CDH20 Gene (Protein Coding)

Cadherin 20

GC18P061333
GIFtS:
36
This gene is a type II classical cadherin from the cadherin superfamily and one of three cadherin 7-like genes located in a cluster on chromosome 18. The encoded membrane protein is a calcium dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Type II (atypical) cadherins are... See more...

Aliases for CDH20 Gene

Aliases for CDH20 Gene

  • Cadherin 20 2 3 5
  • Cadherin 20, Type 2 2 3
  • Cadherin-20 3 4
  • CDH7L3 3 4
  • Cdh7 3

External Ids for CDH20 Gene

Previous GeneCards Identifiers for CDH20 Gene

  • GC18P058988
  • GC18P059130
  • GC18P057306
  • GC18P057308
  • GC18P055867

Summaries for CDH20 Gene

Entrez Gene Summary for CDH20 Gene

  • This gene is a type II classical cadherin from the cadherin superfamily and one of three cadherin 7-like genes located in a cluster on chromosome 18. The encoded membrane protein is a calcium dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Since disturbance of intracellular adhesion is a prerequisite for invasion and metastasis of tumor cells, cadherins are considered prime candidates for tumor suppressor genes. [provided by RefSeq, Jul 2008]

GeneCards Summary for CDH20 Gene

CDH20 (Cadherin 20) is a Protein Coding gene. Diseases associated with CDH20 include Charge Syndrome and Choanal Atresia, Posterior. Among its related pathways are Nanog in Mammalian ESC Pluripotency and S-1P Stimulated Signaling. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is CDH7.

UniProtKB/Swiss-Prot Summary for CDH20 Gene

  • Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.

Additional gene information for CDH20 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CDH20 Gene

Genomics for CDH20 Gene

GeneHancer (GH) Regulatory Elements for CDH20 Gene

Promoters and enhancers for CDH20 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
GH18J061332 Promoter/Enhancer 1.2 Ensembl CraniofacialAtlas dbSUPER 510.7 +0.9 854 2.2 EZH2 SMC3 ZBTB17 ZNF263 CTCF TAF1 ZNF202 TBP POLR2A GLIS2 CDH20 RF00026-492 RNU6-116P
GH18J061398 Enhancer 0.6 Ensembl ENCODE 10 +66.7 66725 2.9 JUND FOS SPI1 GATA2 JUN MNT CDH20 RNU6-116P RF00026-492 lnc-RNF152-10
GH18J061502 Enhancer 0.5 ENCODE 10.8 +169.3 169253 0.2 CTCF RAD21 TRIM22 SMC3 ZNF654 ZNF143 CDH20 piR-33432-258 lnc-RNF152-9
GH18J061503 Enhancer 0.5 Ensembl 10.8 +168.8 168771 0.8 CTCF RAD21 TRIM22 SMC3 ZNF654 ZNF143 CDH20 piR-33432-258 lnc-RNF152-9
GH18J061869 Enhancer 0.7 FANTOM5 Ensembl ENCODE 6.1 +536.9 536908 1.5 USF1 FOXP2 USF2 RNF152 CDH20 PHLPP1 lnc-RNF152-3 lnc-PIGN-6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDH20 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CDH20

Top Transcription factor binding sites by QIAGEN in the CDH20 gene promoter:
  • C/EBPalpha
  • FOXO4
  • LHX3b
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • SRF
  • SRF (504 AA)
  • TGIF
  • YY1

Genomic Locations for CDH20 Gene

Genomic Locations for CDH20 Gene
chr18:61,333,430-61,555,779
(GRCh38/hg38)
Size:
222,350 bases
Orientation:
Plus strand
chr18:59,000,815-59,223,006
(GRCh37/hg19)
Size:
222,192 bases
Orientation:
Plus strand

Genomic View for CDH20 Gene

Genes around CDH20 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDH20 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDH20 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CDH20 Gene

