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CDH3 (Cadherin 3, Type 1, P-Cadherin (Placental))

Written2014-05André Filipe Vieira, Ana Sofia Ribeiro, Joana Paredes
Institute of Pathology, Immunology of the University of Porto, Portugal

(Note : for Links provided by Atlas : click)


Alias_namescadherin 3, P-cadherin (placental)
cadherin 3, type 1, P-cadherin (placental)
Alias_symbol (synonym)CDHP
Other aliasHJMD
HGNC (Hugo) CDH3
LocusID (NCBI) 1001
Atlas_Id 40025
Location 16q22.1  [Link to chromosome band 16q22]
Location_base_pair Starts at 68678739 and ends at 68732970 bp from pter ( according to hg19-Feb_2009)  [Mapping CDH3.png]
  Localization of CDH3 gene (P-cadherin). 5 cadherin genes (CDH1; CDH3; CDH5; CDH8; and CDH11) are clustered in the 16q21-q22.1 region. The CDH3 gene is localized in the larger arm of chromosome 16, just 32Kb upstream of the gene encoding CDH1 (E-cadherin) (Bussemakers et al., 1994; Kremmidiotis et al., 1998).
Fusion genes
(updated 2016)
AFF3 (2q11.2) / CDH3 (16q22.1)CDH3 (16q22.1) / RRM2 (2p25.1)CDH3 (16q22.1) / ZNF608 (5q23.2)
PPP2CA (5q31.1) / CDH3 (16q22.1)TNC (9q33.1) / CDH3 (16q22.1)


  The genomic structure of the CDH3/P-cadherin gene is constituted by 16 coding exons (NCBI Reference Sequence: NM_001793.4): the extracellular part of P-cadherin is encoded by 10 exons (exons 4-13), whereas the transmembrane and the intracellular domains are codified by the last 3 exons (exons 14-16) (Albergaria et al., 2011) (NCBI Reference Sequence: NM_001793.4).
Description DNA contains 54807 bp containing 16 coding exons.
Transcription 4276 bp mRNA transcribed in centromeric to telomeric orientation; 2490 bp open reading frame (CCDS10868.1). Concerning CDH3/P-cadherin gene regulation, the main transcriptional activators described for the CDH3/P-cadherin gene promoter are β-catenin (Faraldo et al., 2007), p63 (Shimomura et al., 2008) and C/EBPβ (Albergaria et al., 2010; Albergaria et al., 2013). In contrast, BRCA1/c-Myc/Sp1 complex acts as a transcriptional repressor of the CDH3 promoter (Gorski et al., 2009). It was also demonstrated that ER can indirectly repress P-cadherin expression by promoting epigenetic changes in the CDH3 gene promoter (Paredes et al., 2004; Albergaria et al., 2010).
This gene has 12 transcripts (splice variants), of which 5 are protein coding transcripts, 4 are transcripts suffering nonsense mediated decay, and 3 transcripts do not code for any protein product (ensemble ENSG00000062038 and vega genome OTTHUMG00000137560).


