Human Gene CDH1 (uc010cfg.1) Description and Page Index
  Description: Homo sapiens cadherin 1, type 1, E-cadherin (epithelial) (CDH1), mRNA.
RefSeq Summary (NM_004360): 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].
Transcript (Including UTRs)
   Position: hg19 chr16:68,771,195-68,869,444 Size: 98,250 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr16:68,771,319-68,867,402 Size: 96,084 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:68,771,195-68,869,444)mRNA (may differ from genome)Protein (821 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Cadherin 1, type 1, E-cadherin (Epithelial), isoform CRA_c; SubName: Full=E-Cad/CTF2; SubName: Full=E-cadherin; SubName: Full=Uncharacterized protein;
FUNCTION: Cadherins are calcium dependent cell adhesion proteins (By similarity).
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (By similarity).

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CDH1
CDC HuGE Published Literature: CDH1
Positive Disease Associations: bladder cancer , colorectal cancer , Colorectal Neoplasms , Crohn Disease| , diffuse gastric cancer , gastric carcinoma risk , prostate cancer , stomach cancer , transitional cell carcinoma of the bladder. , ulcerative colitis , urinary calculus , urothelial cancer
Related Studies:
  1. bladder cancer
    Zhang, X. et al. 2003, Association between a C/A single nucleotide polymorphism of the E-cadherin gene promoter and transitional cell carcinoma of the bladder., The Journal of urology. 2003 Oct;170(4 Pt 1):1379-82. [PubMed 14501773]
    The -160 C/A single nucleotide polymorphism of the E-cadherin gene promoter is associated with TCCB. This single nucleotide polymorphism may serve as a prognostic marker of TCCB.
  2. colorectal cancer
    Shin, Y. et al. 2004, A functional polymorphism (-347 G-->GA) in the E-cadherin gene is associated with colorectal cancer., Carcinogenesis. 2004 Nov;25(11):2173-6. [PubMed 15231691]
    Taken together, our results suggest that the E-cadherin -347 G-->GA polymorphism may be associated with colorectal cancer.
  3. colorectal cancer
    Wheeler JM et al. 2001, Hypermethylation of the promoter region of the E-cadherin gene (CDH1) in sporadic and ulcerative colitis associated colorectal cancer., Gut. 2001 Mar;48(3):367-71. [PubMed 11171827]
    We have demonstrated hypermethylation of the promoter region in CDH1 in 46% of colorectal cancers studied. There was no difference between the UCACRC and SCRC groups. Just as there are specific differences in the genetic changes between UCACRC and SCRC, there is also likely to be a large degree of overlap among the genetic pathways of these cancers.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CDH1
Diseases sorted by gene-association score: gastric cancer risk after h. pylori infection* (1650), breast cancer* (476), endometrial cancer* (252), ovarian cancer, somatic* (190), prostate cancer* (177), diffuse gastric cancer (41), prostate cancer susceptibility* (41), gastric adenocarcinoma (32), inflammatory breast carcinoma (31), lobular neoplasia (26), goblet cell carcinoid (23), gallbladder cancer (23), bladder urothelial carcinoma (21), biphasic synovial sarcoma (21), epstein-barr virus-associated gastric carcinoma (18), breast ductal carcinoma (18), pseudo-meigs syndrome (18), gastric diffuse adenocarcinoma (16), tongue cancer (16), adenoid squamous cell carcinoma (15), ovarian stromal hyperthecosis (15), renal fibrosis (14), sarcomatoid transitional cell carcinoma (14), colorectal cancer (14), thyroid cancer (14), bladder signet ring cell adenocarcinoma (14), cleft lip/palate* (13), stomach cancer (13), microinvasive gastric cancer (12), esophagus squamous cell carcinoma (12), bile duct carcinoma (12), oral squamous cell carcinoma (12), transitional cell carcinoma (12), adenocarcinoma (12), bladder cancer, somatic (11), urinary bladder cancer (11), signet ring cell adenocarcinoma (11), tongue squamous cell carcinoma (11), familial adenomatous polyposis (10), pemphigus vulgaris (10), nasopharyngeal carcinoma (10), colon adenocarcinoma (10), linitis plastica (9), h. pylori infection (9), hailey-hailey disease (9), gastric cardia carcinoma (9), gastric cancer, somatic (9), lung giant cell carcinoma (9), pancreatic ductal adenocarcinoma (9), sarcoma, synovial (8), papillary adenocarcinoma (8), salivary gland adenoid cystic carcinoma (8), cholangiocarcinoma, susceptibility to (8), breast cystic hypersecretory carcinoma (8), parasagittal meningioma (8), darier disease (8), choroid plexus papilloma (8), intrahepatic cholangiocarcinoma (8), oral cancer (8), tubular adenocarcinoma (8), interstitial cystitis (7), cervical squamous cell carcinoma (7), spindle cell carcinoma (7), crohn's colitis (7), oral submucous fibrosis (7), cholecystitis (7), ductal carcinoma in situ (7), cerebral convexity meningioma (7), squamous cell carcinoma of the oral tongue (7), gastric signet ring cell adenocarcinoma (7), colorectal adenocarcinoma (7), diversion colitis (7), hereditary spastic paraplegia 3a (7), hypotrichosis, congenital, with juvenile macular dystrophy (7), squamous cell carcinoma (7), mesothelioma, somatic (6), lung cancer susceptibility 3 (6), pre-malignant neoplasm (6), lymphoepithelioma-like carcinoma (6), extrahepatic bile duct adenocarcinoma (6), squamous cell carcinoma, head and neck (6), infiltrative basal cell carcinoma (6), vulvar intraepithelial neoplasia (6), adenomatous polyposis coli (6), pancreatic cancer (6), listeriosis (6), ovary epithelial cancer (6), malignant ovarian surface epithelial-stromal neoplasm (6), adhesions of uterus (6), familial colorectal cancer (6), cell type cancer (6), chordoma (5), morpheaform basal cell carcinoma (5), gastrointestinal system cancer (5), ureteral disease (5), pharynx cancer (5), hypopharynx cancer (5), reproductive organ cancer (5), lung cancer (5), in situ carcinoma (5), parotid gland cancer (5), breast squamous cell carcinoma (4), malignant epithelial mesothelioma (4), lipid-rich carcinoma (4), chondroid chordoma (4), pancreas adenocarcinoma (4), microcystic meningioma (4), functional diarrhea (4), breast metaplastic carcinoma (4), hepatocellular carcinoma (4), intestinal benign neoplasm (4), esophageal cancer (3), melanoma (3), renal cell carcinoma (2), hepatitis c virus (2), adamantinoma of long bones (2), female reproductive organ cancer (2), male reproductive organ cancer (2), urinary tract obstruction (1), tooth agenesis (1), bile duct adenocarcinoma (1), eye disease (1), gastrointestinal system benign neoplasm (1), endocrine gland cancer (1), pulmonary fibrosis, idiopathic (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 60.97 RPKM in Esophagus - Mucosa
Total median expression: 590.48 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -46.80124-0.377 Picture PostScript Text
3' UTR -622.772042-0.305 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002126 - Cadherin
IPR015919 - Cadherin-like
IPR020894 - Cadherin_CS
IPR000233 - Cadherin_cytoplasmic-dom
IPR014868 - Cadherin_pro_dom

Pfam Domains:
PF00028 - Cadherin domain
PF01049 - Cadherin cytoplasmic region
PF08758 - Cadherin prodomain like

SCOP Domains:
49313 - Cadherin-like

ModBase Predicted Comparative 3D Structure on Q9UII8
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Descriptions from all associated GenBank mRNAs
  AK312551 - Homo sapiens cDNA, FLJ92924, Homo sapiens cadherin 1, type 1, E-cadherin (epithelial) (CDH1),mRNA.
