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Aliases for PCDH1 Gene

Aliases for PCDH1 Gene

  • Protocadherin 1 2 3 5
  • Cadherin-Like Protein 1 3 4
  • PC42 3 4
  • Protocadherin 1 (Cadherin-Like 1) 2
  • Protocadherin 42 3
  • Protocadherin-42 4
  • Cadherin-Like 1 3
  • Protocadherin-1 3
  • PCDH42 3

External Ids for PCDH1 Gene

Previous GeneCards Identifiers for PCDH1 Gene

  • GC05M141056
  • GC05M141816
  • GC05M141215
  • GC05M141261
  • GC05M141212
  • GC05M136376
  • GC05M141232

Summaries for PCDH1 Gene

Entrez Gene Summary for PCDH1 Gene

  • This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDH1 Gene

PCDH1 (Protocadherin 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 PCDH7.

UniProtKB/Swiss-Prot for PCDH1 Gene

  • May be involved in cell-cell interaction processes and in cell adhesion.

Gene Wiki entry for PCDH1 Gene

Additional gene information for PCDH1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH1 Gene

Genomics for PCDH1 Gene

GeneHancer (GH) Regulatory Elements for PCDH1 Gene

Promoters and enhancers for PCDH1 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
GH05J141868 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 652.9 +4.8 4836 11 PKNOX1 FOXA2 ARID4B SIN3A YBX1 ZNF2 ZBTB7B IRF4 YY1 ZNF766 PCDH1 GC05P142308 MRPL11P2 PCDHB19P PCDHB5 PCDHB12 PCDHB3 PCDHB11 DELE1 HDAC3
GH05J141881 Enhancer 0.5 FANTOM5 dbSUPER 650.7 -1.9 -1852 0.1 PCDH1 GC05P142293 PCDHGA9 PCDHGC5 PCDHGC4 NDFIP1 RELL2 PCDHGB6 PCDHGC3
GH05J141679 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 10.6 +197.4 197435 4.7 HDGF ARNT SIN3A ZNF2 YY1 CBX5 ZNF213 FOS SP3 REST ARAP3 PCDHB19P HARS2 DELE1 PCDHB18P PCDHGA7 PCDH1 PCDH12 RNF14 HDAC3
GH05J141837 Enhancer 1.2 Ensembl ENCODE dbSUPER 17.4 +36.9 36862 8.9 ZSCAN4 SIN3A BMI1 RAD21 EGR1 ZNF366 ZNF143 RCOR1 FOS EGR2 PCDH1 MRPL11P2 DELE1 PIR31345 ENSG00000278925
GH05J141847 Enhancer 1.5 Ensembl ENCODE dbSUPER 12.8 +29.7 29711 4.5 HDGF PKNOX1 SMAD1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B GC05P142296 GC05M141848 PCDH1 PCDHB19P DELE1 PIR31345
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDH1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDH1 gene promoter:
  • COMP1
  • Nkx2-5
  • RREB-1
  • GATA-3
  • Elk-1
  • Sp1
  • E47
  • AP-1
  • c-Fos
  • c-Jun

Genomic Locations for PCDH1 Gene

Genomic Locations for PCDH1 Gene
26,928 bases
Minus strand
26,140 bases
Minus strand

Genomic View for PCDH1 Gene

Genes around PCDH1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDH1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDH1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH1 Gene

Proteins for PCDH1 Gene

  • Protein details for PCDH1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q8IUP2

    Protein attributes for PCDH1 Gene

    1060 amino acids
    Molecular mass:
    114743 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAA36419.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};

    Alternative splice isoforms for PCDH1 Gene


neXtProt entry for PCDH1 Gene

Post-translational modifications for PCDH1 Gene

  • Glycosylation at Asn818, isoforms=2813, Asn720, Asn662, Asn618, isoforms=2403, and Asn305
  • Modification sites at PhosphoSitePlus

Antibody Products

  • R&D Systems Antibodies for PCDH1 (Protocadherin-1)
  • Abcam antibodies for PCDH1

No data available for DME Specific Peptides for PCDH1 Gene

Domains & Families for PCDH1 Gene

Gene Families for PCDH1 Gene

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

Suggested Antigen Peptide Sequences for PCDH1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDH1: view

No data available for UniProtKB/Swiss-Prot for PCDH1 Gene

Function for PCDH1 Gene

Molecular function for PCDH1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in cell-cell interaction processes and in cell adhesion.
GENATLAS Biochemistry:
protocadherin 1,cadherin-related neuronal receptor,component of the PCDHG cluster,member C3,expressed in the brain,localized at the synaptic junction and putatively involved in specific neuronal connections and signal transduction

Phenotypes From GWAS Catalog for PCDH1 Gene

Gene Ontology (GO) - Molecular Function for PCDH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDH1: view
genes like me logo Genes that share phenotypes with PCDH1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDH1

CRISPR Products

miRNA for PCDH1 Gene

miRTarBase miRNAs that target PCDH1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDH1 Gene

Localization for PCDH1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH1 Gene

Cell junction. Cell membrane; Single-pass type I membrane protein. Note=Found at cell-cell boundaries and probably at cell-matrix boundaries.

