Human Gene CDH3 (ENST00000264012.9) from GENCODE V44
  Description: Homo sapiens cadherin 3 (CDH3), transcript variant 1, mRNA. (from RefSeq NM_001793)
RefSeq Summary (NM_001793): This gene encodes a classical cadherin of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature glycoprotein. This calcium-dependent cell-cell adhesion protein is comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. This gene is located in a gene cluster in a region on the long arm of chromosome 16 that is involved in loss of heterozygosity events in breast and prostate cancer. In addition, aberrant expression of this protein is observed in cervical adenocarcinomas. Mutations in this gene are associated with hypotrichosis with juvenile macular dystrophy and ectodermal dysplasia, ectrodactyly, and macular dystrophy syndrome (EEMS). [provided by RefSeq, Nov 2015].
Gencode Transcript: ENST00000264012.9
Gencode Gene: ENSG00000062038.15
Transcript (Including UTRs)
   Position: hg38 chr16:68,645,310-68,700,292 Size: 54,983 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg38 chr16:68,645,380-68,698,400 Size: 53,021 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:68,645,310-68,700,292)mRNA (may differ from genome)Protein (829 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Cadherin-3; AltName: Full=Placental cadherin; Short=P-cadherin; Flags: Precursor;
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.
SUBUNIT: Interacts with CDCP1.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Expressed in some normal epithelial tissues and in some carcinoma cell lines.
DISEASE: Defects in CDH3 are the cause of hypotrichosis with juvenile macular dystrophy (HJMD) [MIM:601553]. HJMD is a rare autosomal recessive disorder characterized by early hair loss heralding severe degenerative changes of the retinal macula and culminating in blindness during the second to third decade of life.
DISEASE: Defects in CDH3 are the cause of ectodermal dysplasia with ectrodactyly and macular dystrophy (EEM) [MIM:225280]; also known as EEM syndrome, Albrectsen-Svendsen syndrome or Ohdo- Hirayama-Terawaki syndrome. Ectodermal dysplasia defines a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures. EEM is an autosomal recessive condition characterized by features of ectodermal dysplasia such as sparse eyebrows and scalp hair, and selective tooth agenesis associated with macular dystrophy and ectrodactyly.
SIMILARITY: Contains 5 cadherin domains.
WEB RESOURCE: Name=Mutations of the CDH3 gene; Note=Retina International's Scientific Newsletter; URL="";
WEB RESOURCE: Name=GeneReviews; URL="";

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: CDH3
Diseases sorted by gene-association score: ectodermal dysplasia, ectrodactyly, and macular dystrophy* (1691), hypotrichosis, congenital, with juvenile macular dystrophy* (1587), juvenile macular degeneration and hypotrichosis* (400), hypotrichosis (55), hailey-hailey disease (11), darier disease (10), north american indian childhood cirrhosis (7), diffuse gastric cancer (7), deafness, autosomal recessive 89 (7), telogen effluvium (6), crohn's colitis (6), corneal fleck dystrophy (4), hair disease (4), prostate cancer (2), breast cancer (2), tooth agenesis (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 26.48 RPKM in Ovary
Total median expression: 148.58 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -23.4070-0.334 Picture PostScript Text
3' UTR -602.401892-0.318 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002126 - Cadherin
IPR015919 - Cadherin-like
IPR020894 - Cadherin_CS
IPR000233 - Cadherin_cytoplasmic-dom

Pfam Domains:
PF00028 - Cadherin domain
PF01049 - Cadherin cytoplasmic region

ModBase Predicted Comparative 3D Structure on P22223
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0005509 calcium ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0001895 retina homeostasis
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007601 visual perception
GO:0010628 positive regulation of gene expression
GO:0010838 positive regulation of keratinocyte proliferation
GO:0022405 hair cycle process
GO:0031424 keratinization
GO:0032773 positive regulation of monophenol monooxygenase activity
GO:0032912 negative regulation of transforming growth factor beta2 production
GO:0034332 adherens junction organization
GO:0042060 wound healing
GO:0042493 response to drug
GO:0043568 positive regulation of insulin-like growth factor receptor signaling pathway
GO:0048023 positive regulation of melanin biosynthetic process
GO:0050896 response to stimulus
GO:0051796 negative regulation of catagen
GO:0060070 canonical Wnt signaling pathway
GO:0060901 regulation of hair cycle by canonical Wnt signaling pathway
GO:0098609 cell-cell adhesion
GO:1902910 positive regulation of melanosome transport

