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 PCDHGC5 Gene

Aliases for PCDHGC5 Gene

  • Protocadherin Gamma Subfamily C, 5 2 3 5
  • Protocadherin Gamma-C5 3 4
  • PCDH-GAMMA-C5 2 3
  • PCDH-Gamma-C5 4
  • PCDHGC5 5

External Ids for PCDHGC5 Gene

Previous GeneCards Identifiers for PCDHGC5 Gene

  • GC05P140593
  • GC05P141321
  • GC05P140718
  • GC05P140776
  • GC05P140797
  • GC05P140736
  • GC05P140745
  • GC05P140820
  • GC05P140849
  • GC05P140862
  • GC05P140888
  • GC05P140910
  • GC05P140937
  • GC05P140959
  • GC05P140980
  • GC05P141006
  • GC05P141020
  • GC05P141031
  • GC05P141071
  • GC05P136013
  • GC05P141123
  • GC05P141158
  • GC05P141189
  • GC05P141222
  • GC05P141262
  • GC05P141339
  • GC05P141396
  • GC05P141490
  • GC05P141552
  • GC05P142464
  • GC05P142569
  • GC05P142678
  • GC05P142878
  • GC05P141647
  • GC05P141746
  • GC05P141845
  • GC05P141953
  • GC05P142054
  • GC05P142160
  • GC05P142258
  • GC05P142360

Summaries for PCDHGC5 Gene

Entrez Gene Summary for PCDHGC5 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 PCDHGC5 Gene

PCDHGC5 (Protocadherin Gamma Subfamily C, 5) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGC4.

UniProtKB/Swiss-Prot Summary for PCDHGC5 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 PCDHGC5 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDHGC5 Gene

Genomics for PCDHGC5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCDHGC5 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
GH05J141506 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 613.1 +27.4 27397 20 ZNF221 SP1 HNRNPL CREB1 GATAD2A CTCF TEAD4 PRDM10 ZNF629 REST PCDHGC5 PCDHGC4 PCDHGA7 DIAPH1 PCDHGB6 PCDHGA2 PCDHGA11 PCDHB18P RN7SL68P PCDHGC3
GH05J141475 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 600.4 -11.6 -11595 4.6 CTCF RFX5 PRDM1 ZNF143 ZIC2 RAD21 POLR2A SP1 TRIM22 YY1 PCDHGC3 RF00017-4962 RN7SL68P lnc-PCDHGC4-1 PCDHGC5 PCDHGA6 ARAP3 PCDHGA11 PCDHGA2 HDAC3
GH05J141493 Promoter/Enhancer 1.4 EPDnew FANTOM5 ENCODE CraniofacialAtlas dbSUPER 600.4 +6.0 6009 3.3 ZIC2 YY1 POLR2A GLIS1 RAD21 SMARCA4 GATA2 PCDHGC5 ENSG00000272070 CD14 PCDHB2 DIAPH1 RELL2 TAF7 PCDHB16 RF00017-4963 PCDHGC4
GH05J141488 Promoter/Enhancer 0.9 EPDnew Ensembl ENCODE 600.7 +0.0 20 2.6 CREB1 MAFK ATF2 PCDHGC5 PCDHGA6 PCDHA1 PCDHGA1 PCDHGA2 PCDHGC4 RF00017-4963 PCDHGC3 lnc-DIAPH1-2 PCDHGA12
GH05J141372 Promoter 0.3 EPDnew 600.1 -116.5 -116529 0.1 PCDHGA6 PCDHGC5 PCDHGB3 PCDHGA5 PCDHGB2 PCDHGA4 PCDHGB1 PCDHGA3 PCDHGA2 PCDHG@
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHGC5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDHGC5

Top Transcription factor binding sites by QIAGEN in the PCDHGC5 gene promoter:
  • AML1a
  • AREB6
  • ER-alpha
  • Gfi-1
  • Meis-1
  • Meis-1a
  • Meis-1b
  • NF-1
  • USF-1
  • YY1

Genomic Locations for PCDHGC5 Gene

Genomic Locations for PCDHGC5 Gene
chr5:141,489,081-141,512,975
(GRCh38/hg38)
Size:
23,895 bases
Orientation:
Plus strand
chr5:140,868,808-140,892,546
(GRCh37/hg19)
Size:
23,739 bases
Orientation:
Plus strand

Genomic View for PCDHGC5 Gene

Genes around PCDHGC5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGC5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGC5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGC5 Gene

Proteins for PCDHGC5 Gene

  • Protein details for PCDHGC5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5F6-PCDGM_HUMAN
    Recommended name:
    Protocadherin gamma-C5
    Protein Accession:
    Q9Y5F6
    Secondary Accessions:
    • Q9Y5C2

    Protein attributes for PCDHGC5 Gene

    Size:
    944 amino acids
    Molecular mass:
    101921 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGC5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGC5 Gene

Post-translational modifications for PCDHGC5 Gene

  • Glycosylation at Asn265, Asn443, and Asn547
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGC5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGC5 Gene

