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Aliases for PCDH20 Gene

Aliases for PCDH20 Gene

  • Protocadherin 20 2 3 5
  • PCDH13 3 4
  • Protocadherin 13 3
  • Protocadherin-20 3
  • Protocadherin-13 4

External Ids for PCDH20 Gene

Previous GeneCards Identifiers for PCDH20 Gene

  • GC13M059951
  • GC13M055978
  • GC13M060920
  • GC13M059781
  • GC13M060881
  • GC13M061983
  • GC13M042676

Summaries for PCDH20 Gene

Entrez Gene Summary for PCDH20 Gene

  • This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal receptor is thought to play a role in the establishment and function of specific cell-cell connections in the brain. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDH20 Gene

PCDH20 (Protocadherin 20) is a Protein Coding gene. Diseases associated with PCDH20 include Trichorhinophalangeal Syndrome, Type I. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is ENSG00000197991.

UniProtKB/Swiss-Prot for PCDH20 Gene

  • Potential calcium-dependent cell-adhesion protein.

Gene Wiki entry for PCDH20 Gene

Additional gene information for PCDH20 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH20 Gene

Genomics for PCDH20 Gene

GeneHancer (GH) Regulatory Elements for PCDH20 Gene

Promoters and enhancers for PCDH20 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
GH13J061414 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 650.7 +0.2 213 1.4 TAF1 MAX RAD21 YY1 HIC1 POLR2A ZBTB48 ZNF547 SCRT2 SP3 PCDH20 GC13M061413 ENSG00000197991 GC13P061390
GH13J061411 Promoter 0.5 EPDnew 0.7 +3.9 3882 0.1 PCDH20 ENSG00000197991 GC13P061390
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDH20 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDH20 gene promoter:
  • CUTL1
  • GATA-1
  • FOXO4
  • MEF-2A
  • aMEF-2
  • GATA-3
  • GATA-2
  • HSF2
  • AML1a

Genomic Locations for PCDH20 Gene

Genomic Locations for PCDH20 Gene
5,838 bases
Minus strand
18,403 bases
Minus strand

Genomic View for PCDH20 Gene

Genes around PCDH20 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDH20 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDH20 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH20 Gene

Proteins for PCDH20 Gene

  • Protein details for PCDH20 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A8K1K9
    • B1AQU2
    • Q8NDN4
    • Q9NRT9

    Protein attributes for PCDH20 Gene

    951 amino acids
    Molecular mass:
    104919 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH27907.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for PCDH20 Gene

Post-translational modifications for PCDH20 Gene

  • Glycosylation at Asn849, isoforms=844, isoforms=803, Asn748, Asn680, Asn332, isoforms=326, and Asn135
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDH20 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDH20 Gene

Domains & Families for PCDH20 Gene

Gene Families for PCDH20 Gene

Protein Domains for PCDH20 Gene


Suggested Antigen Peptide Sequences for PCDH20 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDH20: view

No data available for UniProtKB/Swiss-Prot for PCDH20 Gene

Function for PCDH20 Gene

Molecular function for PCDH20 Gene

UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein.

Phenotypes From GWAS Catalog for PCDH20 Gene

Gene Ontology (GO) - Molecular Function for PCDH20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22681889
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDH20: view
genes like me logo Genes that share phenotypes with PCDH20: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDH20 Gene

Localization for PCDH20 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH20 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 PCDH20 gene
Compartment Confidence
plasma membrane 5
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytokinetic bridge (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDH20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDH20: view

Pathways & Interactions for PCDH20 Gene

SuperPathways for PCDH20 Gene

No Data Available

Interacting Proteins for PCDH20 Gene

Gene Ontology (GO) - Biological Process for PCDH20 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 --
genes like me logo Genes that share ontologies with PCDH20: view

No data available for Pathways by source and SIGNOR curated interactions for PCDH20 Gene

Drugs & Compounds for PCDH20 Gene

(1) Drugs for PCDH20 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 PCDH20: view

Transcripts for PCDH20 Gene

mRNA/cDNA for PCDH20 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(36) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PCDH20 Gene

Protocadherin 20:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH20 Gene

No ASD Table

Relevant External Links for PCDH20 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDH20 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDH20 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PCDH20 Gene

This gene is overexpressed in Brain - Hippocampus (x5.1) and Brain - Anterior cingulate cortex (BA24) (x4.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDH20 Gene

Protein tissue co-expression partners for PCDH20 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDH20 Gene:


SOURCE GeneReport for Unigene cluster for PCDH20 Gene:


Evidence on tissue expression from TISSUES for PCDH20 Gene

  • Nervous system(4.4)
  • Lung(4.1)
genes like me logo Genes that share expression patterns with PCDH20: view

No data available for Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDH20 Gene

Orthologs for PCDH20 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH20 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDH20 33
  • 97.52 (n)
(Canis familiaris)
Mammalia LOC100686939 33
  • 89.84 (n)
(Bos Taurus)
Mammalia PCDH20 33
  • 88.42 (n)
(Mus musculus)
Mammalia Pcdh20 16 33
  • 87.21 (n)
(Rattus norvegicus)
Mammalia Pcdh20 33
  • 86.89 (n)
(Gallus gallus)
Aves PCDH20 33
  • 76.32 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh20 33
  • 70.52 (n)
(Danio rerio)
Actinopterygii pcdh20 33
  • 60.72 (n)
Species where no ortholog for PCDH20 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)
  • 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 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 PCDH20 Gene

Gene Tree for PCDH20 (if available)
Gene Tree for PCDH20 (if available)
Evolutionary constrained regions (ECRs) for PCDH20: view image

Paralogs for PCDH20 Gene

(5) SIMAP similar genes for PCDH20 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PCDH20: view

Variants for PCDH20 Gene

Sequence variations from dbSNP and Humsavar for PCDH20 Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
VAR_036111 A breast cancer sample p.Val523Met
rs1000110480 -- 61,418,109(-) A/C genic_upstream_transcript_variant, intron_variant
rs1000153815 -- 61,414,197(-) T/A intron_variant
rs1000327707 -- 61,426,273(-) T/A 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1000541028 -- 61,412,807(-) A/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDH20 Gene

Variant ID Type Subtype PubMed ID
esv2761266 CNV gain 21179565
esv3892365 CNV gain 25118596
nsv510587 CNV deletion 20534489
nsv832628 CNV loss 17160897

Variation tolerance for PCDH20 Gene

Residual Variation Intolerance Score: 13.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.98; 74.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDH20 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDH20 Gene

Disorders for PCDH20 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDH20 Gene - From: DISEASES

Disorder Aliases PubMed IDs
trichorhinophalangeal syndrome, type i
  • trps1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDH20

genes like me logo Genes that share disorders with PCDH20: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDH20 Gene

Publications for PCDH20 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. 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
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. Decreased expression of protocadherin 20 is associated with poor prognosis in hepatocellular carcinoma. (PMID: 27935871) Wu Y … Zhong B (Oncotarget 2017) 3 58
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58

Products for PCDH20 Gene

Sources for PCDH20 Gene

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