U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

    CDH1 cadherin 1 [ Homo sapiens (human) ]

    Gene ID: 999, updated on 13-May-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

    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 IEA
    Inferred from Electronic Annotation
    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 migration 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)