Domains & Families for PCDHGC5 Gene

Gene Families for PCDHGC5 Gene

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

Protein Domains for PCDHGC5 Gene

Suggested Antigen Peptide Sequences for PCDHGC5 Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin gamma-C5 (PCDGM_HUMAN)
  • Protocadherin gamma subfamily C, 5, isoform 2 (Q2M272_HUMAN)
genes like me logo Genes that share domains with PCDHGC5: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCDHGC5 Gene

Function for PCDHGC5 Gene

Molecular function for PCDHGC5 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 PCDHGC5 Gene

Gene Ontology (GO) - Molecular Function for PCDHGC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGC5: view
genes like me logo Genes that share phenotypes with PCDHGC5: view

Animal Model Products

CRISPR Products

miRNA for PCDHGC5 Gene

miRTarBase miRNAs that target PCDHGC5

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHGC5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHGC5 Gene

Localization for PCDHGC5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGC5 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 PCDHGC5 gene
Compartment Confidence
plasma membrane 3
extracellular 1
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1

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 PCDHGC5 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 PCDHGC5: view

Pathways & Interactions for PCDHGC5 Gene

PathCards logo

SuperPathways for PCDHGC5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHGC5 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 --
GO:0050808 synapse organization IEA --
genes like me logo Genes that share ontologies with PCDHGC5: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGC5 Gene

Drugs & Compounds for PCDHGC5 Gene

(1) Drugs for PCDHGC5 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6556
genes like me logo Genes that share compounds with PCDHGC5: view

Transcripts for PCDHGC5 Gene

mRNA/cDNA for PCDHGC5 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHGC5

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGC5 Gene

No ASD Table

Relevant External Links for PCDHGC5 Gene

GeneLoc Exon Structure for
PCDHGC5

Expression for PCDHGC5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHGC5 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHGC5 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x6.5), Brain - Nucleus accumbens (basal ganglia) (x6.4), Brain - Anterior cingulate cortex (BA24) (x6.0), and Brain - Cortex (x5.1).

Protein differential expression in normal tissues from HIPED for PCDHGC5 Gene

This gene is overexpressed in Cerebrospinal fluid (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHGC5 Gene



Protein tissue co-expression partners for PCDHGC5 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDHGC5

Evidence on tissue expression from TISSUES for PCDHGC5 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with PCDHGC5: 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 PCDHGC5 Gene

Orthologs for PCDHGC5 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGC5 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PCDHGC5 30
  • 99.61 (n)
Mouse
(Mus musculus)
Mammalia Pcdhga9 31
  • 93 (a)
OneToOne
Pcdhgc5 30 17
  • 88.45 (n)
Dog
(Canis familiaris)
Mammalia PCDHGC5 31
  • 93 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pcdhgc5 30
  • 88.27 (n)
Chicken
(Gallus gallus)
Aves -- 31
  • 42 (a)
ManyToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pcdhga11 30
  • 58.33 (n)
Zebrafish
(Danio rerio)
Actinopterygii pcdh1g26 31
  • 47 (a)
ManyToMany
BX119910.6 31
  • 46 (a)
ManyToMany
BX119910.4 31 31
  • 46 (a)
ManyToMany
BX119910.9 31
  • 45 (a)
ManyToMany
pcdh1g32 31
  • 45 (a)
ManyToMany
zgc:162322 31
  • 45 (a)
ManyToMany
BX119910.3 31
  • 45 (a)
ManyToMany
pcdh1g22 31
  • 44 (a)
ManyToMany
pcdh1gc5 31
  • 38 (a)
ManyToMany
Species where no ortholog for PCDHGC5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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 PCDHGC5 Gene

ENSEMBL:
Gene Tree for PCDHGC5 (if available)
TreeFam:
Gene Tree for PCDHGC5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDHGC5: view image

Paralogs for PCDHGC5 Gene

genes like me logo Genes that share paralogs with PCDHGC5: view

Variants for PCDHGC5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDHGC5 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
723584 Benign: not provided 141,511,014(+) A/G SYNONYMOUS_VARIANT
729017 Benign: not provided 141,491,361(+) C/A SYNONYMOUS_VARIANT,INTRON_VARIANT
739048 Likely Benign: not provided 141,511,002(+) C/T SYNONYMOUS_VARIANT
751089 Likely Benign: not provided 141,511,035(+) C/T SYNONYMOUS_VARIANT
776070 Benign: not provided 141,490,413(+) G/A SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for PCDHGC5 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCDHGC5 Gene

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

Variation tolerance for PCDHGC5 Gene

Residual Variation Intolerance Score: 5.78% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.76; 78.90% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHGC5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGC5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGC5 Gene

Disorders for PCDHGC5 Gene

Additional Disease Information for PCDHGC5

No disorders were found for PCDHGC5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGC5 Gene

Publications for PCDHGC5 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
  2. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. (PMID: 23376485) Prunotto M … Moll S (Journal of proteomics 2013) 3
  3. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PMID: 21832049) Oláh J … Ovádi J (The Journal of biological chemistry 2011) 3
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3
  5. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L … Andersson-Svahn H (Molecular & cellular proteomics : MCP 2008) 3

Products for PCDHGC5 Gene

  • Biorbyt antibodies for PCDHGC5
  • Signalway ELISA kits for PCDHGC5

Sources for PCDHGC5 Gene