CDH1 cadherin 1 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

Location:: 16q22.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (68737292..68835537)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (74533467..74631804)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (68771195..68869440)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

IL-8 promotes lens capsular residual cells migration by down-regulates expression of E-cadherin and ZO-1 via the CXCR1/2-NF-kappaB-RhoA signal pathway.
Title: IL-8 promotes lens capsular residual cells migration by down-regulates expression of E-cadherin and ZO-1 via the CXCR1/2-NF-κB-RhoA signal pathway.
Associations between CDH1 gene polymorphisms and the risk of gastric cancer: A meta-analysis based on 44 studies.
Title: Associations between CDH1 gene polymorphisms and the risk of gastric cancer: A meta-analysis based on 44 studies.
Molecular Crosstalk Between Adherens Junction Proteins, E-cadherin and Nectin-4.
Title: Molecular Crosstalk Between Adherens Junction Proteins, E-cadherin and Nectin-4.
CDH1 methylation analysis in invasive lobular breast carcinomas with and without gene mutation.
Title: CDH1 methylation analysis in invasive lobular breast carcinomas with and without gene mutation.
RAC1-mediated integrin alpha-6 expression in E-cadherin-deficient gastric cancer cells promotes interactions with the stroma and peritoneal dissemination.
Title: RAC1-mediated integrin alpha-6 expression in E-cadherin-deficient gastric cancer cells promotes interactions with the stroma and peritoneal dissemination.
Biomarkers of epithelial-mesenchymal transition: E-cadherin and beta-catenin in malignant transformation of oral lesions.
Title: Biomarkers of epithelial-mesenchymal transition: E-cadherin and beta-catenin in malignant transformation of oral lesions.
A novel noncanonical function for IRF6 in the recycling of E-cadherin.
Title: A novel noncanonical function for IRF6 in the recycling of E-cadherin.
E-cadherin expression and gene expression profiles in corticotroph pituitary neuroendocrine tumor subtypes.
Title: E-cadherin expression and gene expression profiles in corticotroph pituitary neuroendocrine tumor subtypes.
Cell division-dependent dissemination following E-cadherin loss underlies initiation of diffuse-type gastric cancer.
Title: Cell division-dependent dissemination following E-cadherin loss underlies initiation of diffuse-type gastric cancer.
CDH1 Genotype Exploration in Women With Hereditary Lobular Breast Cancer Phenotype.
Title: CDH1 Genotype Exploration in Women With Hereditary Lobular Breast Cancer Phenotype.

Submit: New GeneRIF Correction See all GeneRIFs (1930)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Blepharocheilodontic syndrome 1 MedGen: C4551988 OMIM: 119580 GeneReviews: Not available	not available
Endometrial carcinoma MedGen: C0476089 OMIM: 608089 GeneReviews: Not available	not available
Familial cancer of breast MedGen: C0346153 OMIM: 114480 GeneReviews: BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer	not available
Hereditary diffuse gastric adenocarcinoma MedGen: C1708349 OMIM: 137215 GeneReviews: Diffuse Gastric and Lobular Breast Cancer Syndrome	not available
Malignant tumor of prostate MedGen: C0376358 GeneReviews: Not available	not available
Ovarian neoplasm MedGen: C0919267 GeneReviews: Not available	not available

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 EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

PMC84611P1 (e-PCR)
- UniSTS:273449

GDB:361044 (e-PCR)
- UniSTS:156724

GDB:361074 (e-PCR)
- UniSTS:156725

GDB:361084 (e-PCR)
- UniSTS:156726

GDB:361089 (e-PCR)
- UniSTS:156727

GDB:361093 (e-PCR)
- UniSTS:156728

GDB:361098 (e-PCR)
- UniSTS:156729

GDB:361103 (e-PCR)
- UniSTS:156730

GDB:361109 (e-PCR)
- UniSTS:156731

GDB:361113 (e-PCR)
- UniSTS:156732

SHGC-33499 (e-PCR)
- UniSTS:23613

GDB:361120 (e-PCR)
- UniSTS:156733

GDB:361125 (e-PCR)
- UniSTS:156734

GDB:361128 (e-PCR)
- UniSTS:156735

GDB:361131 (e-PCR)
- UniSTS:156736

Cdh1 (e-PCR), detects polymorphism
- UniSTS:472904

RH64967 (e-PCR)
- UniSTS:89433

CDH1_96.2 (e-PCR)
- UniSTS:277087

D1S1423 (e-PCR)
- UniSTS:149619

RH68244 (e-PCR)
- UniSTS:1912

RH64971 (e-PCR)
- UniSTS:91522

STS-T85105 (e-PCR)
- UniSTS:9091

RH91417 (e-PCR)
- UniSTS:88196

PMC134726P1 (e-PCR)
- UniSTS:270747

A008N17 (e-PCR)
- UniSTS:11680

PMC135805P1 (e-PCR)
- UniSTS:270774

PMC135805P2 (e-PCR)
- UniSTS:270775

PMC135805P3 (e-PCR)
- UniSTS:270776

PMC135805P4 (e-PCR)
- UniSTS:270777

PMC135805P5 (e-PCR)
- UniSTS:270778

RH65826 (e-PCR)
- UniSTS:19434

SHGC-149254 (e-PCR)
- UniSTS:176889

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 beta-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
enables cadherin binding	HDA more info	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 adhesion mediated by cadherin	IDA Inferred from Direct Assay more info	PubMed
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 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 heparin	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
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	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 desmosome	IEA Inferred from Electronic Annotation more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	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

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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)

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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

NG_008021.1 RefSeqGene

Range

5001..103250

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_301

mRNA and Protein(s)

NM_001317184.2 → NP_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:158 → 258

CA_like; Cadherin repeat-like domain

cd11304
Location:431 → 530

Cadherin_repeat; Cadherin tandem repeat domain

pfam00028
Location:537 → 625

Cadherin; Cadherin domain

pfam01049
Location:680 → 816

Cadherin_C; Cadherin cytoplasmic region

pfam08758
Location:27 → 116

Cadherin_pro; Cadherin prodomain like
NM_001317185.2 → NP_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:3 → 75

Cadherin_repeat; Cadherin tandem repeat domain

pfam00028
Location:82 → 170

Cadherin; Cadherin domain

pfam01049
Location:225 → 361

Cadherin_C; Cadherin cytoplasmic region
NM_001317186.2 → NP_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:83 → 224

Cadherin_C; Cadherin cytoplasmic region
NM_004360.5 → NP_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:158 → 258

CA_like; Cadherin repeat-like domain

cd11304
Location:492 → 591

Cadherin_repeat; Cadherin tandem repeat domain

pfam01049
Location:738 → 879

Cadherin_C; Cadherin cytoplasmic region

pfam08758
Location:27 → 116

Cadherin_pro; Cadherin prodomain like

cl09101
Location:598 → 686

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus