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CDH3 cadherin 3 [ Homo sapiens (human) ]

Gene ID: 1001, updated on 13-Mar-2020

Summary

Official Symbol
CDH3provided by HGNC
Official Full Name
cadherin 3provided by HGNC
Primary source
HGNC:HGNC:1762
See related
Ensembl:ENSG00000062038 MIM:114021
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CDHP; HJMD; PCAD
Summary
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]
Expression
Broad expression in skin (RPKM 13.2), ovary (RPKM 12.3) and 15 other tissues See more
Orthologs

Genomic context

See CDH3 in Genome Data Viewer
Location:
16q22.1
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (68644914..68727573)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68678151..68732959)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371321 Neighboring gene RNA, U4 small nuclear 36, pseudogene Neighboring gene ZFP90 zinc finger protein Neighboring gene calponin 2 pseudogene Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 5 Neighboring gene RNA, 5S ribosomal pseudogene 429 Neighboring gene Sharpr-MPRA regulatory region 4224 Neighboring gene cadherin 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cadherin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoskeletal protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
adherens junction organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
adherens junction organization TAS
Traceable Author Statement
more info
 
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell adhesion TAS
Traceable Author Statement
more info
PubMed 
cell morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell adhesion mediated by cadherin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell junction assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
hair cycle process IMP
Inferred from Mutant Phenotype
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
keratinization IMP
Inferred from Mutant Phenotype
more info
PubMed 
multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of timing of catagen IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transforming growth factor beta2 production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of canonical Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of insulin-like growth factor receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of keratinocyte proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of melanin biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of melanosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of monophenol monooxygenase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of hair cycle by canonical Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to drug IEA
Inferred from Electronic Annotation
more info
 
retina homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
visual perception IEA
Inferred from Electronic Annotation
more info
 
wound healing IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catenin complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell junction IDA
Inferred from Direct Assay
more info
 
cell surface IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
cadherin-3
Names
cadherin 3, type 1, P-cadherin (placental)
calcium-dependent adhesion protein, placental

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009096.1 RefSeqGene

    Range
    6063..61045
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001317195.2NP_001304124.1  cadherin-3 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift and an early stop codon. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1. This isoform (2) may undergo proteolytic processing similar to isoform (1).
    Source sequence(s)
    AW339148, BC014462, BQ945506, BU543746, CA489015, CN365479
    Consensus CDS
    CCDS82004.1
    UniProtKB/Swiss-Prot
    P22223
    Related
    ENSP00000398485.2, ENST00000429102.6
    Conserved Domains (4) summary
    cd11304
    Location:219324
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam01049
    Location:687765
    Cadherin_C; Cadherin cytoplasmic region
    cl07391
    Location:2696
    Cadherin_pro; Cadherin prodomain like
    cl09101
    Location:113211
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  2. NM_001317196.2NP_001304125.1  cadherin-3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in its 5' UTR, resulting in the use of a downstream translation start site compared to variant 1. The encoded isoform (3) has a shorter N-terminus and lacks a predicted signal peptide compared to isoform 1.
    Source sequence(s)
    AC099314, AK296968, AW339148, BQ945506, BU543746, CA489015, CN365479
    UniProtKB/Swiss-Prot
    P22223
    UniProtKB/TrEMBL
    B4DLF0
    Conserved Domains (3) summary
    cd11304
    Location:164269
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam01049
    Location:632769
    Cadherin_C; Cadherin cytoplasmic region
    cl09101
    Location:58156
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  3. NM_001793.6NP_001784.2  cadherin-3 isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_001784.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC099314, AW339148, BC014462, BC041846, BQ945506, BU543746, CA489015, CN365479
    Consensus CDS
    CCDS10868.1
    UniProtKB/Swiss-Prot
    P22223
    Related
    ENSP00000264012.4, ENST00000264012.9
    Conserved Domains (4) summary
    cd11304
    Location:219324
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam01049
    Location:687824
    Cadherin_C; Cadherin cytoplasmic region
    cl07391
    Location:2696
    Cadherin_pro; Cadherin prodomain like
    cl09101
    Location:113211
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    68644914..68727573
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522800.3XP_011521102.1  cadherin-3 isoform X1

    Conserved Domains (4) summary
    cd11304
    Location:219324
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam01049
    Location:687762
    Cadherin_C; Cadherin cytoplasmic region
    cl07391
    Location:2696
    Cadherin_pro; Cadherin prodomain like
    cl09101
    Location:113211
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
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