  Image of a classical type I cadherin, adapted with permission from the RCSB PDB March 2008 Molecule of the Month feature by David Goodsell (doi: 10.2210/rcsb_pdb/mom_2008_3).
P-cadherin is a transmembrane protein included in the classical cadherin family, with an ectodomain containing 5 cadherin repeats (which interacts with another cadherin's ectodomain in a cis or trans manner) and a highly conserved cytoplasmic domain that binds to catenins. Sharing about 67% of homology with the CDH1/E-cadherin gene, P-cadherin differs mainly in the extracellular portion and it is far less characterized.
Description Described for the first time in 1986, as "a novel class of cadherin that appeared in developing mouse embryos", this adhesion molecule was found in the tissues that gave rise to its name, the placenta (Nose and Takeichi, 1986). P-cadherin is a transmembrane glycoprotein that belongs to a large family of molecules that mediate calcium-dependent homophilic cell-cell adhesion. It plays a role in many cellular processes such as embryonic development, differentiation, cell polarity, growth and migration (Larue et al., 1996).
P-cadherin is composed by three domains: 1) an extracellular portion responsible for calcium-dependent homotypic cadherin-cadherin interaction (which has 5 repeated cadherin domains); 2) a single pass transmembrane domain; and 3) a highly conserved cytoplasmic domain that binds to the intracellular catenins p120-catenin and β-catenin. Catenins have a dual role, acting as signalling mediators or as adaptor molecules that stabilize the cadherin complex at the membrane and link the cadherin molecule to the actin filaments of the cytoskeleton (Wheelock et al., 2001).
Expression It is expressed in the placenta of mice (hence, its name). It is also expressed in human placental tissues, albeit at lower levels (Shimoyama et al., 1989; Sahin et al., 2014).
Despite being expressed in several human fetal structures, in the adult it is only expressed in certain tissues, usually co-expressed with E-cadherin, such as the basal layer of the epidermis, the breast and the prostate, as well as the mesothelium, the ovary, the hair follicle, and the corneal endothelium (Nose and Takeichi, 1986; Imai et al., 2008).
According to human protein reference database (HPRD:00227), the major sites of expression include endometrium, the glomerulus, hair follicle, keratinocytes, mammary myoepithelium, melanocytes, oocytes, spermatozoa, placenta, prostate, retina, serum, skin. An 80 KDa fragment of P-cadherin (known as soluble P-cadherin) is also found in human breast milk (Soler et al., 2002), nipple aspirates (Mannello et al., 2008), semen (De Paul et al., 2005) and urine (Adachi et al., 2006).
Localisation Cell junctions: a single-pass type I membrane protein anchored to actin microfilaments through association with α-catenin, β-catenin and γ-catenin. Sequential proteolysis induced by apoptosis or calcium influx, results in translocation from sites of cell-cell contact to the cytoplasm.
Function Cell-cell adhesion: cadherin mediated cell-cell adhesion is accomplished by homophilic interactions between two cadherin molecules at the surface of the respective cells in a cis and/or trans manner (Cavallaro and Dejana, 2011) and the cadherin-catenin complex constitutes the main building block of the adherens-type junctions. These complexes also represent a major regulatory mechanism that guides cell fate decisions, influencing cell growth, differentiation, cell motility and survival (Cavallaro and Dejana, 2011).
Cell signalling: P-cadherin shares common interplayers with the wnt signalling pathway (eg. : β-catenin) (Kamposioras et al., 2013; Samuelov et al., 2013) and Integrin signalling (Vieira et al., 2014).
In cancer, it may have a tumour suppressive or a cancer promoting function, depending on the cellular and tissue context (see below).
Homology Sharing about 67% of homology with the CDH1/E-cadherin gene, P-cadherin differs mainly in the extracellular portion and it is far less characterized.
64 organisms have orthologs with the human CDH3 gene. For example, the CDH3 gene is conserved in chimpanzee, dog, cow, mouse, rat and chicken (HomoloGene:20425).


Note According to the Human Gene Mutation Database, 21 mutations have been described for the P-cadherin/CDH3 gene, namely 9 missense/nonsense mutations, 4 splicing mutations, 1 regulatory mutation, 1 gross deletion, 5 small deletions and 1 small insertion (The Human Gene Mutation Database).
There are no reported descriptions of small indels, gross insertions/duplications, complex rearrangements or repeat variations.
16 mutations are associated with Hypotricosis with Juvenile Macular Dystrophy (HJMD) and 2 mutations are implicated with Ectodermal dysplasia, Ectrodactyly and Macular dystrophy (EEM) syndrome (The Human Gene Mutation Database).
Regarding polymorphisms, several SNPs have been reported for the CDH3 gene that have no clinical significance because they code for synonymous codons or related residues (ClinVar).
  Summary of the human CDH3 gene mutations. 21 mutations have been described for the P-cadherin/CDH3 gene, namely 9 missense/nonsense mutations, 4 splicing mutations, 1 regulatory mutation, 5 small deletions, 1 small insertion and 1 gross deletion (The Human Gene Mutation Database).
Germinal Human germline mutations for the CDH3 gene have been reported to carry the phenotype of HJMD and EEM syndromes (Sprecher et al., 2001;Kjaer et al., 2005; Avitan-Hersh et al., 2012; Halford et al., 2012). The germline deletion of CDH3 in the mouse causes breast secretory immaturity and premature mammary gland differentiation. The P-cadherin mutant mice develop hyperplasia and dysplasia of the mammary epithelium with age and, in contrast to humans, no reports regarding development defects have been described (Radice et al., 1997).

