mutLBSgeneDB |
Gene summary for PMS2 |
Gene summary |
Basic gene Info. | Gene symbol | PMS2 |
Gene name | PMS2 postmeiotic segregation increased 2 (S. cerevisiae) | |
Synonyms | HNPCC4|PMS2CL|PMSL2 | |
Cytomap | UCSC genome browser: 7p22.2 | |
Type of gene | protein-coding | |
RefGenes | NM_000535.5, NR_003085.2, | |
Description | DNA mismatch repair protein PMS2H_DJ0042M02.9PMS1 protein homolog 2mismatch repair endonuclease PMS2 | |
Modification date | 20141222 | |
dbXrefs | MIM : 600259 | |
HGNC : HGNC | ||
Ensembl : ENSG00000122512 | ||
HPRD : 02598 | ||
Vega : OTTHUMG00000023135 | ||
Protein | UniProt: P54278 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PMS2 | |
BioGPS: 5395 | ||
Pathway | NCI Pathway Interaction Database: PMS2 | |
KEGG: PMS2 | ||
REACTOME: PMS2 | ||
Pathway Commons: PMS2 | ||
Context | iHOP: PMS2 | |
ligand binding site mutation search in PubMed: PMS2 | ||
UCL Cancer Institute: PMS2 | ||
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:0006298 | mismatch repair | 10871409 |
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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 |
LBS | AAchange of nsSNV | Cancer type | # samples | A49 | G50R | BLCA | 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. |
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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. |
LBS | AAchange of nsSNV | Relative stability change | A49 | G50R | -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) |
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Phenotype information for PMS2 |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0265325 | Turcot syndrome | 15 | Biomarker, GeneticVariation |
umls:C0009405 | Colorectal Neoplasms, Hereditary Nonpolyposis | 6 | Biomarker, GeneticVariation |
umls:C0027627 | Neoplasm Metastasis | 2 | Biomarker |
umls:C0035412 | Rhabdomyosarcoma | 1 | Biomarker |
umls:C0221263 | Cafe-au-Lait Spots | 1 | Biomarker |
umls:C0206663 | Neuroectodermal Tumors, Primitive | 1 | Biomarker |
umls:C0038874 | Supratentorial Neoplasms | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for PMS2 |
Gene-centered drug-gene interaction network |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Experimental | DB02930 | Phosphothiophosphoric Acid-Adenylate Ester | Small molecule |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of PMS2 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ADP | ADP | 1ea6 | A | A49 | ADP | ADP | 1ea6 | B | A49 | AGS | ADENOSINE 5'-[GAMMA-THIO]TRIPHOSPHATE | 1h7u | A | A49 | AGS | ADENOSINE 5'-[GAMMA-THIO]TRIPHOSPHATE | 1h7u | B | A49 |
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Conservation information for LBS of PMS2 |
Multiple alignments for P54278 in multiple species |
LBS | AA sequence | # species | Species |
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