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Aliases for PCDHGC3 Gene

Aliases for PCDHGC3 Gene

  • Protocadherin Gamma Subfamily C, 3 2 3 5
  • Protocadherin 43 2 3
  • Protocadherin-2 3 4
  • Cadherin-Like 2 2 3
  • PCDH2 3 4
  • Protocadherin Gamma-C3 3
  • Protocadherin-43 4
  • Protocadherin 2 2
  • PCDH-Gamma-C3 4
  • PC-43 4
  • PC43 3

External Ids for PCDHGC3 Gene

Previous HGNC Symbols for PCDHGC3 Gene

  • PCDH2

Previous GeneCards Identifiers for PCDHGC3 Gene

  • GC05P140591
  • GC05P141319
  • GC05P140716
  • GC05P140774
  • GC05P140795
  • GC05P140734
  • GC05P140743
  • GC05P140856
  • GC05P140860
  • GC05P140886
  • GC05P140908
  • GC05P140918
  • GC05P140940
  • GC05P140961
  • GC05P140983
  • GC05P141012
  • GC05P141055
  • GC05P141076
  • GC05P136000
  • GC05P141122
  • GC05P141137
  • GC05P141188
  • GC05P141221
  • GC05P141261
  • GC05P141338
  • GC05P141395

Summaries for PCDHGC3 Gene

Entrez Gene Summary for PCDHGC3 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 PCDHGC3 Gene

PCDHGC3 (Protocadherin Gamma Subfamily C, 3) is a Protein Coding gene. Diseases associated with PCDHGC3 include Nonsyndromic Deafness. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB2.

UniProtKB/Swiss-Prot for PCDHGC3 Gene

  • Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Gene Wiki entry for PCDHGC3 Gene

Additional gene information for PCDHGC3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGC3 Gene

Genomics for PCDHGC3 Gene

GeneHancer (GH) Regulatory Elements for PCDHGC3 Gene

Promoters and enhancers for PCDHGC3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J141475 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 650.7 +1.1 1107 3.8 PKNOX1 NFIB SIN3A BATF RAD21 RFX5 YY1 ZNF335 ZNF143 BCLAF1 PCDHGC3 PCDHGC5 PCDHGA6 ARAP3 PCDHGA2 HDAC3 PCDHGA1 RN7SL68P PCDHGA12 PCDHGA11
GH05J140717 Promoter/Enhancer 1.6 Ensembl ENCODE 12.5 -756.8 -756811 2.7 MLX IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GC05P142304 VTRNA1-2 ANKHD1 PURA HARS2 PCDHB18P PCDHB19P HDAC3 WDR55 PCDHGA6
GH05J140710 Promoter/Enhancer 1.6 Ensembl ENCODE 12.5 -765.0 -764963 1.9 CLOCK FEZF1 IRF4 YY1 ZNF213 ZNF143 SP3 SSRP1 ZNF610 GLIS1 GC05P142295 LOC105378198 VTRNA1-1 HARS2 ANKHD1 WDR55 LOC102723915 HDAC3 PCDHB18P PURA
GH05J141563 Enhancer 1.4 Ensembl ENCODE dbSUPER 12.7 +88.5 88466 1.4 FOXA2 PKNOX1 ARNT SIN3A DMAP1 ZNF2 IRF4 YY1 ZNF213 ZNF207 HARS2 IK PCDHB8 PCDHB3 PCDHA6 PCDHB9 PCDHB7 ENSG00000272108 PCDHB15 PCDHGC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHGC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHGC3 gene promoter:
  • Meis-1b
  • Meis-1a
  • Meis-1
  • YY1
  • NF-1
  • Gfi-1
  • AML1a
  • USF1
  • USF-1
  • NF-kappaB1

Genomic Locations for PCDHGC3 Gene

Genomic Locations for PCDHGC3 Gene
37,033 bases
Plus strand
36,978 bases
Plus strand

Genomic View for PCDHGC3 Gene

Genes around PCDHGC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGC3 Gene

Proteins for PCDHGC3 Gene

  • Protein details for PCDHGC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin gamma-C3
    Protein Accession:
    Secondary Accessions:
    • O60622
    • Q08192
    • Q9Y5C4

    Protein attributes for PCDHGC3 Gene

    934 amino acids
    Molecular mass:
    101077 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAA36421.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. The C-terminus matches chromosome 8 region.; Evidence={ECO:0000305}; Sequence=AAA75391.1; Type=Frameshift; Positions=254, 259, 905, 914, 918, 930; Evidence={ECO:0000305};

    Alternative splice isoforms for PCDHGC3 Gene


neXtProt entry for PCDHGC3 Gene

Post-translational modifications for PCDHGC3 Gene

  • Glycosylation at isoforms=2689, isoforms=2643, Asn615, isoforms=2550, Asn478, Asn424, and isoforms=2245
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGC3 Gene

Antibody Products

  • R&D Systems Antibodies for PCDHGC3 (Protocadherin gamma C3)
  • Boster Bio Antibodies for PCDHGC3

No data available for DME Specific Peptides for PCDHGC3 Gene

Domains & Families for PCDHGC3 Gene

Gene Families for PCDHGC3 Gene

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

Protein Domains for PCDHGC3 Gene

Suggested Antigen Peptide Sequences for PCDHGC3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGC3: view