Implicated in

Entity Various cancers
Note P-cadherin is altered in various human tumours, but its effective role in the carcinogenesis process remains object of debate, since it can behave differently depending on the studied tumour cell model and context. For example, in melanoma, P-cadherin seems to have a tumour suppressive function, exactly as E-cadherin (Van Marck et al., 2005). In breast cancer P-cadherin is often overexpressed and it is reported to exhibit tumour promoting effects (Paredes et al., 2012). Importantly, P-cadherin upregulation is also found in other malignancies such as gastric, endometrial, colorectal and pancreatic carcinomas (Hardy et al., 2002; Stefansson et al., 2004; Taniuchi et al., 2005; Imai et al., 2008).
Entity Breast cancer
Note P-cadherin aberrant expression is found in 20% to 40% of invasive breast carcinomas, as well as in 25% of pre-invasive (in situ) ductal carcinomas. Aberrant P-cadherin expression was shown to be associated with tumours of high histological grade, as well as with well established markers of poor prognosis, like Ki-67, EGFR, CK5, vimentin, p53 and HER-2 expression, and negatively associated with age at prognosis and hormonal receptors (ER and PgR) expression. None of these reports showed a significant association with tumour size and lymph node metastasis (Turashvili et al., 2011; Peralta Soler et al., 1999; Gamallo et al., 2001; Paredes et al., 2002; Paredes et al., 2005). P-cadherin aggressive behaviour in breast cancer is dependent on an E-cadherin positive background (Ribeiro et al., 2013) and it is substantially attributed to an increased migratory and invasive capacity of cancer cells (Ribeiro et al., 2010), increased stem cell activity (Vieira et al., 2012) and cross-talk with integrin oncogenic signalling pathways (Vieira et al., 2014).
P-cadherin up-regulation is predominantly found in the basal-like subgroup of breast cancers (Matos et al., 2005; Paredes et al., 2007a; Paredes et al., 2007b) and it is strongly associated with the presence of BRCA1 mutation (Arnes et al., 2005) and poor clinical outcome (Paredes et al., 2005; Turashvili et al., 2011). It has been proposed that P-cadherin in conjugation with vimentin and CK14 constitutes a better criterion for the identification of basal-like breast carcinomas by immunohistochemistry (Sousa et al., 2010).
Prognosis P-cadherin overexpression in breast cancer is an independent factor of poor prognosis (poor disease free and overall survival) (Paredes et al., 2005; Turashvili et al., 2011).
Entity Hypotrichosis with juvenile macular dystrophy (HJMD)
Note In humans, the loss of P-cadherin induces characteristic genetic syndromes.
CDH3 gene mutations have been shown to cause P-cadherin functional inactivation, leading to developmental defects associated with hypotrichosis with juvenile macular dystrophy (HJMD) (Sprecher et al., 2001; Avitan-Hersh et al., 2012; Halford et al., 2012).
Disease Hypotrichosis with juvenile macular dystrophy (HJMD; OMIM: 601553) is a rare recessive disorder, characterized by hair loss heralding progressive macular degeneration and early blindness. Affected HJMD individuals are born with seemingly normal hair but develop alopecia of the scalp at around 3 months. After the age of 3 years, affected individuals develop progressive macular degeneration with slight peripheral retinal dystrophy. The severe degenerative changes of the retinal macula culminate in blindness during the second to third decade of life. Since Sprech er et al. (2001) first established a link between this disease and a mutation in gene encoding CDH3/P-cadherin (Sprecher et al., 2001), several other mutations were found, which essentially disturb the Ca2+ binding and the cadherin functional domains or result in the synthesis of a truncated form of P-cadherin or in the absence of P-cadherin expression.
Cytogenetics The following allelic variants are responsible for HJMD:
- CDH3, c981delG - (Sprecher et al., 2001)
- CDH3, Arg503His - (Indelman et al., 2002)
- CDH3, Leu168Term - (Indelman et al., 2003)
- CDH3, Arg221Term - (Indelman et al., 2007)
- CDH3, Tyr249Term - (Avitan-Hersh et al., 2012)
- CDH3, Glu504Lys - (Indelman et al., 2007)
- CDH3, His575Arg - (Indelman et al., 2007)
- CDH3, Tyr615Term - (Indelman et al., 2005)
- CDH3, IVS2 ds G-A +1 - (Indelman et al., 2007)
- CDH3, IVS10 as G-A -1 - (Jelani et al., 2009; Kamran-ul-Hassan Naqvi et al., 2010)
- CDH3, IVS12 as A-G -2 - (Shimomura et al., 2010)
- CDH3, c.462delT - (Indelman et al., 2003)
- CDH3, c.2117delG - (Indelman et al., 2003)
- CDH3, gDNA 8815bp deleted incl exons 12-13 - (Halford et al., 2012)
Entity Ectodermal dysplasia, ectrodactyly and macular dystrophy (EEM)
Note CDH3 gene mutations have been shown to cause P-cadherin functional inactivation, leading to ectodermal dysplasia, ectrodactyly, and macular dystrophy (EEM syndrome ), a developmental defect associated syndrome. This inherited disease is characterized by sparse hair and macular dystrophy of the retina, and split hand/foot malformation (Kjaer et al., 2005).
Disease This ectodermal defect is characterised by hypotrichosis with sparse and short hair on the scalp, sparse and short eyebrows and eyelashes, and partial anodontia. Different degrees of absence deformities as well as syndactyly have been described, the hands often being more severely affected than the feet. The retinal lesion appears as a central geographic atrophy of the retinal pigment epithelium and choriocapillary layer of the macular area with coarse hyperpigmentations and sparing of the larger choroidal vessels.
Kjaer et al. (2005) first established a link between families with ectodermal dysplasia, ectrodactyly, and macular dystrophy (EEM; OMIM: 225280) and homozygous mutations in CDH3/P-cadherin in affected individuals: a missense mutation (114021.0003) and a deletion (114021.0004), respectively (Kjaer et al., 2005).
Cytogenetics The following allelic variants are responsible for EEM:
- CDH3, Asn322Ile - (Kjaer et al., 2005)
- CDH3, c.829delG - (Kjaer et al., 2005)
- CDH3, Gly277Val - (Basel-Vanagaite et al., 2010)


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PMID 11547897


This paper should be referenced as such :
AF Vieira, AS Ribeiro, J Paredes
CDH3 (Cadherin 3, Type 1, P-Cadherin (Placental))
Atlas Genet Cytogenet Oncol Haematol. 2015;19(2):85-92.
Free journal version : [ pdf ]   [ DOI ]
On line version :

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Soft Tissues: Alveolar rhabdomyosarcoma

External links

HGNC (Hugo)CDH3   1762
Entrez_Gene (NCBI)CDH3  1001  cadherin 3
GeneCards (Weizmann)CDH3
Ensembl hg19 (Hinxton)ENSG00000062038 [Gene_View]  chr16:68678739-68732970 [Contig_View]  CDH3 [Vega]
Ensembl hg38 (Hinxton)ENSG00000062038 [Gene_View]  chr16:68678739-68732970 [Contig_View]  CDH3 [Vega]
ICGC DataPortalENSG00000062038
TCGA cBioPortalCDH3
AceView (NCBI)CDH3
Genatlas (Paris)CDH3
SOURCE (Princeton)CDH3
Genetics Home Reference (NIH)CDH3
Genomic and cartography
GoldenPath hg19 (UCSC)CDH3  -     chr16:68678739-68732970 +  16q22.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)CDH3  -     16q22.1   [Description]    (hg38-Dec_2013)
EnsemblCDH3 - 16q22.1 [CytoView hg19]  CDH3 - 16q22.1 [CytoView hg38]
Mapping of homologs : NCBICDH3 [Mapview hg19]  CDH3 [Mapview hg38]
OMIM114021   225280   601553   
Gene and transcription
Genbank (Entrez)AI149268 AK225396 AK296968 AK312554 AW339148
RefSeq transcript (Entrez)NM_001317195 NM_001317196 NM_001793
RefSeq genomic (Entrez)NC_000016 NC_018927 NG_009096 NT_010498 NW_004929402
Consensus coding sequences : CCDS (NCBI)CDH3
Cluster EST : UnigeneHs.191842 [ NCBI ]
CGAP (NCI)Hs.191842
Alternative Splicing GalleryENSG00000062038
Gene ExpressionCDH3 [ NCBI-GEO ]   CDH3 [ EBI - ARRAY_EXPRESS ]   CDH3 [ SEEK ]   CDH3 [ MEM ]
Gene Expression Viewer (FireBrowse)CDH3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1001
GTEX Portal (Tissue expression)CDH3
Protein : pattern, domain, 3D structure
UniProt/SwissProtP22223   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP22223  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP22223
Splice isoforms : SwissVarP22223
Domaine pattern : Prosite (Expaxy)CADHERIN_1 (PS00232)    CADHERIN_2 (PS50268)   
Domains : Interpro (EBI)Cadherin    Cadherin-like    Cadherin_CS    Cadherin_cytoplasmic-dom    Catenin_binding_dom   
Domain families : Pfam (Sanger)Cadherin (PF00028)    Cadherin_C (PF01049)   
Domain families : Pfam (NCBI)pfam00028    pfam01049   
Domain families : Smart (EMBL)CA (SM00112)  
Conserved Domain (NCBI)CDH3
DMDM Disease mutations1001
Blocks (Seattle)CDH3
PDB (SRS)4OY9   
PDB (PDBSum)4OY9   
PDB (IMB)4OY9   
Structural Biology KnowledgeBase4OY9   
SCOP (Structural Classification of Proteins)4OY9   
CATH (Classification of proteins structures)4OY9   
Human Protein AtlasENSG00000062038
Peptide AtlasP22223
IPIIPI00747243   IPI00645614   IPI01010390   
Protein Interaction databases
IntAct (EBI)P22223
Ontologies - Pathways
Ontology : AmiGOretina homeostasis  molecular_function  calcium ion binding  cytoplasm  plasma membrane  plasma membrane  cell-cell adherens junction  cell adhesion  homophilic cell adhesion via plasma membrane adhesion molecules  visual perception  positive regulation of gene expression  positive regulation of keratinocyte proliferation  integral component of membrane  single organismal cell-cell adhesion  hair cycle process  keratinization  positive regulation of monophenol monooxygenase activity  negative regulation of transforming growth factor beta2 production  adherens junction organization  wound healing  response to drug  positive regulation of insulin-like growth factor receptor signaling pathway  positive regulation of melanin biosynthetic process  negative regulation of catagen  canonical Wnt signaling pathway  regulation of hair cycle by canonical Wnt signaling pathway  positive regulation of melanosome transport  
