Atlas of Genetics and Cytogenetics in Oncology and Haematology


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PMS2 (PMS1 homolog 2, mismatch repair system component)

Identity

Other namesHNPCC4
MLH4
PMS2CL
PMSL2
HGNC (Hugo) PMS2
LocusID (NCBI) 5395
Atlas_Id 328
Location 7p22.1
Location_base_pair Starts at 6012870 and ends at 6048737 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2015)
PMS2 7p22.1 / AIMP2 7p22.1

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Solid tumors implicated (Data extracted from papers in the Atlas)
  Breast tumors : an overview
Colon: Colorectal adenocarcinoma

Other Cancer prone implicated (Data extracted from papers in the Atlas)
  Familial nervous system tumour syndromes Hereditary non polyposis colorectal carcinoma (HNPCC Syndrome) Turcot syndrome

External links

Nomenclature
HGNC (Hugo)PMS2   9122
Cards
Entrez_Gene (NCBI)PMS2  5395  PMS1 homolog 2, mismatch repair system component
GeneCards (Weizmann)PMS2
Ensembl hg19 (Hinxton)ENSG00000122512 [Gene_View]  chr7:6012870-6048737 [Contig_View]  PMS2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000122512 [Gene_View]  chr7:6012870-6048737 [Contig_View]  PMS2 [Vega]
ICGC DataPortalENSG00000122512
TCGA cBioPortalPMS2
AceView (NCBI)PMS2
Genatlas (Paris)PMS2
WikiGenes5395
SOURCE (Princeton)PMS2
Genomic and cartography
GoldenPath hg19 (UCSC)PMS2  -     chr7:6012870-6048737 -  7p22.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PMS2  -     7p22.1   [Description]    (hg38-Dec_2013)
EnsemblPMS2 - 7p22.1 [CytoView hg19]  PMS2 - 7p22.1 [CytoView hg38]
Mapping of homologs : NCBIPMS2 [Mapview hg19]  PMS2 [Mapview hg38]
OMIM276300   600259   614337   
Gene and transcription
Genbank (Entrez)AB103082 AB103083 AB103085 AB103086 AB103087
RefSeq transcript (Entrez)NM_000535
RefSeq genomic (Entrez)NC_000007 NC_018918 NG_008466 NT_007819 NW_004929329
Consensus coding sequences : CCDS (NCBI)PMS2
Cluster EST : UnigeneHs.715590 [ NCBI ]
CGAP (NCI)Hs.715590
Alternative Splicing : Fast-db (Paris)GSHG0027991
Alternative Splicing GalleryENSG00000122512
Gene ExpressionPMS2 [ NCBI-GEO ]     PMS2 [ SEEK ]   PMS2 [ MEM ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)5395
Protein : pattern, domain, 3D structure
UniProt/SwissProtP54278 (Uniprot)
NextProtP54278  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP54278
Splice isoforms : SwissVarP54278 (Swissvar)
Catalytic activity : Enzyme3.1.-.- [ Enzyme-Expasy ]   3.1.-.- [ Enzyme-SRS ]   3.1.-.- [ IntEnz-EBI ]   3.1.-.- [ PRIAM ]   3.1.-.- [ BRENDA ]   3.1.-.- [ KEGG ]   3.1.-.- [ IUBMB ]
PhosPhoSitePlusP54278
Domaine pattern : Prosite (Expaxy)DNA_MISMATCH_REPAIR_1 (PS00058)   
Domains : Interpro (EBI)DNA_mismatch_repair_C    DNA_mismatch_repair_CS    DNA_mismatch_repair_fam    HATPase_C    MutL_C    Pms1/Pms2/PMS2L    Ribosomal_S5_D2-typ_fold    Ribosomal_S5_D2-typ_fold_subgr   
Domain families : Pfam (Sanger)DNA_mis_repair (PF01119)    MutL_C (PF08676)   
Domain families : Pfam (NCBI)pfam01119    pfam08676   
Domain families : Smart (EMBL)HATPase_c (SM00387)  MutL_C (SM00853)  
DMDM Disease mutations5395
Blocks (Seattle)PMS2
PDB (SRS)1EA6    1H7S    1H7U   
PDB (PDBSum)1EA6    1H7S    1H7U   
PDB (IMB)1EA6    1H7S    1H7U   
PDB (RSDB)1EA6    1H7S    1H7U   
Structural Biology KnowledgeBase1EA6    1H7S    1H7U   
SCOP (Structural Classification of Proteins)1EA6    1H7S    1H7U   
CATH (Classification of proteins structures)1EA6    1H7S    1H7U   
Human Protein AtlasENSG00000122512