AK297913 - Homo sapiens cDNA FLJ60313 complete cds, highly similar to Epithelial-cadherin precursor.
EU709494 - Homo sapiens truncated E-cadherin (CDH1) mRNA, complete cds.
GQ891411 - Homo sapiens clone HEL-S-131 epididymis secretory sperm binding protein mRNA, complete cds.
LF384443 - JP 2014500723-A/191946: Polycomb-Associated Non-Coding RNAs.
L08599 - Human uvomorulin (E-cadherin) (UVO) mRNA, complete cds.
BC141838 - Homo sapiens cadherin 1, type 1, E-cadherin (epithelial), mRNA (cDNA clone MGC:165111 IMAGE:40148986), complete cds.
BC146662 - Homo sapiens cadherin 1, type 1, E-cadherin (epithelial), mRNA (cDNA clone MGC:164884 IMAGE:40148047), complete cds.
BC144283 - Homo sapiens cDNA clone IMAGE:9052803, containing frame-shift errors.
AK290012 - Homo sapiens cDNA FLJ78203 complete cds, highly similar to Homo sapiens cadherin 1, type 1, E-cadherin (epithelial) (CDH1), mRNA.
Z13009 - H.sapiens mRNA for E-cadherin.
BC015576 - Homo sapiens mRNA similar to cadherin 1, type 1, E-cadherin (epithelial) (cDNA clone IMAGE:3959042).
AB025105 - Homo sapiens mRNA for E-cadherin, complete cds.
AB025106 - Homo sapiens mRNA for E-cadherin, complete cds.
Z18923 - H.sapiens mRNA for E-cadherin.
AK309703 - Homo sapiens cDNA, FLJ99744.
AK311198 - Homo sapiens cDNA, FLJ18240.
MA620020 - JP 2018138019-A/191946: Polycomb-Associated Non-Coding RNAs.
JD287654 - Sequence 268678 from Patent EP1572962.
JD104639 - Sequence 85663 from Patent EP1572962.
LF374261 - JP 2014500723-A/181764: Polycomb-Associated Non-Coding RNAs.
LF374263 - JP 2014500723-A/181766: Polycomb-Associated Non-Coding RNAs.
X12790 - Human mRNA for uvomorulin (put. CAM 120/80).
LF374264 - JP 2014500723-A/181767: Polycomb-Associated Non-Coding RNAs.
LF374265 - JP 2014500723-A/181768: Polycomb-Associated Non-Coding RNAs.
LF374267 - JP 2014500723-A/181770: Polycomb-Associated Non-Coding RNAs.
X52279 - H.sapiens mRNA for ARC-1/uvomorulin.
LF374269 - JP 2014500723-A/181772: Polycomb-Associated Non-Coding RNAs.
LF374270 - JP 2014500723-A/181773: Polycomb-Associated Non-Coding RNAs.
LF374273 - JP 2014500723-A/181776: Polycomb-Associated Non-Coding RNAs.
LF374275 - JP 2014500723-A/181778: Polycomb-Associated Non-Coding RNAs.
LF374278 - JP 2014500723-A/181781: Polycomb-Associated Non-Coding RNAs.
LF374282 - JP 2014500723-A/181785: Polycomb-Associated Non-Coding RNAs.
LF374284 - JP 2014500723-A/181787: Polycomb-Associated Non-Coding RNAs.
LF374286 - JP 2014500723-A/181789: Polycomb-Associated Non-Coding RNAs.
LF374287 - JP 2014500723-A/181790: Polycomb-Associated Non-Coding RNAs.
JD058481 - Sequence 39505 from Patent EP1572962.
JD466853 - Sequence 447877 from Patent EP1572962.
JD330340 - Sequence 311364 from Patent EP1572962.
JD241004 - Sequence 222028 from Patent EP1572962.
LF374289 - JP 2014500723-A/181792: Polycomb-Associated Non-Coding RNAs.
