHGC4 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
GH05I141483 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 550.8 -0.5 -463 1.4 SP1 E2F1 POLR2A L3MBTL2 SIN3A RFX5 GC05P142209 PCDHGC4 PIR35622 PCDHGA6 PCDHGA11 IK PCDHGC3 RN7SL68P PCDHGA12 PCDHGB7
GH05I141506 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 23.6 +31.5 31481 20 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 ZNF2 IRF4 YY1 PCDHGC4 PCDHGA7 DIAPH1 PCDHGB6 PCDHGA2 PCDHGC5 PCDHGA11 PCDHB18P RN7SL68P PCDHGC3
GH05I140717 Promoter/Enhancer 1.6 Ensembl ENCODE 10.8 -765.9 -765861 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 -774.0 -774013 1.9 CLOCK FEZF1 IRF4 YY1 ZNF213 ZNF143 SP3 SSRP1 ZNF610 GLIS1 GC05P142198 LOC105378198 VTRNA1-1 HARS2 PCDHB18P PURA WDR55 LOC102723915 HDAC3 PCDHGA6
GH05I141563 Enhancer 1.4 Ensembl ENCODE dbSUPER 11 +79.4 79416 1.4 FOXA2 PKNOX1 ARNT DMAP1 ZNF2 IRF4 YY1 ZNF213 ZNF207 ZNF143 HARS2 IK PCDHB8 PCDHB3 PCDHA6 PCDHB9 PCDHB7 ENSG00000272108 PCDHB15 PCDHGC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHGC4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHGC4 gene promoter:

Genomic Locations for PCDHGC4 Gene

Genomic Locations for PCDHGC4 Gene
chr5:141,484,997-141,512,979
(GRCh38/hg38)
Size:
27,983 bases
Orientation:
Plus strand
chr5:140,864,741-140,892,546
(GRCh37/hg19)

Genomic View for PCDHGC4 Gene

Genes around PCDHGC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGC4 Gene

Proteins for PCDHGC4 Gene

  • Protein details for PCDHGC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5F7-PCDGL_HUMAN
    Recommended name:
    Protocadherin gamma-C4
    Protein Accession:
    Q9Y5F7
    Secondary Accessions:
    • Q495T2
    • Q9Y5C3

    Protein attributes for PCDHGC4 Gene

    Size:
    938 amino acids
    Molecular mass:
    101214 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGC4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGC4 Gene

Post-translational modifications for PCDHGC4 Gene

  • Glycosylation at Asn265, isoforms=2276, and Asn444

Other Protein References for PCDHGC4 Gene

No data available for DME Specific Peptides for PCDHGC4 Gene

Domains & Families for PCDHGC4 Gene

Gene Families for PCDHGC4 Gene

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

Protein Domains for PCDHGC4 Gene

Suggested Antigen Peptide Sequences for PCDHGC4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGC4: view

No data available for UniProtKB/Swiss-Prot for PCDHGC4 Gene

Function for PCDHGC4 Gene

Molecular function for PCDHGC4 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 PCDHGC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGC4: view

miRNA for PCDHGC4 Gene

miRTarBase miRNAs that target PCDHGC4

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHGC4 Gene

Localization for PCDHGC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGC4 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 PCDHGC4 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 PCDHGC4 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 PCDHGC4: view

Pathways & Interactions for PCDHGC4 Gene

SuperPathways for PCDHGC4 Gene

No Data Available

Interacting Proteins for PCDHGC4 Gene

Gene Ontology (GO) - Biological Process for PCDHGC4 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 PCDHGC4: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGC4 Gene

Drugs & Compounds for PCDHGC4 Gene

(1) Drugs for PCDHGC4 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 PCDHGC4: view

Transcripts for PCDHGC4 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGC4 Gene

No ASD Table

Relevant External Links for PCDHGC4 Gene

GeneLoc Exon Structure for
PCDHGC4
ECgene alternative splicing isoforms for
PCDHGC4

Expression for PCDHGC4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGC4 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHGC4 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x11.4) and Brain - Cerebellum (x8.3).

Protein differential expression in normal tissues from HIPED for PCDHGC4 Gene

This gene is overexpressed in Platelet (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCDHGC4 Gene



Protein tissue co-expression partners for PCDHGC4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGC4 Gene:

PCDHGC4

Evidence on tissue expression from TISSUES for PCDHGC4 Gene

  • Nervous system(5)
  • Skin(3.1)
  • Eye(2.9)
genes like me logo Genes that share expression patterns with PCDHGC4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHGC4 Gene

Orthologs for PCDHGC4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGC4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHGC4 33
  • 99.68 (n)
-- 34
  • 33 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Pcdhgc4 33 16
  • 91.22 (n)
cow
(Bos Taurus)
Mammalia -- 34
  • 33 (a)
ManyToMany
dog
(Canis familiaris)
Mammalia -- 34
  • 31 (a)
ManyToMany
chicken
(Gallus gallus)
Aves PCDH10 34
  • 33 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100491009 33
  • 52.47 (n)
zebrafish
(Danio rerio)
Actinopterygii pcdh1g26 34
  • 43 (a)
ManyToMany
BX119910.3 34
  • 42 (a)
ManyToMany
BX119910.4 34 34
  • 42 (a)
ManyToMany
BX119910.6 34
  • 42 (a)
ManyToMany
pcdh1g32 34
  • 42 (a)
ManyToMany
zgc:162322 34
  • 42 (a)
ManyToMany
BX119910.9 34
  • 41 (a)
ManyToMany
pcdh1g22 34
  • 41 (a)
ManyToMany
pcdh1gc5 34
  • 39 (a)
ManyToMany
Species where no ortholog for PCDHGC4 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 PCDHGC4 Gene

ENSEMBL:
Gene Tree for PCDHGC4 (if available)
TreeFam:
Gene Tree for PCDHGC4 (if available)

Paralogs for PCDHGC4 Gene

genes like me logo Genes that share paralogs with PCDHGC4: view

Variants for PCDHGC4 Gene

Sequence variations from dbSNP and Humsavar for PCDHGC4 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs386352347 uncertain-significance, not provided 141,485,635(+) G/A coding_sequence_variant, synonymous_variant
rs1000138324 -- 141,499,091(+) A/C genic_downstream_transcript_variant, intron_variant
rs1000179570 -- 141,485,122(+) G/C upstream_transcript_variant
rs1000330093 -- 141,511,812(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000400491 -- 141,499,457(+) T/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGC4 Gene

Variant ID Type Subtype PubMed ID
nsv599923 CNV loss 21841781
nsv462470 CNV loss 19166990
esv25744 CNV gain 19812545

Variation tolerance for PCDHGC4 Gene

Residual Variation Intolerance Score: 6.42% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.42; 63.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHGC4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGC4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGC4 Gene

Disorders for PCDHGC4 Gene

Additional Disease Information for PCDHGC4

No disorders were found for PCDHGC4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGC4 Gene

Publications for PCDHGC4 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. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L … Andersson-Svahn H (Molecular & cellular proteomics : MCP 2008) 3 58
  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 58
  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 58

Products for PCDHGC4 Gene

Sources for PCDHGC4 Gene

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