mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for APC
Gene summary
Basic gene Info.Gene symbolAPC
Gene nameadenomatous polyposis coli
SynonymsBTPS2|DP2|DP2.5|DP3|GS|PPP1R46
CytomapUCSC genome browser: 5q21-q22
Type of geneprotein-coding
RefGenesNM_000038.5,
NM_001127510.2,NM_001127511.2,
Descriptionadenomatosis polyposis coli tumor suppressoradenomatous polyposis coli proteindeleted in polyposis 2.5protein phosphatase 1, regulatory subunit 46
Modification date20141222
dbXrefs MIM : 611731
HGNC : HGNC
Ensembl : ENSG00000134982
HPRD : 01439
Vega : OTTHUMG00000128806
ProteinUniProt: P25054
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_APC
BioGPS: 324
PathwayNCI Pathway Interaction Database: APC
KEGG: APC
REACTOME: APC
Pathway Commons: APC
ContextiHOP: APC
ligand binding site mutation search in PubMed: APC
UCL Cancer Institute: APC
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0006461protein complex assembly16188939
GO:0006974cellular response to DNA damage stimulus14728717
GO:0007026negative regulation of microtubule depolymerization11166179
GO:0007050cell cycle arrest8521819
GO:0008285negative regulation of cell proliferation8521819
GO:0045736negative regulation of cyclin-dependent protein serine/threonine kinase activity8521819


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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
LBSAAchange of nsSNVCancer type# samples
R463H464RCOAD2
R640R640WCOAD2
R463A465TCOAD2
A597S596LCOAD2
R499R499LCOAD1
R554R554LCOAD1
R499Y500FCOAD1
K603D605NKIRC1
N550N550HLUAD1
W593W593LOV1
N507L508FSKCM1
S546S546GSTAD1
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.
LBSAAchange of nsSNVRelative stability change
W593W593L0.18743253
A597S596L0.10812767
K603D605N-1.2502356
N507L508F-1.2169578
R463A465T-1.0278937
N550N550H-0.99310902
R640R640W-0.97209751
S546S546G-0.96058467
R499R499L-0.88073409
R554R554L-0.83930795
R499Y500F-0.82131991
R463H464R-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 IDPDB titlePDB structure
1DEBCRYSTAL 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)
* Left PPI network was created from samples with mutations in the LBS of APC and the right PPI network was created from samples without mutations in the LBS of APC. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for APC
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0032580Adenomatous Polyposis Coli630AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification
umls:C0001430Adenoma142AlteredExpression, Biomarker, GeneticVariation
umls:C0009404Colorectal Neoplasms109AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification
umls:C0699790Colon Carcinoma89Biomarker, GeneticVariation
umls:C0001418Adenocarcinoma47Biomarker, GeneticVariation, PostTranslationalModification
umls:C0079218Fibromatosis, Aggressive44Biomarker, GeneticVariation
umls:C0009375Colonic Neoplasms42AlteredExpression, Biomarker, GeneticVariation
umls:C0699791STOMACH CARCINOMA22Biomarker, GeneticVariation
umls:C2239176Carcinoma, Hepatocellular18Biomarker, GeneticVariation
umls:C0206677Adenomatous Polyps17Biomarker, GeneticVariation
umls:C0025149Medulloblastoma16Biomarker, GeneticVariation
umls:C0021846Intestinal Polyps16Biomarker, GeneticVariation
umls:C0021841Intestinal Neoplasms15Biomarker
umls:C0206624Hepatoblastoma13Biomarker, GeneticVariation
umls:C0007131Carcinoma, Non-Small-Cell Lung10Biomarker
umls:C0265325Turcot syndrome9Biomarker
umls:C0017097Gardner Syndrome9Biomarker, GeneticVariation
umls:C0034885Rectal Neoplasms7Biomarker, GeneticVariation
umls:C0021390Inflammatory Bowel Diseases6Biomarker, GeneticVariation
umls:C0206646Fibromatosis, Abdominal5Biomarker, GeneticVariation
umls:C1851124Desmoid disease, hereditary4Biomarker, GeneticVariation
umls:C0038356Stomach Neoplasms3Biomarker, GeneticVariation
umls:C0033578Prostatic Neoplasms3Biomarker, PostTranslationalModification
umls:C0024667Mammary Neoplasms, Animal3Biomarker, GeneticVariation
umls:C0024121Lung Neoplasms3Biomarker, PostTranslationalModification
umls:C0007621Cell Transformation, Neoplastic3Biomarker, GeneticVariation
umls:C0017185Gastrointestinal Neoplasms3Biomarker
umls:C0004352Autistic Disorder2Biomarker, GeneticVariation
umls:C0017636Glioblastoma2Biomarker
umls:C0027672Neoplastic Syndromes, Hereditary2Biomarker, GeneticVariation
umls:C1879526Aberrant Crypt Foci1Biomarker
umls:C0009405Colorectal Neoplasms, Hereditary Nonpolyposis1Biomarker
umls:C0015393Eye Abnormalities1Biomarker
umls:C0020473Hyperlipidemias1Biomarker
umls:C3714756Intellectual Disability1Biomarker
umls:C0025500Mesothelioma1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs
180181H464RUncertain significanceGermlineMedGen: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 statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of APC go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (SER,TYR,GLU,GLY,TYR,GLU,GLY,TYR,TYR,SER,GLN)3qheCR463 N507 N550 R554 W593 A597 K603 R640
IIIPeptide ligand (SER,TYR,GLU,GLY,TYR,GLU,GLY,TYR,TYR,SER)3qheAR463 N507 N550 R554 W593 A597 R640
IIIPeptide ligand (GLY,GLY,GLY,GLU,GLN,LEU,ALA,ILE,ASN,GLU,LEU,ILE,SER)3nmxCR463 N507 S546 N550 W593
IIIPeptide ligand (GLY,GLY,GLY,GLU,GLN,LEU,ALA,ILE,ASN,GLU,LEU,ILE,SER)3nmxAR463 R499 N507 S546 N550 W593
IIIPeptide ligand (GLY,GLY,GLY,GLU,GLN,LEU,ALA,ILE,ASN,GLU,LEU,ILE,SER)3nmxBR463 R499 N507 S546 N550 W593


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Conservation information for LBS of APC
Multiple alignments for P25054 in multiple species
LBSAA sequence# speciesSpecies


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