LF208297 - JP 2014500723-A/15800: Polycomb-Associated Non-Coding RNAs.
JD554654 - Sequence 535678 from Patent EP1572962.
JD112473 - Sequence 93497 from Patent EP1572962.
JD320565 - Sequence 301589 from Patent EP1572962.
JD320853 - Sequence 301877 from Patent EP1572962.
LF374290 - JP 2014500723-A/181793: Polycomb-Associated Non-Coding RNAs.
JD566358 - Sequence 547382 from Patent EP1572962.
JD358287 - Sequence 339311 from Patent EP1572962.
JD289756 - Sequence 270780 from Patent EP1572962.
JD351089 - Sequence 332113 from Patent EP1572962.
JD513039 - Sequence 494063 from Patent EP1572962.
JD317670 - Sequence 298694 from Patent EP1572962.
JD371347 - Sequence 352371 from Patent EP1572962.
JD337731 - Sequence 318755 from Patent EP1572962.
JD367707 - Sequence 348731 from Patent EP1572962.
JD535557 - Sequence 516581 from Patent EP1572962.
JD252516 - Sequence 233540 from Patent EP1572962.
JD197676 - Sequence 178700 from Patent EP1572962.
JD197447 - Sequence 178471 from Patent EP1572962.
JD071874 - Sequence 52898 from Patent EP1572962.
JD350553 - Sequence 331577 from Patent EP1572962.
JD486130 - Sequence 467154 from Patent EP1572962.
JD488125 - Sequence 469149 from Patent EP1572962.
JD560764 - Sequence 541788 from Patent EP1572962.
JD476887 - Sequence 457911 from Patent EP1572962.
JD397387 - Sequence 378411 from Patent EP1572962.
JD415497 - Sequence 396521 from Patent EP1572962.
JD415498 - Sequence 396522 from Patent EP1572962.
JD180408 - Sequence 161432 from Patent EP1572962.
JD346071 - Sequence 327095 from Patent EP1572962.
JD504824 - Sequence 485848 from Patent EP1572962.
JD438601 - Sequence 419625 from Patent EP1572962.
JD532122 - Sequence 513146 from Patent EP1572962.
JD464193 - Sequence 445217 from Patent EP1572962.
JD149859 - Sequence 130883 from Patent EP1572962.
JD251500 - Sequence 232524 from Patent EP1572962.
JD386123 - Sequence 367147 from Patent EP1572962.
JD351637 - Sequence 332661 from Patent EP1572962.
JD522975 - Sequence 503999 from Patent EP1572962.
JD457290 - Sequence 438314 from Patent EP1572962.
JD457291 - Sequence 438315 from Patent EP1572962.
JD388668 - Sequence 369692 from Patent EP1572962.
JD277462 - Sequence 258486 from Patent EP1572962.
JD248836 - Sequence 229860 from Patent EP1572962.
JD337764 - Sequence 318788 from Patent EP1572962.
JD160203 - Sequence 141227 from Patent EP1572962.
JD490864 - Sequence 471888 from Patent EP1572962.
JD245803 - Sequence 226827 from Patent EP1572962.
JD544149 - Sequence 525173 from Patent EP1572962.
JD310956 - Sequence 291980 from Patent EP1572962.
JD255536 - Sequence 236560 from Patent EP1572962.
JD124312 - Sequence 105336 from Patent EP1572962.
JD312232 - Sequence 293256 from Patent EP1572962.
JD283009 - Sequence 264033 from Patent EP1572962.
JD424306 - Sequence 405330 from Patent EP1572962.
JD046813 - Sequence 27837 from Patent EP1572962.
LF374291 - JP 2014500723-A/181794: Polycomb-Associated Non-Coding RNAs.
BC013851 - Homo sapiens cadherin 1, type 1, E-cadherin (epithelial), mRNA (cDNA clone IMAGE:3864475).
JD146835 - Sequence 127859 from Patent EP1572962.
