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mutLBSgeneDB |
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| Gene summary for CDH1 |
 Gene summary |
| Basic gene Info. | Gene symbol | CDH1 |
| Gene name | cadherin 1, type 1, E-cadherin (epithelial) | |
| Synonyms | Arc-1|CD324|CDHE|ECAD|LCAM|UVO | |
| Cytomap | UCSC genome browser: 16q22.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_004360.3, | |
| Description | CAM 120/80E-Cadherincadherin 1, E-cadherin (epithelial)cadherin-1calcium-dependent adhesion protein, epithelialcell-CAM 120/80epithelial cadherinuvomorulin | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 192090 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000039068 | ||
| HPRD : 01885 | ||
| Vega : OTTHUMG00000137561 | ||
| Protein | UniProt: P12830 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_CDH1 | |
| BioGPS: 999 | ||
| Pathway | NCI Pathway Interaction Database: CDH1 | |
| KEGG: CDH1 | ||
| REACTOME: CDH1 | ||
| Pathway Commons: CDH1 | ||
| Context | iHOP: CDH1 | |
| ligand binding site mutation search in PubMed: CDH1 | ||
| UCL Cancer Institute: CDH1 | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0016337 | single organismal cell-cell adhesion | 16338932 | GO:0042993 | positive regulation of transcription factor import into nucleus | 16338932 | GO:0045893 | positive regulation of transcription, DNA-templated | 16338932 | GO:0071285 | cellular response to lithium ion | 12937339 | GO:0071681 | cellular response to indole-3-methanol | 10868478 | GO:0072659 | protein localization to plasma membrane | 17620337 |
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| Ligand binding site mutations for CDH1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | D254 | D254Y | STAD | 2 | N258 | P260H | BRCA | 1 | D288,D290 | A289V | COAD | 1 | D349 | A347D | COAD | 1 | D290 | D291N | COAD | 1 | N297 | A298V | COAD | 1 | D288 | D288G | COAD | 1 | N297 | T295I | COAD | 1 | D257 | D257N | COAD | 1 | Q255 | Q255L | COAD | 1 | E223 | R224H | HNSC | 1 | D221 | D221V | OV | 1 | D221,E223 | R222G | STAD | 1 | D288 | A286V | STAD | 1 | D257 | D257N | STAD | 1 | E336 | E336K | STAD | 1 | D290 | D290G | STAD | 1 | N297 | A299S | STAD | 1 | E223 | R224H | UCEC | 1 |
| cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
| Clinical information for CDH1 from My Cancer Genome. |
| Cadherin 1, type 1, E-cadherin (epithelial) (CDH1) is a gene that encodes a protein that functions as a calcium dependent cell-cell adhesion glycoprotein that mediates bacterial adhesion to mammalian cells. Missense mutations, nonsense mutations, silent mutations, whole gene deletions, frameshift deletions and insertions, and in-frame deletions and insertions are observed in cancers such as breast cancer, intestinal cancer, and stomach cancer. Modified: July 1, 2015 |
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| Protein structure related information for CDH1 |
| Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
 : nsSNV at non-LBS : nsSNV at LBS |
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| nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
| LBS | AAchange of nsSNV | Relative stability change | D290 | D290G | -1.6052582 | E223 | R224H | -1.4569748 | E336 | E336K | -1.4160759 | E223 | R222G | -1.2972737 | D221 | R222G | -1.2972737 | N297 | A299S | -1.1807462 | N258 | P260H | -1.125433 | D290 | D291N | -1.0354579 | D290 | A289V | -0.84714582 | D288 | A289V | -0.84714582 | D257 | D257N | -0.74281147 | Q255 | Q255L | -0.63474168 | D349 | A347D | -0.57943641 | D221 | D221V | -0.5189889 | N297 | T295I | -0.50982583 | D288 | D288G | -0.42631728 | D254 | D254Y | -0.39970676 | N297 | A298V | -0.20174976 | D288 | A286V | -0.052885222 |