Cellular Component:
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005913 cell-cell adherens junction
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  BC041846 - Homo sapiens cadherin 3, type 1, P-cadherin (placental), mRNA (cDNA clone MGC:43574 IMAGE:5269523), complete cds.
BC014462 - Homo sapiens cadherin 3, type 1, P-cadherin (placental), mRNA (cDNA clone MGC:23083 IMAGE:4870356), complete cds.
AK296968 - Homo sapiens cDNA FLJ50795 complete cds, highly similar to Cadherin-3 precursor.
AK312554 - Homo sapiens cDNA, FLJ92927, highly similar to Homo sapiens cadherin 3, type 1, P-cadherin (placental) (CDH3),mRNA.
AK225396 - Homo sapiens mRNA for Cadherin-3 precursor variant, clone: HRC02858.
X63629 - H.sapiens mRNA for p cadherin.
AB527800 - Synthetic construct DNA, clone: pF1KB5787, Homo sapiens CDH3 gene for cadherin 3, type 1, P-cadherin, without stop codon, in Flexi system.
KJ904433 - Synthetic construct Homo sapiens clone ccsbBroadEn_13827 CDH3 gene, encodes complete protein.
EU832319 - Synthetic construct Homo sapiens clone HAIB:100067348; DKFZo008E0227 cadherin 3, type 1, P-cadherin (placental) protein (CDH3) gene, encodes complete protein.
EU832404 - Synthetic construct Homo sapiens clone HAIB:100067433; DKFZo004E0228 cadherin 3, type 1, P-cadherin (placental) protein (CDH3) gene, encodes complete protein.
JD039187 - Sequence 20211 from Patent EP1572962.
JD187670 - Sequence 168694 from Patent EP1572962.
JD156157 - Sequence 137181 from Patent EP1572962.
JD524926 - Sequence 505950 from Patent EP1572962.
JD403723 - Sequence 384747 from Patent EP1572962.
JD314394 - Sequence 295418 from Patent EP1572962.
JD067867 - Sequence 48891 from Patent EP1572962.
JD185553 - Sequence 166577 from Patent EP1572962.
JD209590 - Sequence 190614 from Patent EP1572962.
JD075330 - Sequence 56354 from Patent EP1572962.
JD136956 - Sequence 117980 from Patent EP1572962.
JD535372 - Sequence 516396 from Patent EP1572962.
DM110841 - Novel Cancer Marker and Use Thereof.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)

Reactome (by CSHL, EBI, and GO)

Protein P22223 (Reactome details) participates in the following event(s):

R-HSA-419001 Connection of adjacent cells through calcium-dependent trans-dimerization of cadherin
R-HSA-419002 Interaction of cadherin with Beta/gamma catenin, alpha catenin and p120 catenin
R-HSA-418990 Adherens junctions interactions
R-HSA-421270 Cell-cell junction organization
R-HSA-446728 Cell junction organization
R-HSA-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6F4, CADH3_HUMAN, CDHP, ENST00000264012.1, ENST00000264012.2, ENST00000264012.3, ENST00000264012.4, ENST00000264012.5, ENST00000264012.6, ENST00000264012.7, ENST00000264012.8, NM_001793, P22223, Q05DI6, uc002ewf.1, uc002ewf.2, uc002ewf.3, uc002ewf.4
UCSC ID: ENST00000264012.9
RefSeq Accession: NM_001793
Protein: P22223 (aka CADH3_HUMAN or CAD3_HUMAN)
CCDS: CCDS10868.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.