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CDH1 cadherin 1 [ Homo sapiens (human) ]

Gene ID: 999, updated on 24-May-2020

Summary

Official Symbol
CDH1provided by HGNC
Official Full Name
cadherin 1provided by HGNC
Primary source
HGNC:HGNC:1748
See related
Ensembl:ENSG00000039068 MIM:192090
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
UVO; CDHE; ECAD; LCAM; Arc-1; BCDS1; CD324
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. Mutations in this gene are correlated with gastric, breast, colorectal, thyroid and ovarian cancer. Loss of function of this gene is thought to contribute to cancer progression by increasing proliferation, invasion, and/or metastasis. The ectodomain of this protein mediates bacterial adhesion to mammalian cells and the cytoplasmic domain is required for internalization. This gene is present in a gene cluster with other members of the cadherin family on chromosome 16. [provided by RefSeq, Nov 2015]
Annotation information
Note: CDH1 (GeneID 999) and FZR1 (GeneID 51343) share the CDH1 symbol. CDH1 is sometimes used as an abbreviation for 'CDC20 homolog 1' which is an alternate name for the FZR1 gene and thus can be confused with the official symbol for cadherin 1 (CDH1). [16 Jul 2018]
Expression
Broad expression in thyroid (RPKM 81.8), colon (RPKM 70.0) and 17 other tissues See more
Orthologs

Genomic context

See CDH1 in Genome Data Viewer
Location:
16q22.1
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (68737292..68835537)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68771128..68869445)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene calponin 2 pseudogene Neighboring gene cadherin 3 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 ferritin light chain pseudogene 14 Neighboring gene transport and golgi organization 6 homolog Neighboring gene RNA, U7 small nuclear 42 pseudogene Neighboring gene RNA, U6 small nuclear 898, pseudogene

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?

Phenotypes

Associated conditions

Description Tests
Blepharocheilodontic syndrome 1
MedGen: C4551988 OMIM: 119580 GeneReviews: Not available
Compare labs
Endometrial carcinoma
MedGen: C0476089 OMIM: 608089 GeneReviews: Not available
Compare labs
Familial cancer of breast Compare labs
Hereditary diffuse gastric cancer Compare labs
Malignant tumor of prostate
MedGen: C0376358 OMIM: 176807 GeneReviews: Not available
Compare labs
Neoplasm of ovary
MedGen: C0919267 OMIM: 167000 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2020-04-10)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2020-04-10)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.
NHGRI GWA Catalog
Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 inhibits the expression of E-cadherin and changes its localization from cell membrane to cytoplasm in polarized oral epithelial cells PubMed
Tat tat HIV-1 Tat C treated human brain microvascular endothelial cells result in downregulation and dissociation of VE-PTP and SHP2 from VE-cadherin PubMed
tat HIV-1 Tat C induces phosphorylation of adherens junction proteins VE-cadherin and beta-catenin in human brain microvascular endothelial cells PubMed
tat HIV-1 Tat inhibits the expression of E-cadherin and changes its localization from cell membrane to cytoplasm in polarized oral epithelial cells PubMed
Vpr vpr HIV-1 Vpr-expressing Jurkat T cell clones showed upregulated expression of cadherin, suggesting a role of Vpr in modulating the cell adhesion process PubMed
Vpu vpu HIV-1 Vpu reduces the beta-catenin interaction with E-cadherin and the Vpu-mediated dissociation of beta-catenin with E-cadherin enhances particle release PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase activating protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ankyrin binding IPI
Inferred from Physical Interaction
more info
PubMed 
beta-catenin binding IDA
Inferred from Direct Assay
more info
PubMed 
cadherin binding HDA PubMed 
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 
cell adhesion molecule binding IPI
Inferred from Physical Interaction
more info
PubMed 
cell adhesion molecule binding NAS
Non-traceable Author Statement
more info
PubMed 
gamma-catenin binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
adherens junction organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
adherens junction organization IMP
Inferred from Mutant Phenotype
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 morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
cell-cell adhesion mediated by cadherin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell adhesion via plasma-membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell junction assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to indole-3-methanol IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to lithium ion IDA
Inferred from Direct Assay
more info
PubMed 
entry of bacterium into host cell TAS
Traceable Author Statement
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
homophilic cell adhesion via plasma membrane adhesion molecules NAS
Non-traceable Author Statement
more info
PubMed 
multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell-cell adhesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron projection development IEA
Inferred from Electronic Annotation
more info
 