| (MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
| Structure image for CDH1 from PDB |
| PDB ID | PDB title | PDB structure | 2O72 | Crystal Structure Analysis of human E-cadherin (1-213) |  |
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| Differential gene expression and gene-gene network for CDH1 |
| Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
| Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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| Phenotype information for CDH1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C1708349 | GASTRIC CANCER, HEREDITARY DIFFUSE | 96 | Biomarker, GeneticVariation |
| umls:C0007097 | Carcinoma | 80 | AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification |
| umls:C0027627 | Neoplasm Metastasis | 64 | AlteredExpression, Biomarker |
| umls:C0038356 | Stomach Neoplasms | 43 | AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification |
| umls:C0007137 | Carcinoma, Squamous Cell | 25 | AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification |
| umls:C0033578 | Prostatic Neoplasms | 22 | AlteredExpression, Biomarker, GeneticVariation |
| umls:C0009404 | Colorectal Neoplasms | 19 | AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification |
| umls:C1458155 | Breast Neoplasms | 16 | AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification, Therapeutic |
| umls:C0206692 | Carcinoma, Lobular | 15 | AlteredExpression, Biomarker, GeneticVariation |
| umls:C0009324 | Colitis, Ulcerative | 8 | Biomarker, GeneticVariation |
| umls:C1134719 | Carcinoma, Ductal, Breast | 7 | Biomarker |
| umls:C0005695 | Urinary Bladder Neoplasms | 6 | AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification |
| umls:C0030297 | Pancreatic Neoplasms | 6 | AlteredExpression, Biomarker, GeneticVariation |
| umls:C0919267 | Ovarian Neoplasms | 4 | AlteredExpression, Biomarker, GeneticVariation |
| umls:C0010606 | Carcinoma, Adenoid Cystic | 4 | AlteredExpression, Biomarker |
| umls:C0079487 | Helicobacter Infections | 3 | Biomarker, GeneticVariation |
| umls:C0032927 | Precancerous Conditions | 3 | Biomarker |
| umls:C0014170 | Endometrial Neoplasms | 2 | AlteredExpression, Biomarker |
| umls:C2931456 | Prostate cancer, familial | 2 | Biomarker |
| umls:C0027626 | Neoplasm Invasiveness | 2 | Biomarker, Therapeutic |
| umls:C0242656 | Disease Progression | 1 | Biomarker |
| umls:C0023904 | Liver Neoplasms, Experimental | 1 | Biomarker |
| umls:C0024667 | Mammary Neoplasms, Animal | 1 | Biomarker |
| umls:C0024668 | Mammary Neoplasms, Experimental | 1 | Biomarker |
| umls:C0025500 | Mesothelioma | 1 | Biomarker |
| umls:C0026936 | Mycoplasma Infections | 1 | Biomarker |
| umls:C0027746 | Nerve Degeneration | 1 | Biomarker |
| umls:C0282612 | Prostatic Intraepithelial Neoplasia | 1 | Biomarker |
| umls:C0036095 | Salivary Gland Neoplasms | 1 | Biomarker |
| umls:C0027672 | Neoplastic Syndromes, Hereditary | 1 | GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
| 50225 | R224H | Uncertain significance | Germline | MedGen:C0027672 SNOMED CT:699346009 MedGen:CN221809 |
| 213200 | A289V | Uncertain significance | Germline | GeneReviews:NBK1139 MedGen:C1708349 OMIM:137215 Orphanet:ORPHA26106 |
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| Pharmacological information for CDH1 |
| Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of CDH1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of CDH1 |
| Multiple alignments for P12830 in multiple species |
