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 PMS2
Gene summary
Basic gene Info.Gene symbolPMS2
Gene namePMS2 postmeiotic segregation increased 2 (S. cerevisiae)
SynonymsHNPCC4|PMS2CL|PMSL2
CytomapUCSC genome browser: 7p22.2
Type of geneprotein-coding
RefGenesNM_000535.5,
NR_003085.2,
DescriptionDNA mismatch repair protein PMS2H_DJ0042M02.9PMS1 protein homolog 2mismatch repair endonuclease PMS2
Modification date20141222
dbXrefs MIM : 600259
HGNC : HGNC
Ensembl : ENSG00000122512
HPRD : 02598
Vega : OTTHUMG00000023135
ProteinUniProt: P54278
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PMS2
BioGPS: 5395
PathwayNCI Pathway Interaction Database: PMS2
KEGG: PMS2
REACTOME: PMS2
Pathway Commons: PMS2
ContextiHOP: PMS2
ligand binding site mutation search in PubMed: PMS2
UCL Cancer Institute: PMS2
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:0006298mismatch repair10871409


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Ligand binding site mutations for PMS2
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
A49G50RBLCA1
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.


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Protein structure related information for PMS2
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
A49G50R-0.83618327
(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 PMS2 from PDB

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Differential gene expression and gene-gene network for PMS2
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 PMS2 and the right PPI network was created from samples without mutations in the LBS of PMS2. 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 PMS2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0265325Turcot syndrome15Biomarker, GeneticVariation
umls:C0009405Colorectal Neoplasms, Hereditary Nonpolyposis6Biomarker, GeneticVariation
umls:C0027627Neoplasm Metastasis2Biomarker
umls:C0035412Rhabdomyosarcoma1Biomarker
umls:C0221263Cafe-au-Lait Spots1Biomarker
umls:C0206663Neuroectodermal Tumors, Primitive1Biomarker
umls:C0038874Supratentorial Neoplasms1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for PMS2

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
ExperimentalDB02930Phosphothiophosphoric Acid-Adenylate EsterSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PMS2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ADPADP1ea6AA49
ADPADP1ea6BA49
AGSADENOSINE 5'-[GAMMA-THIO]TRIPHOSPHATE1h7uAA49
AGSADENOSINE 5'-[GAMMA-THIO]TRIPHOSPHATE1h7uBA49


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Conservation information for LBS of PMS2
Multiple alignments for P54278 in multiple species
LBSAA sequence# speciesSpecies


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