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 cytoplasmi... See more...

Aliases for PCDH1 Gene

Aliases for PCDH1 Gene

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

External Ids for PCDH1 Gene

Previous GeneCards Identifiers for PCDH1 Gene

  • GC05M141056
  • GC05M141816
  • GC05M141215
  • GC05M141261
  • GC05M141212
  • GC05M136376
  • GC05M141232
  • GC05M141853

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. Diseases associated with PCDH1 include Corneal Dystrophy, Endothelial, X-Linked and Hantavirus Pulmonary Syndrome. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH7.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification 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
Score
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 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 502.8 +4.7 4701 11.3 HNRNPK EP300 CTCF SIN3A TCF12 NRF1 MYC SP1 TEAD4 PHB2 PCDH1 lnc-KIAA0141-4 PCDHB19P PCDHB5 PCDHB12 PCDHB3 PCDHB11 DELE1 HDAC3 PCDHGA4
GH05J141881 Enhancer 0.6 FANTOM5 dbSUPER 500.7 -1.9 -1852 0.1 SMC3 ZNF449 ENSG00000287726 PCDH1 PCDHGA9 PCDHGC5 PCDHGC4 NDFIP1 RELL2 PCDHGB6 PCDHGC3 RF00017-4964
GH05J141880 Promoter/Enhancer 0.5 Ensembl dbSUPER 500.7 -1.3 -1255 0.2 PCDH1 ENSG00000287726 RF00017-4964
GH05J141679 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.6 +197.4 197435 4.7 NRF1 TCF12 GTF2E2 FOS ZFX ZNF639 ZIC2 REST POLR2A ZBTB10 ARAP3 PCDHB19P HARS2 DELE1 PCDHB18P PCDHGA7 PCDH1 RNF14 PCDH12 HDAC3
GH05J141847 Promoter/Enhancer 1.7 ENCODE CraniofacialAtlas dbSUPER 12.8 +29.7 29711 4.5 ZNF217 NRF1 POLR2G GTF2E2 PHF8 ZFX ZNF639 ZIC2 POLR2A ZBTB10 lnc-KIAA0141-1 lnc-PCDH1-2 PCDH1 PCDHB19P DELE1 piR-30346 RF00017-4964
- 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

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDH1

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

Genomic Locations for PCDH1 Gene

Genomic Locations for PCDH1 Gene
chr5:141,852,319-141,879,246
(GRCh38/hg38)
Size:
26,928 bases
Orientation:
Minus strand
chr5:141,232,672-141,258,811
(GRCh37/hg19)
Size:
26,140 bases
Orientation:
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:
    Q08174-PCDH1_HUMAN
    Recommended name:
    Protocadherin-1
    Protein Accession:
    Q08174
    Secondary Accessions:
    • Q8IUP2

    Protein attributes for PCDH1 Gene

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

    Three dimensional structures from OCA and Proteopedia for PCDH1 Gene

    Alternative splice isoforms for PCDH1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDH1 Gene

Post-translational modifications for PCDH1 Gene

  • Glycosylation at Asn305, Asn403, Asn618, Asn662, Asn720, 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

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

Protein Domains for PCDH1 Gene

Blocks:
  • Cadherin
  • Prokaryotic transcription elongation factor GreA/GreB
  • Protocadherin
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PCDH1 Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin-42 (PCDH1_HUMAN)
genes like me logo Genes that share domains with PCDH1: view

No data available for Graphical View of Domain Structure and 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

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

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 PCDH1 gene
Compartment Confidence
plasma membrane 5
nucleus 4
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (3)
  • Nucleoli (1)
  • Nucleoplasm (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:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IDA --
GO:0005886 plasma membrane IEA,TAS 8508762
GO:0005887 integral component of plasma membrane IBA,TAS 21873635
genes like me logo Genes that share ontologies with PCDH1: view

Pathways & Interactions for PCDH1 Gene

PathCards logo

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,IBA 21873635
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

mRNA/cDNA for PCDH1 Gene

4 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
8 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 PCDH1

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

No ASD Table

Relevant External Links for PCDH1 Gene

GeneLoc Exon Structure for
PCDH1

Expression for PCDH1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDH1

SOURCE GeneReport for Unigene cluster for PCDH1 Gene:

Hs.79769

mRNA Expression by UniProt/SwissProt for PCDH1 Gene:

Q08174-PCDH1_HUMAN
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
chimpanzee
(Pan troglodytes)
Mammalia PCDH1 31 30
  • 99.65 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PCDH1 31
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PCDH1 31 30
  • 92.48 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PCDH1 31 30
  • 90.75 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pcdh1 30
  • 88.97 (n)
mouse
(Mus musculus)
Mammalia Pcdh1 17 31 30
  • 88.7 (n)
chicken
(Gallus gallus)
Aves PCDH1 31 30
  • 78.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PCDH1 31
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh1 30
  • 69.56 (n)
Str.20430 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.12097 30
zebrafish
(Danio rerio)
Actinopterygii pcdh1a 31
  • 68 (a)
OneToMany
pcdh1b 31
  • 68 (a)
OneToMany
pcdh1 30
  • 66.89 (n)
Dr.26174 30
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

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

Paralogs for PCDH1 Gene

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

  • PCDH1_HUMAN
  • D6RAX3_HUMAN
  • D6RBG2_HUMAN
  • 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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDH1 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
776073 Likely Benign: not provided 141,864,528(-) A/C MISSENSE_VARIANT
779244 Benign: not provided 141,869,429(-) G/A MISSENSE_VARIANT
787045 Likely Benign: not provided 141,854,406(-) G/A MISSENSE_VARIANT
rs12515587 - p.His25Pro
rs12517385 - p.Leu15Phe

Additional dbSNP identifiers (rs#s) for PCDH1 Gene

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
PCDH1

SNP Genotyping and Copy Number Assay Products

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

Disorders for PCDH1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PCDH1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
corneal dystrophy, endothelial, x-linked
  • xecd
hantavirus pulmonary syndrome
  • four corners hantavirus
- elite association - COSMIC cancer census association via MalaCards
Search PCDH1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PCDH1

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

No data available for 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 54
  2. The Functional Proximal Proteome of Oncogenic Ras Includes mTORC2. (PMID: 30639242) Kovalski JR … Khavari PA (Molecular cell 2019) 3 54
  3. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 54
  4. Protocadherin-1 is essential for cell entry by New World hantaviruses. (PMID: 30464266) Jangra RK … Chandran K (Nature 2018) 3 54
  5. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. (PMID: 28611215) Fei T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2017) 3 54

Products for PCDH1 Gene

Sources for PCDH1 Gene