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 PCDH1 gene
Compartment Confidence
plasma membrane 5
nucleus 4
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (3)
  • Nucleoli (1)
  • Nucleus (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IDA --
GO:0005886 plasma membrane TAS,IEA 8508762
GO:0005887 integral component of plasma membrane TAS 8508762
GO:0005911 cell-cell junction TAS 8508762
genes like me logo Genes that share ontologies with PCDH1: view

Pathways & Interactions for PCDH1 Gene

SuperPathways for PCDH1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDH1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling TAS 8508762
GO:0007399 nervous system development TAS 8508762
genes like me logo Genes that share ontologies with PCDH1: view

No data available for Pathways by source and SIGNOR curated interactions for PCDH1 Gene

Drugs & Compounds for PCDH1 Gene

No Compound Related Data Available

Transcripts for PCDH1 Gene

Unigene Clusters for PCDH1 Gene

Protocadherin 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDH1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH1 Gene

No ASD Table

Relevant External Links for PCDH1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDH1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDH1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDH1 Gene

This gene is overexpressed in Heart (29.2) and Frontal cortex (10.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDH1 Gene

Protein tissue co-expression partners for PCDH1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDH1 Gene:


SOURCE GeneReport for Unigene cluster for PCDH1 Gene:


mRNA Expression by UniProt/SwissProt for PCDH1 Gene:

Tissue specificity: Highly expressed in the brain and neuro-glial cells.

Evidence on tissue expression from TISSUES for PCDH1 Gene

  • Nervous system(4.4)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with PCDH1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDH1 Gene

Orthologs for PCDH1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDH1 34 33
  • 99.65 (n)
(Monodelphis domestica)
Mammalia PCDH1 34
  • 94 (a)
(Canis familiaris)
Mammalia PCDH1 34 33
  • 92.48 (n)
(Bos Taurus)
Mammalia PCDH1 34 33
  • 90.75 (n)
(Rattus norvegicus)
Mammalia Pcdh1 33
  • 88.97 (n)
(Mus musculus)
Mammalia Pcdh1 16 34 33
  • 88.7 (n)
(Gallus gallus)
Aves PCDH1 34 33
  • 78.4 (n)
(Anolis carolinensis)
Reptilia PCDH1 34
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh1 33
  • 69.56 (n)
Str.20430 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.12097 33
(Danio rerio)
Actinopterygii pcdh1a 34
  • 68 (a)
pcdh1b 34
  • 68 (a)
pcdh1 33
  • 66.89 (n)
Dr.26174 33
Species where no ortholog for PCDH1 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)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)

Evolution for PCDH1 Gene

Gene Tree for PCDH1 (if available)
Gene Tree for PCDH1 (if available)
Evolutionary constrained regions (ECRs) for PCDH1: view image

Paralogs for PCDH1 Gene

(47) SIMAP similar genes for PCDH1 Gene using alignment to 7 proteins:

  • F5H3L5_HUMAN
  • H0Y2Z9_HUMAN
  • H0Y9F5_HUMAN
  • H0Y9I5_HUMAN
genes like me logo Genes that share paralogs with PCDH1: view

Variants for PCDH1 Gene

Sequence variations from dbSNP and Humsavar for PCDH1 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000130420 -- 141,871,152(-) A/G 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000204620 -- 141,866,849(-) C/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000233559 -- 141,857,918(-) A/C genic_downstream_transcript_variant, intron_variant
rs1000416037 -- 141,877,396(-) G/T genic_upstream_transcript_variant, intron_variant
rs1000470118 -- 141,877,538(-) G/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDH1 Gene

Variant ID Type Subtype PubMed ID
dgv1654e212 CNV loss 25503493
esv3369680 CNV duplication 20981092
nsv1154058 CNV deletion 26484159
nsv509093 CNV insertion 20534489
nsv950418 CNV deletion 24416366

Variation tolerance for PCDH1 Gene

Residual Variation Intolerance Score: 2.66% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.96; 87.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDH1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDH1 Gene

Disorders for PCDH1 Gene

Additional Disease Information for PCDH1

No disorders were found for PCDH1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDH1 Gene

Publications for PCDH1 Gene

  1. 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
  2. Protocadherin-1 Localization and Cell-Adhesion Function in Airway Epithelial Cells in Asthma. (PMID: 27701444) Faura Tellez G … Koppelman GH (PloS one 2016) 3 58
  3. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58
  4. Protocadherin-1 binds to SMAD3 and suppresses TGF-β1-induced gene transcription. (PMID: 26209277) Faura Tellez G … Nawijn MC (American journal of physiology. Lung cellular and molecular physiology 2015) 3 58
  5. Protocadherin-1 is a glucocorticoid-responsive critical regulator of airway epithelial barrier function. (PMID: 26227965) Kozu Y … Hashimoto S (BMC pulmonary medicine 2015) 3 58

Products for PCDH1 Gene

Sources for PCDH1 Gene

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