Proteins for CDH20 Gene

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  • Protein details for CDH20 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HBT6-CAD20_HUMAN
    Recommended name:
    Cadherin-20
    Protein Accession:
    Q9HBT6
    Secondary Accessions:
    • Q495S3

    Protein attributes for CDH20 Gene

    Size:
    801 amino acids
    Molecular mass:
    88993 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CDH20 Gene

Protein Expression for CDH20 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CDH20 Gene

  • Glycosylation at Asn261, Asn420, Asn461, and Asn542
  • Modification sites at PhosphoSitePlus

Other Protein References for CDH20 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CDH20 Gene

Domains & Families for CDH20 Gene

Gene Families for CDH20 Gene

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

Protein Domains for CDH20 Gene

Blocks:
  • Cadherin cytoplasmic region
  • Cadherin
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CDH20 Gene

GenScript: Design optimal peptide antigens:
  • Cadherin-20 (CAD20_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9HBT6

UniProtKB/Swiss-Prot:

CAD20_HUMAN :
  • Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
Domain:
  • Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
genes like me logo Genes that share domains with CDH20: view

Function for CDH20 Gene

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Molecular function for CDH20 Gene

UniProtKB/Swiss-Prot Function:
Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.

Phenotypes From GWAS Catalog for CDH20 Gene

Gene Ontology (GO) - Molecular Function for CDH20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CDH20: view
genes like me logo Genes that share phenotypes with CDH20: view

Animal Model Products

CRISPR Products

miRNA for CDH20 Gene

miRTarBase miRNAs that target CDH20

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDH20

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CDH20 Gene

Localization for CDH20 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDH20 Gene

Cell membrane; Single-pass type I membrane protein.

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 CDH20 gene
Compartment Confidence
plasma membrane 5
extracellular 2
nucleus 2
cytoskeleton 1
mitochondrion 1
peroxisome 0
cytosol 0

Gene Ontology (GO) - Cellular Components for CDH20 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 CDH20: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDH20 Gene

Pathways & Interactions for CDH20 Gene

PathCards logo

SuperPathways for CDH20 Gene

SuperPathway Contained pathways
1 G12-G13 in Cellular Signaling
G12-G13 in Cellular Signaling
-
2 Nanog in Mammalian ESC Pluripotency
GSK3 Signaling
.61
3 ERK Signaling
ILK Signaling
.49
4 S-1P Stimulated Signaling
S-1P Stimulated Signaling
-
5 WNT Signaling
WNT Signaling
-
genes like me logo Genes that share pathways with CDH20: view

Pathways by source for CDH20 Gene

5 Qiagen pathways for CDH20 Gene
  • G12-G13 in Cellular Signaling
  • GSK3 Signaling
  • ILK Signaling
  • S-1P Stimulated Signaling
  • WNT Signaling

Gene Ontology (GO) - Biological Process for CDH20 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:0098609 cell-cell adhesion IEA --
genes like me logo Genes that share ontologies with CDH20: view

No data available for SIGNOR curated interactions for CDH20 Gene

Drugs & Compounds for CDH20 Gene

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  1. Drug

(1) Drugs for CDH20 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
genes like me logo Genes that share compounds with CDH20: view

Transcripts for CDH20 Gene

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  1. CRISPR
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mRNA/cDNA for CDH20 Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
4 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 CDH20

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDH20 Gene

No ASD Table

Relevant External Links for CDH20 Gene

GeneLoc Exon Structure for
CDH20

Expression for CDH20 Gene

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  1. Primer
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CDH20 Gene

mRNA expression in normal human tissues for CDH20 Gene
mRNA expression by BioGPS for CDH20 GenemRNA expression by GTEx for CDH20 Gene

mRNA differential expression in normal tissues according to GTEx for CDH20 Gene

This gene is overexpressed in Brain - Amygdala (x5.4), Brain - Caudate (basal ganglia) (x5.0), Brain - Spinal cord (cervical c-1) (x4.9), Brain - Nucleus accumbens (basal ganglia) (x4.5), Brain - Substantia nigra (x4.5), Brain - Hippocampus (x4.3), and Brain - Putamen (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for CDH20 Gene

This gene is overexpressed in Frontal cortex (37.0) and Spinal cord (29.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CDH20 Gene



Protein tissue co-expression partners for CDH20 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CDH20

SOURCE GeneReport for Unigene cluster for CDH20 Gene:

Hs.671510

mRNA Expression by UniProt/SwissProt for CDH20 Gene:

Q9HBT6-CAD20_HUMAN
Tissue specificity: Expressed in placenta, adult brain, and fetal brain.