No data available for UniProtKB/Swiss-Prot for PCDHGC3 Gene

Function for PCDHGC3 Gene

Molecular function for PCDHGC3 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 PCDHGC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGC3: view
genes like me logo Genes that share phenotypes with PCDHGC3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDHGC3

CRISPR Products

miRNA for PCDHGC3 Gene

miRTarBase miRNAs that target PCDHGC3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHGC3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHGC3 Gene

Localization for PCDHGC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGC3 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

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 PCDHGC3 gene
Compartment Confidence
extracellular 5
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 PCDHGC3 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 NAS 8508762
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome HDA --
genes like me logo Genes that share ontologies with PCDHGC3: view

Pathways & Interactions for PCDHGC3 Gene

SuperPathways for PCDHGC3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHGC3 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 --
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS 8508762
genes like me logo Genes that share ontologies with PCDHGC3: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGC3 Gene

Drugs & Compounds for PCDHGC3 Gene

(1) Drugs for PCDHGC3 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 PCDHGC3: view

Transcripts for PCDHGC3 Gene

mRNA/cDNA for PCDHGC3 Gene

Unigene Clusters for PCDHGC3 Gene

Protocadherin gamma subfamily C, 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHGC3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGC3 Gene

No ASD Table

Relevant External Links for PCDHGC3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHGC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGC3 Gene

Protein differential expression in normal tissues from HIPED for PCDHGC3 Gene

This gene is overexpressed in Gallbladder (35.9), Urine (18.1), and Ovary (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCDHGC3 Gene

Protein tissue co-expression partners for PCDHGC3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHGC3 Gene:


SOURCE GeneReport for Unigene cluster for PCDHGC3 Gene:


Evidence on tissue expression from TISSUES for PCDHGC3 Gene

  • Nervous system(4.2)
  • Liver(4)
  • Skin(4)
genes like me logo Genes that share expression patterns with PCDHGC3: 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 PCDHGC3 Gene

Orthologs for PCDHGC3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGC3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHGC3 33
  • 99.54 (n)
(Bos Taurus)
Mammalia PCDHGC3 33
  • 89.55 (n)
(Mus musculus)
Mammalia Pcdhgc3 16 33
  • 87.99 (n)
(Rattus norvegicus)
Mammalia Pcdhgc3 33
  • 87.7 (n)
(Canis familiaris)
Mammalia -- 34
  • 39 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 37 (a)
(Gallus gallus)
Aves PCDHGC3 33
  • 66.4 (n)
-- 34
  • 37 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 45 (a)
-- 34
  • 41 (a)
-- 34
  • 39 (a)
-- 34
  • 38 (a)
-- 34
  • 38 (a)
-- 34
  • 38 (a)
-- 34
  • 37 (a)
(Danio rerio)
Actinopterygii AL929558.1 34
  • 41 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
CSA.7308 34
  • 18 (a)
Species where no ortholog for PCDHGC3 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)
  • oppossum (Monodelphis domestica)
  • 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 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)

Evolution for PCDHGC3 Gene

Gene Tree for PCDHGC3 (if available)
Gene Tree for PCDHGC3 (if available)
Evolutionary constrained regions (ECRs) for PCDHGC3: view image

Paralogs for PCDHGC3 Gene

genes like me logo Genes that share paralogs with PCDHGC3: view

Variants for PCDHGC3 Gene

Sequence variations from dbSNP and Humsavar for PCDHGC3 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
rs1000138324 -- 141,499,091(+) A/C genic_downstream_transcript_variant, intron_variant
rs1000179570 -- 141,485,122(+) G/C genic_downstream_transcript_variant, intron_variant
rs1000222118 -- 141,482,017(+) A/G genic_downstream_transcript_variant, intron_variant
rs1000330093 -- 141,511,812(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGC3 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
nsv1123990 CNV deletion 24896259
nsv1125852 CNV tandem duplication 24896259
nsv462470 CNV loss 19166990
nsv599923 CNV loss 21841781

Variation tolerance for PCDHGC3 Gene

Residual Variation Intolerance Score: 7.77% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.67; 31.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHGC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGC3 Gene

Disorders for PCDHGC3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDHGC3 Gene - From: GeneCards

Disorder Aliases PubMed IDs
nonsyndromic deafness
  • nonsyndromic hearing loss
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHGC3

genes like me logo Genes that share disorders with PCDHGC3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHGC3 Gene

Publications for PCDHGC3 Gene

  1. Nonsyndromic deafness DFNA1 associated with mutation of a human homolog of the Drosophila gene diaphanous. (PMID: 9360932) Lynch ED … King MC (Science (New York, N.Y.) 1997) 2 3 4 58
  2. Protocadherins: a large family of cadherin-related molecules in central nervous system. (PMID: 8508762) Sano K … Suzuki S (The EMBO journal 1993) 2 3 4 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) 3 4 58
  4. A striking organization of a large family of human neural cadherin-like cell adhesion genes. (PMID: 10380929) Wu Q … Maniatis T (Cell 1999) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for PCDHGC3 Gene

Sources for PCDHGC3 Gene

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