mutLBSgeneDB |
Gene summary for APC |
Gene summary |
Basic gene Info. | Gene symbol | APC |
Gene name | adenomatous polyposis coli | |
Synonyms | BTPS2|DP2|DP2.5|DP3|GS|PPP1R46 | |
Cytomap | UCSC genome browser: 5q21-q22 | |
Type of gene | protein-coding | |
RefGenes | NM_000038.5, NM_001127510.2,NM_001127511.2, | |
Description | adenomatosis polyposis coli tumor suppressoradenomatous polyposis coli proteindeleted in polyposis 2.5protein phosphatase 1, regulatory subunit 46 | |
Modification date | 20141222 | |
dbXrefs | MIM : 611731 | |
HGNC : HGNC | ||
Ensembl : ENSG00000134982 | ||
HPRD : 01439 | ||
Vega : OTTHUMG00000128806 | ||
Protein | UniProt: P25054 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_APC | |
BioGPS: 324 | ||
Pathway | NCI Pathway Interaction Database: APC | |
KEGG: APC | ||
REACTOME: APC | ||
Pathway Commons: APC | ||
Context | iHOP: APC | |
ligand binding site mutation search in PubMed: APC | ||
UCL Cancer Institute: APC | ||
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:0006461 | protein complex assembly | 16188939 | GO:0006974 | cellular response to DNA damage stimulus | 14728717 | GO:0007026 | negative regulation of microtubule depolymerization | 11166179 | GO:0007050 | cell cycle arrest | 8521819 | GO:0008285 | negative regulation of cell proliferation | 8521819 | GO:0045736 | negative regulation of cyclin-dependent protein serine/threonine kinase activity | 8521819 |
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Ligand binding site mutations for APC |
Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.) : non-synonymous mutation on LBS, Circle size denotes number of samples. |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | R463 | H464R | COAD | 2 | R640 | R640W | COAD | 2 | R463 | A465T | COAD | 2 | A597 | S596L | COAD | 2 | R499 | R499L | COAD | 1 | R554 | R554L | COAD | 1 | R499 | Y500F | COAD | 1 | K603 | D605N | KIRC | 1 | N550 | N550H | LUAD | 1 | W593 | W593L | OV | 1 | N507 | L508F | SKCM | 1 | S546 | S546G | STAD | 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 APC from My Cancer Genome. |
Adenomatous polyposis coli (APC) is a gene that encodes a tumor suppressor protein that is involved in the β-Catenin/Wnt signaling pathway. Missense mutations, nonsense mutations, silent mutations, and frameshift deletions are observed in cancers such as intestinal cancer, stomach cancer, and thymus cancer. Related Pathways: β-catenin/Wnt signaling. Modified: December 4, 2015 |
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Protein structure related information for APC |
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 |
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 | W593 | W593L | 0.18743253 | A597 | S596L | 0.10812767 | K603 | D605N | -1.2502356 | N507 | L508F | -1.2169578 | R463 | A465T | -1.0278937 | N550 | N550H | -0.99310902 | R640 | R640W | -0.97209751 | S546 | S546G | -0.96058467 | R499 | R499L | -0.88073409 | R554 | R554L | -0.83930795 | R499 | Y500F | -0.82131991 | R463 | H464R | -0.36347865 |
(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 APC from PDB |
PDB ID | PDB title | PDB structure | 1DEB | CRYSTAL STRUCTURE OF THE N-TERMINAL COILED COIL DOMAIN FROM APC |
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Differential gene expression and gene-gene network for APC |
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 APC |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0032580 | Adenomatous Polyposis Coli | 630 | AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification |
umls:C0001430 | Adenoma | 142 | AlteredExpression, Biomarker, GeneticVariation |