Evidence on tissue expression from TISSUES for CDH20 Gene

  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with CDH20: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDH20 Gene

Orthologs for CDH20 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CDH20 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia CDH20 31 30
  • 99.38 (n)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia CDH20 31
  • 93 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia CDH20 31 30
  • 92.68 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia CDH20 31 30
  • 89.89 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Cdh20 17 31 30
  • 89.76 (n)
rat
(Rattus norvegicus)
 Mammalia Cdh20 30
  • 89.39 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia CDH20 31
  • 75 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves CDH20 31 30
  • 81.43 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia CDH20 31
  • 86 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia cdh20 30
  • 72.61 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.153 30
Species where no ortholog for CDH20 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)
  • 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)
  • zebrafish (Danio rerio)

Evolution for CDH20 Gene

ENSEMBL:
Gene Tree for CDH20 (if available)
TreeFam:
Gene Tree for CDH20 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CDH20: view image

Paralogs for CDH20 Gene

Paralogs for CDH20 Gene

(18) SIMAP similar genes for CDH20 Gene using alignment to 3 proteins:

  • CAD20_HUMAN
  • K7ESP2_HUMAN
  • L8EAG9_HUMAN
genes like me logo Genes that share paralogs with CDH20: view

Variants for CDH20 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CDH20 Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
VAR_036103 A breast cancer sample p.Met228Ile
VAR_036104 A breast cancer sample p.Pro416Thr
VAR_036105 A breast cancer sample p.Gln746His
rs17068463 - p.Pro391Leu
rs1943330 - p.Pro328His

Additional dbSNP identifiers (rs#s) for CDH20 Gene

Structural Variations from Database of Genomic Variants (DGV) for CDH20 Gene

Variant ID Type Subtype PubMed ID
esv1603313 CNV deletion 17803354
esv2664717 CNV deletion 23128226
esv3307059 CNV mobile element insertion 20981092
esv3343786 CNV insertion 20981092
esv3376534 CNV insertion 20981092
esv3555490 CNV deletion 23714750
esv3642733 CNV loss 21293372
nsv524346 CNV loss 19592680

Variation tolerance for CDH20 Gene

Residual Variation Intolerance Score: 6.42% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.23; 70.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDH20 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDH20

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDH20 Gene

Disorders for CDH20 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CDH20 Gene - From: DISEASES

Disorder Aliases PubMed IDs
charge syndrome
  • hhs
choanal atresia, posterior
  • pca
coloboma of macula
  • agenesis of macula
- elite association - COSMIC cancer census association via MalaCards
Search CDH20 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDH20

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CDH20: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDH20 Gene

Publications for CDH20 Gene

  1. Characterization of three novel human cadherin genes (CDH7, CDH19, and CDH20) clustered on chromosome 18q22-q23 and with high homology to chicken cadherin-7. (PMID: 10995570) Kools P … van Roy F (Genomics 2000) 2 3 4 23 54
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  3. Genetic analysis of diabetic nephropathy on chromosome 18 in African Americans: linkage analysis and dense SNP mapping. (PMID: 19690890) McDonough CW … Bowden DW (Human genetics 2009) 3 41 54
  4. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. (PMID: 29676528) Khanna R … Parnaik VK (The FEBS journal 2018) 3 54
  5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PMID: 23251661) Comuzzie AG … Butte NF (PloS one 2012) 3 54

ExternalLinks

View latest publications for CDH20 gene in Mastermind

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