Peptide AtlasP54278
HPRD02598
IPIIPI00746337   IPI00873034   IPI00418329   IPI00874088   IPI01012773   IPI00604708   IPI00743812   
Protein Interaction databases
DIP (DOE-UCLA)P54278
IntAct (EBI)P54278
FunCoupENSG00000122512
BioGRIDPMS2
IntegromeDBPMS2
STRING (EMBL)PMS2
ZODIACPMS2
Ontologies - Pathways
QuickGOP54278
Ontology : AmiGODNA binding  single-stranded DNA binding  endonuclease activity  protein binding  ATP binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytoplasm  DNA repair  mismatch repair  mismatch repair  microtubule cytoskeleton  somatic hypermutation of immunoglobulin genes  somatic recombination of immunoglobulin gene segments  ATPase activity  single base insertion or deletion binding  MutLalpha complex  MutSalpha complex binding  nucleic acid phosphodiester bond hydrolysis  nucleic acid phosphodiester bond hydrolysis  
Ontology : EGO-EBIDNA binding  single-stranded DNA binding  endonuclease activity  protein binding  ATP binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytoplasm  DNA repair  mismatch repair  mismatch repair  microtubule cytoskeleton  somatic hypermutation of immunoglobulin genes  somatic recombination of immunoglobulin gene segments  ATPase activity  single base insertion or deletion binding  MutLalpha complex  MutSalpha complex binding  nucleic acid phosphodiester bond hydrolysis  nucleic acid phosphodiester bond hydrolysis  
Pathways : KEGGMismatch repair    Fanconi anemia pathway   
Protein Interaction DatabasePMS2
Atlas of Cancer Signalling NetworkPMS2
Wikipedia pathwaysPMS2
Orthology - Evolution
OrthoDB5395
GeneTree (enSembl)ENSG00000122512
Phylogenetic Trees/Animal Genes : TreeFamPMS2
Homologs : HomoloGenePMS2
Homology/Alignments : Family Browser (UCSC)PMS2
Gene fusions - Rearrangements
Fusion: TCGAPMS2 7p22.1 AIMP2 7p22.1 LUAD
Polymorphisms : SNP, variants
NCBI Variation ViewerPMS2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PMS2
dbVarPMS2
ClinVarPMS2
1000_GenomesPMS2 
Exome Variant ServerPMS2
Exome Aggregation Consortium (ExAC)ENSG00000122512
SNP (GeneSNP Utah)PMS2
SNP : HGBasePMS2
Genetic variants : HAPMAPPMS2
Genomic Variants (DGV)PMS2 [DGVbeta]
Mutations
ICGC Data PortalPMS2 
TCGA Data PortalPMS2 
Tumor PortalPMS2
TCGA Copy Number PortalPMS2
Cancer Gene: CensusPMS2 
Somatic Mutations in Cancer : COSMICPMS2 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Colon cancer gene variant databases
LOVD (Leiden Open Variation Database)LOVD - human mismatch repair genes
LOVD (Leiden Open Variation Database)Zhejiang University Center for Genetic and Genomic Medicine (ZJU-CGGM)
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch PMS2
DgiDB (Drug Gene Interaction Database)PMS2
DoCM (Curated mutations)PMS2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PMS2 (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)7:6012870-6048737
CONAN: Copy Number AnalysisPMS2 
Mutations and Diseases : HGMDPMS2
OMIM276300    600259    614337   
MedgenPMS2
NextProtP54278 [Medical]
TSGene5395
GENETestsPMS2
Huge Navigator PMS2 [HugePedia]  PMS2 [HugeCancerGEM]
snp3D : Map Gene to Disease5395
BioCentury BCIQPMS2
General knowledge
Chemical/Protein Interactions : CTD5395
Chemical/Pharm GKB GenePA33448
Clinical trialPMS2
Other databases
Probes
Litterature
PubMed155 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePMS2
GoPubMedPMS2
iHOPPMS2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Jan 16 19:16:30 CET 2016

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