umls:C0009404 | Colorectal Neoplasms | 109 | AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification |
umls:C0699790 | Colon Carcinoma | 89 | Biomarker, GeneticVariation |
umls:C0001418 | Adenocarcinoma | 47 | Biomarker, GeneticVariation, PostTranslationalModification |
umls:C0079218 | Fibromatosis, Aggressive | 44 | Biomarker, GeneticVariation |
umls:C0009375 | Colonic Neoplasms | 42 | AlteredExpression, Biomarker, GeneticVariation |
umls:C0699791 | STOMACH CARCINOMA | 22 | Biomarker, GeneticVariation |
umls:C2239176 | Carcinoma, Hepatocellular | 18 | Biomarker, GeneticVariation |
umls:C0206677 | Adenomatous Polyps | 17 | Biomarker, GeneticVariation |
umls:C0025149 | Medulloblastoma | 16 | Biomarker, GeneticVariation |
umls:C0021846 | Intestinal Polyps | 16 | Biomarker, GeneticVariation |
umls:C0021841 | Intestinal Neoplasms | 15 | Biomarker |
umls:C0206624 | Hepatoblastoma | 13 | Biomarker, GeneticVariation |
umls:C0007131 | Carcinoma, Non-Small-Cell Lung | 10 | Biomarker |
umls:C0265325 | Turcot syndrome | 9 | Biomarker |
umls:C0017097 | Gardner Syndrome | 9 | Biomarker, GeneticVariation |
umls:C0034885 | Rectal Neoplasms | 7 | Biomarker, GeneticVariation |
umls:C0021390 | Inflammatory Bowel Diseases | 6 | Biomarker, GeneticVariation |
umls:C0206646 | Fibromatosis, Abdominal | 5 | Biomarker, GeneticVariation |
umls:C1851124 | Desmoid disease, hereditary | 4 | Biomarker, GeneticVariation |
umls:C0038356 | Stomach Neoplasms | 3 | Biomarker, GeneticVariation |
umls:C0033578 | Prostatic Neoplasms | 3 | Biomarker, PostTranslationalModification |
umls:C0024667 | Mammary Neoplasms, Animal | 3 | Biomarker, GeneticVariation |
umls:C0024121 | Lung Neoplasms | 3 | Biomarker, PostTranslationalModification |
umls:C0007621 | Cell Transformation, Neoplastic | 3 | Biomarker, GeneticVariation |
umls:C0017185 | Gastrointestinal Neoplasms | 3 | Biomarker |
umls:C0004352 | Autistic Disorder | 2 | Biomarker, GeneticVariation |
umls:C0017636 | Glioblastoma | 2 | Biomarker |
umls:C0027672 | Neoplastic Syndromes, Hereditary | 2 | Biomarker, GeneticVariation |
umls:C1879526 | Aberrant Crypt Foci | 1 | Biomarker |
umls:C0009405 | Colorectal Neoplasms, Hereditary Nonpolyposis | 1 | Biomarker |
umls:C0015393 | Eye Abnormalities | 1 | Biomarker |
umls:C0020473 | Hyperlipidemias | 1 | Biomarker |
umls:C3714756 | Intellectual Disability | 1 | Biomarker |
umls:C0025500 | Mesothelioma | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
180181 | H464R | Uncertain significance | Germline | MedGen:C0027672 SNOMED CT:699346009 |
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Pharmacological information for APC |
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. |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of APC go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (SER,TYR,GLU,GLY,TYR,GLU,GLY,TYR,TYR,SER,GLN) | 3qhe | C | R463 N507 N550 R554 W593 A597 K603 R640 | III | Peptide ligand (SER,TYR,GLU,GLY,TYR,GLU,GLY,TYR,TYR,SER) | 3qhe | A | R463 N507 N550 R554 W593 A597 R640 | III | Peptide ligand (GLY,GLY,GLY,GLU,GLN,LEU,ALA,ILE,ASN,GLU,LEU,ILE,SER) | 3nmx | C | R463 N507 S546 N550 W593 | III | Peptide ligand (GLY,GLY,GLY,GLU,GLN,LEU,ALA,ILE,ASN,GLU,LEU,ILE,SER) | 3nmx | A | R463 R499 N507 S546 N550 W593 | III | Peptide ligand (GLY,GLY,GLY,GLU,GLN,LEU,ALA,ILE,ASN,GLU,LEU,ILE,SER) | 3nmx | B | R463 R499 N507 S546 N550 W593 |
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Conservation information for LBS of APC |
Multiple alignments for P25054 in multiple species |
LBS | AA sequence | # species | Species |
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