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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. 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

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

Genomics for PCDH1 Gene

Regulatory Elements for PCDH1 Gene

Enhancers for PCDH1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G141837 1.4 Ensembl ENCODE dbSUPER 17.4 +36.9 36863 8.9 ZSCAN4 BMI1 RAD21 ZNF335 EGR1 ZNF366 FOS EGR2 ZNF654 REST PCDH1 KIAA0141 PIR31345 ENSG00000278925
GH05G141821 1.7 FANTOM5 Ensembl ENCODE dbSUPER 13.4 +57.2 57243 1.9 TBP ATF1 ZNF366 RCOR1 FOS NFYA CEBPB HDAC8 NFIC SMARCA4 PCDH1 ARAP3 ENSG00000278925
GH05G141940 1.4 Ensembl ENCODE 16 -63.0 -63024 2.9 PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 CBX5 HDAC3 LOC102723915 PCDH1 PCDHB17P PCDH12 PCDHAC2 ENSG00000272070 ARAP3 PCDHGB2 GNPDA1
GH05G141847 1.6 Ensembl ENCODE dbSUPER 12.8 +29.7 29711 4.5 HDGF PKNOX1 FOXA2 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B PCDH1 KIAA0141 GC05M141848 PIR31345
GH05G141832 1 ENCODE dbSUPER 17.1 +46.4 46372 1.5 NFIB ETV1 ZNF23 GATA3 GATA2 ZMIZ1 PRDM10 TCF7L2 STAT1 CEBPB PCDH1 ARAP3 KIAA0141 ENSG00000278925 PIR31345
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDH1 on UCSC Golden Path with GeneCards custom track

Promoters for PCDH1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187928 1146 1401 SIN3A YBX1 ZNF2 YY1 ZNF766 GLIS2 SP3 TSHZ1 REST ZNF579

Genomic Location for PCDH1 Gene

141,852,319 bp from pter
141,879,246 bp from pter
26,928 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 Asn305, posLast=403403, Asn618, posLast=662662, posLast=720720, Asn813, and Asn818
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PCDH1 Gene

Domains & Families for PCDH1 Gene

Gene Families for PCDH1 Gene

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

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
UniProtKB/Swiss-Prot Function:
May be involved in cell-cell interaction processes and in cell adhesion.

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

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

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 IEA,TAS 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

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, PaxDb, 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

Primer Products

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 35
  • 99.65 (n)
(Monodelphis domestica)
Mammalia PCDH1 35
  • 94 (a)
(Canis familiaris)
Mammalia PCDH1 34 35
  • 92.48 (n)
(Bos Taurus)
Mammalia PCDH1 34 35
  • 90.75 (n)
(Rattus norvegicus)
Mammalia Pcdh1 34
  • 88.97 (n)
(Mus musculus)
Mammalia Pcdh1 34 16 35
  • 88.7 (n)
(Gallus gallus)
Aves PCDH1 34 35
  • 78.4 (n)
(Anolis carolinensis)
Reptilia PCDH1 35
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh1 34
  • 69.56 (n)
Str.20430 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.12097 34
(Danio rerio)
Actinopterygii pcdh1a 35
  • 68 (a)
pcdh1b 35
  • 68 (a)
pcdh1 34
  • 66.89 (n)
Dr.26174 34
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)

Paralogs for PCDH1 Gene

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 Sequence Context AA Info Type
rs1000130420 -- 141,871,152(+) GCACT(A/G)CGAAG intron-variant, upstream-variant-2KB, utr-variant-5-prime
rs1000204620 -- 141,866,849(+) CCCGC(C/G)TGCCT intron-variant, upstream-variant-2KB
rs1000233559 -- 141,857,918(+) AGCTC(A/C)GCCTC intron-variant
rs1000416037 -- 141,877,396(+) GTGCT(G/T)TGTAC intron-variant
rs1000470118 -- 141,877,538(+) AGATT(A/G)TGTTT 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)

Relevant External Links for PCDH1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for PCDH1 Gene

Relevant External Links for PCDH1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

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. (EMBO J. 1993) 2 3 4 64
  2. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3 64
  3. Protocadherin-1 binds to SMAD3 and suppresses TGF-I^1-induced gene transcription. (PMID: 26209277) Faura Tellez G. … Nawijn M.C. (Am. J. Physiol. Lung Cell Mol. Physiol. 2015) 3 64
  4. Protocadherin-1 is a glucocorticoid-responsive critical regulator of airway epithelial barrier function. (PMID: 26227965) Kozu Y. … Hashimoto S. (BMC Pulm Med 2015) 3 64
  5. E-cadherin interactome complexity and robustness resolved by quantitative proteomics. (PMID: 25468996) Guo Z. … Zaidel-Bar R. (Sci Signal 2014) 3 64

Products for PCDH1 Gene

Sources for PCDH1 Gene

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