pituitary gland development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein import into nucleus IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
protein localization to plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
protein localization to plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein catabolic process at postsynapse, modulating synaptic transmission IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IEA
Inferred from Electronic Annotation
more info
 
synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
actin cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
adherens junction IDA
Inferred from Direct Assay
more info
PubMed 
apical junction complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apical junction complex IDA
Inferred from Direct Assay
more info
PubMed 
catenin complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catenin complex IDA
Inferred from Direct Assay
more info
PubMed 
cell junction IDA
Inferred from Direct Assay
more info
PubMed 
cell junction TAS
Traceable Author Statement
more info
PubMed 
colocalizes_with cortical actin cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasmic side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
endosome IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
flotillin complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
flotillin complex IDA
Inferred from Direct Assay
more info
PubMed 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
lateral plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
postsynapse IEA
Inferred from Electronic Annotation
more info
 
trans-Golgi network IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
cadherin-1
Names
CAM 120/80
E-cadherin 1
cadherin 1, E-cadherin (epithelial)
cadherin 1, type 1, E-cadherin (epithelial)
calcium-dependent adhesion protein, epithelial
cell-CAM 120/80
epididymis secretory sperm binding protein
epithelial cadherin
uvomorulin

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_008021.1 RefSeqGene

    Range
    5001..103250
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_301

mRNA and Protein(s)

  1. NM_001317184.2NP_001304113.1  cadherin-1 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1. This isoform (2) may undergo proteolytic processing similar to isoform 1.
    Source sequence(s)
    AB025105, AK312551, EU709494
    Consensus CDS
    CCDS82005.1
    UniProtKB/Swiss-Prot
    P12830
    UniProtKB/TrEMBL
    B3GN61
    Related
    ENSP00000414946.2, ENST00000422392.6
    Conserved Domains (5) summary
    cd00031
    Location:158258
    CA_like; Cadherin repeat-like domain
    cd11304
    Location:431530
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam00028
    Location:537625
    Cadherin; Cadherin domain
    pfam01049
    Location:680816
    Cadherin_C; Cadherin cytoplasmic region
    pfam08758
    Location:27116
    Cadherin_pro; Cadherin prodomain like
  2. NM_001317185.2NP_001304114.1  cadherin-1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in an exon in its 5' UTR, resulting in a different 5' UTR and the use of a downstream 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)
    AB025106, AC099314, AK312551, EU709494
    UniProtKB/Swiss-Prot
    P12830
    UniProtKB/TrEMBL
    B3GN61, Q9UII7
    Conserved Domains (3) summary
    cd11304
    Location:375
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam00028
    Location:82170
    Cadherin; Cadherin domain
    pfam01049
    Location:225361
    Cadherin_C; Cadherin cytoplasmic region
  3. NM_001317186.2NP_001304115.1  cadherin-1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an exon in its 5' UTR, resulting in a different 5' UTR and the use of a downstream start site compared to variant 1. The encoded isoform (4) has a shorter N-terminus and lacks a predicted signal peptide compared to isoform 1.
    Source sequence(s)
    AK312551, BC144283, EU709494
    UniProtKB/Swiss-Prot
    P12830
    UniProtKB/TrEMBL
    B3GN61
    Conserved Domains (1) summary
    pfam01049
    Location:86222
    Cadherin_C; Cadherin cytoplasmic region
  4. NM_004360.5NP_004351.1  cadherin-1 isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_004351.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK290012, AK312551, EU709494
    Consensus CDS
    CCDS10869.1
    UniProtKB/Swiss-Prot
    P12830
    UniProtKB/TrEMBL
    A0A0U2ZQU7, B3GN61
    Related
    ENSP00000261769.4, ENST00000261769.10
    Conserved Domains (5) summary
    cd00031
    Location:158258
    CA_like; Cadherin repeat-like domain
    cd11304
    Location:492591
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam01049
    Location:738879
    Cadherin_C; Cadherin cytoplasmic region
    pfam08758
    Location:27116
    Cadherin_pro; Cadherin prodomain like
    cl09101
    Location:598686
    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
    68737292..68835537
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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