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CDH1 cadherin 1 [ Homo sapiens (human) ]

Gene ID: 999, updated on 4-Feb-2024

Summary

Official Symbol
CDH1provided by HGNC
Official Full Name
cadherin 1provided by HGNC
Primary source
HGNC:HGNC:1748
See related
Ensembl:ENSG00000039068 MIM:192090; AllianceGenome:HGNC:1748
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See CDH1 in Genome Data Viewer
Location:
16q22.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (68737292..68835537)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (74533467..74631804)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (68771195..68869440)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene calponin 2 pseudogene Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68688677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68691962-68692462 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68710737 Neighboring gene cadherin 3 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68733646 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68737269-68737769 Neighboring gene Sharpr-MPRA regulatory region 3013 Neighboring gene Sharpr-MPRA regulatory region 1210 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68741769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68744771-68745272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68745273-68745772 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68748223 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68749055 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11024 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68757572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68762277-68762796 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68766493-68767168 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68770288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7650 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68776246 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68778919-68779504 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68780069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68787439-68788396 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68790502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11025 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68791231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11026 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68792712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11028 Neighboring gene RNA, 5S ribosomal pseudogene 429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11027 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68799944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68800316-68800990 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 16:68802068 and 16:68802072 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68803726 Neighboring gene Sharpr-MPRA regulatory region 4224 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68808283 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68813037-68813640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68813641-68814242 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68814316 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68815000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11032 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68818245 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68818709 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68820718 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:68825333-68825902 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 16:68826109 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:68827591-68828091 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68829108-68829608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:68829609-68830109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11033 Neighboring gene ferritin light chain pseudogene 14 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:68900664-68900823 Neighboring gene transport and golgi organization 6 homolog Neighboring gene MPRA-validated peak2625 silencer Neighboring gene RNA, U7 small nuclear 42 pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:69006410-69006910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:69011625-69012125 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69022345-69022846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69022847-69023346 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

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

EBI GWAS Catalog

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

Gene Ontology Provided by GOA

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

NEW Try the new Transcript table

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/TrEMBL
    A0A0E3XJU3, D3XNU5
    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:83224
    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
    A8K1U7, P12830, Q13799, Q14216, Q15855, Q16194, Q4PJ14, Q9UII8
    UniProtKB/TrEMBL
    A0A0E3XJU3, A0A0U2ZQU7, D3XNU5
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    68737292..68835537
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    74533467..74631804
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)