Ontology : EGO-EBIretina homeostasis  molecular_function  calcium ion binding  cytoplasm  plasma membrane  plasma membrane  cell-cell adherens junction  cell adhesion  homophilic cell adhesion via plasma membrane adhesion molecules  visual perception  positive regulation of gene expression  positive regulation of keratinocyte proliferation  integral component of membrane  single organismal cell-cell adhesion  hair cycle process  keratinization  positive regulation of monophenol monooxygenase activity  negative regulation of transforming growth factor beta2 production  adherens junction organization  wound healing  response to drug  positive regulation of insulin-like growth factor receptor signaling pathway  positive regulation of melanin biosynthetic process  negative regulation of catagen  canonical Wnt signaling pathway  regulation of hair cycle by canonical Wnt signaling pathway  positive regulation of melanosome transport  
Pathways : KEGGCell adhesion molecules (CAMs)   
REACTOMEP22223 [protein]
REACTOME Pathways418990 [pathway]   
NDEx NetworkCDH3
Atlas of Cancer Signalling NetworkCDH3
Wikipedia pathwaysCDH3
Orthology - Evolution
GeneTree (enSembl)ENSG00000062038
Phylogenetic Trees/Animal Genes : TreeFamCDH3
Homologs : HomoloGeneCDH3
Homology/Alignments : Family Browser (UCSC)CDH3
Gene fusions - Rearrangements
Fusion : MitelmanPPP2CA/CDH3 [5q31.1/16q22.1]  [t(5;16)(q31;q22)]  
Fusion : MitelmanTNC/CDH3 [9q33.1/16q22.1]  [t(9;16)(q33;q22)]  
Fusion: TCGAPPP2CA 5q31.1 CDH3 16q22.1 LUAD
Fusion: TCGATNC 9q33.1 CDH3 16q22.1 LUAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCDH3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CDH3
Exome Variant ServerCDH3
ExAC (Exome Aggregation Consortium)CDH3 (select the gene name)
Genetic variants : HAPMAP1001
Genomic Variants (DGV)CDH3 [DGVbeta]
DECIPHER (Syndromes)16:68678739-68732970  ENSG00000062038
CONAN: Copy Number AnalysisCDH3 
ICGC Data PortalCDH3 
TCGA Data PortalCDH3 
Broad Tumor PortalCDH3
OASIS PortalCDH3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCDH3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCDH3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Eye diseases - LOVD
BioMutasearch CDH3
DgiDB (Drug Gene Interaction Database)CDH3
DoCM (Curated mutations)CDH3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CDH3 (select a term)
NCG5 (London)CDH3
Cancer3DCDH3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
OMIM114021    225280    601553   
Orphanet1731    1865   
Genetic Testing Registry CDH3
NextProtP22223 [Medical]
Huge Navigator CDH3 [HugePedia]
snp3D : Map Gene to Disease1001
BioCentury BCIQCDH3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1001
Chemical/Pharm GKB GenePA26299
Clinical trialCDH3
canSAR (ICR)CDH3 (select the gene name)
PubMed99 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Apr 12 11:29:23 CEST 2017

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