LF374292 - JP 2014500723-A/181795: Polycomb-Associated Non-Coding RNAs.
JD146953 - Sequence 127977 from Patent EP1572962.
JD551766 - Sequence 532790 from Patent EP1572962.
JD305888 - Sequence 286912 from Patent EP1572962.
LF374294 - JP 2014500723-A/181797: Polycomb-Associated Non-Coding RNAs.
JD121137 - Sequence 102161 from Patent EP1572962.
JD433326 - Sequence 414350 from Patent EP1572962.
JD363575 - Sequence 344599 from Patent EP1572962.
LF374295 - JP 2014500723-A/181798: Polycomb-Associated Non-Coding RNAs.
JD073189 - Sequence 54213 from Patent EP1572962.
LF374296 - JP 2014500723-A/181799: Polycomb-Associated Non-Coding RNAs.
JD556984 - Sequence 538008 from Patent EP1572962.
MA609838 - JP 2018138019-A/181764: Polycomb-Associated Non-Coding RNAs.
MA609840 - JP 2018138019-A/181766: Polycomb-Associated Non-Coding RNAs.
MA609841 - JP 2018138019-A/181767: Polycomb-Associated Non-Coding RNAs.
MA609842 - JP 2018138019-A/181768: Polycomb-Associated Non-Coding RNAs.
MA609844 - JP 2018138019-A/181770: Polycomb-Associated Non-Coding RNAs.
MA609846 - JP 2018138019-A/181772: Polycomb-Associated Non-Coding RNAs.
MA609847 - JP 2018138019-A/181773: Polycomb-Associated Non-Coding RNAs.
MA609850 - JP 2018138019-A/181776: Polycomb-Associated Non-Coding RNAs.
MA609852 - JP 2018138019-A/181778: Polycomb-Associated Non-Coding RNAs.
MA609855 - JP 2018138019-A/181781: Polycomb-Associated Non-Coding RNAs.
MA609859 - JP 2018138019-A/181785: Polycomb-Associated Non-Coding RNAs.
MA609861 - JP 2018138019-A/181787: Polycomb-Associated Non-Coding RNAs.
MA609863 - JP 2018138019-A/181789: Polycomb-Associated Non-Coding RNAs.
MA609864 - JP 2018138019-A/181790: Polycomb-Associated Non-Coding RNAs.
MA609866 - JP 2018138019-A/181792: Polycomb-Associated Non-Coding RNAs.
MA443874 - JP 2018138019-A/15800: Polycomb-Associated Non-Coding RNAs.
MA609867 - JP 2018138019-A/181793: Polycomb-Associated Non-Coding RNAs.
MA609868 - JP 2018138019-A/181794: Polycomb-Associated Non-Coding RNAs.
MA609869 - JP 2018138019-A/181795: Polycomb-Associated Non-Coding RNAs.
MA609871 - JP 2018138019-A/181797: Polycomb-Associated Non-Coding RNAs.
MA609872 - JP 2018138019-A/181798: Polycomb-Associated Non-Coding RNAs.
MA609873 - JP 2018138019-A/181799: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)
hsa04520 - Adherens junction
hsa05100 - Bacterial invasion of epithelial cells
hsa05130 - Pathogenic Escherichia coli infection
hsa05200 - Pathways in cancer
hsa05213 - Endometrial cancer
hsa05216 - Thyroid cancer
hsa05218 - Melanoma
hsa05219 - Bladder cancer

-  Other Names for This Gene
  Alternate Gene Symbols: AB025105, hCG_28201, NM_004360, NP_004351, Q9UII8, Q9UII8_HUMAN
UCSC ID: uc010cfg.1
RefSeq Accession: NM_004360
Protein: Q9UII8

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CDH1:
hgc (Hereditary Diffuse Gastric Cancer)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: AB025105.1
exon count: 15CDS single in 3' UTR: no RNA size: 2567
ORF size: 2466CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 4907.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.