| LBS | AA sequence | # species | Species | D183 | IKSNKDKEGKV | 1 | Homo sapiens | D183 | IKSNKDKESKV | 1 | Gallus gallus | D183 | IKSNRDKETKV | 1 | Mus musculus | D183 | IKSNRDKETTV | 1 | Rattus norvegicus | D183 | IKSNKEKETQV | 1 | Bos taurus | D221 | VTEPLDRERIA | 1 | Homo sapiens | D221 | VTEQLDREKID | 1 | Gallus gallus | D221 | VTQPLDREAIA | 1 | Mus musculus | D221 | VTQPLDREAID | 1 | Rattus norvegicus | D221 | VTQPLDREQIA | 1 | Bos taurus | D254 | LITVTDQNDNK | 1 | Homo sapiens | D254 | IITVMDQNDNK | 1 | Gallus gallus | D254 | VITVTDQNDNR | 1 | Mus musculus | D254 | VVTVTDQNDNR | 1 | Rattus norvegicus | D254 | VITVTDQNDNK | 1 | Bos taurus | D257 | VTDQNDNRPEF | 2 | Mus musculus, Rattus norvegicus | D257 | VTDQNDNKPEF | 1 | Homo sapiens | D257 | VMDQNDNKPVF | 1 | Gallus gallus | D257 | VTDQNDNKPQF | 1 | Bos taurus | D288 | EVTATDADDDV | 1 | Homo sapiens | D288 | TVNATDADDAV | 1 | Gallus gallus | D288 | KVSATDADDDV | 1 | Mus musculus | D288 | QVSATDADDDI | 1 | Rattus norvegicus | D288 | QVTATDIDDEV | 1 | Bos taurus | D290 | TATDADDDVNT | 1 | Homo sapiens | D290 | NATDADDAVNT | 1 | Gallus gallus | D290 | SATDADDDVNT | 1 | Mus musculus | D290 | SATDADDDINT | 1 | Rattus norvegicus | D290 | TATDIDDEVNT | 1 | Bos taurus | D33 | CHPGFDAESYT | 1 | Homo sapiens | D33 | CQPGFAAETFS | 1 | Gallus gallus | D33 | CSPGFSSEVYT | 1 | Mus musculus | D33 | CRPGFSSEVYT | 1 | Rattus norvegicus | D33 | CIPGFGAESYT | 1 | Bos taurus | D334 | VTTGLDRESFP | 1 | Homo sapiens | D334 | LGTGLDRETTP | 1 | Gallus gallus | D334 | LTSGLDRESYP | 1 | Mus musculus | D334 | VTSGLDRESYP | 1 | Rattus norvegicus | D334 | LTTGLDRESFP | 1 | Bos taurus | D349 | VVQAADLQGEG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D349 | IVQATDQEGKG | 1 | Gallus gallus | D349 | MVQAADLNGEG | 1 | Bos taurus | E165 | PISCPENEKGP | 2 | Homo sapiens, Bos taurus | E165 | PISCLENHRGP | 1 | Gallus gallus | E165 | PISCPENEKGE | 1 | Mus musculus | E165 | PINCPENQKGE | 1 | Rattus norvegicus | E223 | EPLDRERIATY | 1 | Homo sapiens | E223 | EQLDREKIDRY | 1 | Gallus gallus | E223 | QPLDREAIAKY | 1 | Mus musculus | E223 | QPLDREAIDKY | 1 | Rattus norvegicus | E223 | QPLDREQIAKY | 1 | Bos taurus | E273 | KGSVMEGALPG | 1 | Homo sapiens | E273 | VGYIEENAKPG | 1 | Gallus gallus | E273 | EGSVAEGAVPG | 1 | Mus musculus | E273 | EGSVAEGALPG | 1 | Rattus norvegicus | E273 | KASALEGALPG | 1 | Bos taurus | E336 | TGLDRESFPTY | 2 | Homo sapiens, Bos taurus | E336 | SGLDRESYPTY | 2 | Mus musculus, Rattus norvegicus | E336 | TGLDRETTPNY | 1 | Gallus gallus | K179 | NLVQIKSNKDK | 1 | Homo sapiens | K179 | RLVQIKSNKDK | 1 | Gallus gallus | K179 | NLVQIKSNRDK | 1 | Mus musculus | K179 | RLVQIKSNRDK | 1 | Rattus norvegicus | K179 | SLVQIKSNKEK | 1 | Bos taurus | N166 | ISCPENEKGPF | 2 | Homo sapiens, Bos taurus | N166 | ISCLENHRGPY | 1 | Gallus gallus | N166 | ISCPENEKGEF | 1 | Mus musculus | N166 | INCPENQKGEF | 1 | Rattus norvegicus | N256 | TVTDQNDNRPE | 2 | Mus musculus, Rattus norvegicus | N256 | TVTDQNDNKPE | 1 | Homo sapiens | N256 | TVMDQNDNKPV | 1 | Gallus gallus | N256 | TVTDQNDNKPQ | 1 | Bos taurus | N258 | TDQNDNKPEFT | 1 | Homo sapiens | N258 | MDQNDNKPVFI | 1 | Gallus gallus | N258 | TDQNDNRPEFT | 1 | Mus musculus | N258 | TDQNDNRPEFI | 1 | Rattus norvegicus | N258 | TDQNDNKPQFT | 1 | Bos taurus | N297 | DVNTYNAAIAY | 2 | Homo sapiens, Mus musculus | N297 | AVNTDNGIVSY | 1 | Gallus gallus | N297 | DINTYNAAIAY | 1 | Rattus norvegicus | N297 | EVNTYTAAIGY | 1 | Bos taurus | Q255 | ITVTDQNDNKP | 2 | Homo sapiens, Bos taurus | Q255 | ITVMDQNDNKP | 1 | Gallus gallus | Q255 | ITVTDQNDNRP | 1 | Mus musculus | Q255 | VTVTDQNDNRP | 1 | Rattus norvegicus | R335 | TTGLDRESFPT | 2 | Homo sapiens, Bos taurus | R335 | TSGLDRESYPT | 2 | Mus musculus, Rattus norvegicus | R335 | GTGLDRETTPN | 1 | Gallus gallus |
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