Atlas of Genetics and Cytogenetics in Oncology and Haematology

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   
X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

SMARCA2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2)

Identity

Alias_namesSNF2L2
Alias_symbol (synonym)BAF190
hSNF2a
hBRM
Sth1p
SNF2LA
BRM
SNF2
SWI2
Other aliasNCBRS
HGNC (Hugo) SMARCA2
LocusID (NCBI) 6595
Atlas_Id 42331
Location 9p24.3  [Link to chromosome band 9p24]
Location_base_pair Starts at 2015219 and ends at 2193623 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
FGFR1OP2 (12p11.23) / SMARCA2 (9p24.3)GFM1 (3q25.32) / SMARCA2 (9p24.3)KCNMA1 (10q22.3) / SMARCA2 (9p24.3)
PVT1 (8q24.21) / SMARCA2 (9p24.3)RFX3 (9p24.2) / SMARCA2 (9p24.3)SMARCA2 (9p24.3) / AC074212.3 ()
SMARCA2 (9p24.3) / DMRT1 (9p24.3)SMARCA2 (9p24.3) / SMARCA2 (9p24.3)TMEM181 (6q25.3) / SMARCA2 (9p24.3)
RFX3 9p24.2 / SMARCA2 9p24.3SMARCA2 9p24.3 AC074212.3SMARCA2 9p24.3 / DMRT1 9p24.3

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 Leukemias implicated (Data extracted from papers in the Atlas)

Leukemias TL_t0109p35p24ID3215 TL_t0109p35p24ID3359 TL_t0909p24p24ID3214 TL_t0912p24p13ID3216

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]

Solid Tumors TT_t0909p24p24ID108457 TT_t0909p24p24ID108459

External links

Nomenclature
HGNC (Hugo)SMARCA2   11098
LRG (Locus Reference Genomic)LRG_882
Cards
Entrez_Gene (NCBI)SMARCA2  6595  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
AliasesBAF190; BRM; NCBRS; SNF2; 
SNF2L2; SNF2LA; SWI2; Sth1p; hBRM; hSNF2a
GeneCards (Weizmann)SMARCA2
Ensembl hg19 (Hinxton)ENSG00000080503 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000080503 [Gene_View]  ENSG00000080503 [Sequence]  chr9:2015219-2193623 [Contig_View]  SMARCA2 [Vega]
ICGC DataPortalENSG00000080503
TCGA cBioPortalSMARCA2
AceView (NCBI)SMARCA2
Genatlas (Paris)SMARCA2
WikiGenes6595
SOURCE (Princeton)SMARCA2
Genetics Home Reference (NIH)SMARCA2
Genomic and cartography
GoldenPath hg38 (UCSC)SMARCA2  -     chr9:2015219-2193623 +  9p24.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMARCA2  -     9p24.3   [Description]    (hg19-Feb_2009)
GoldenPathSMARCA2 - 9p24.3 [CytoView hg19]  SMARCA2 - 9p24.3 [CytoView hg38]
ImmunoBaseENSG00000080503
Mapping of homologs : NCBISMARCA2 [Mapview hg19]  SMARCA2 [Mapview hg38]
OMIM600014   601358   
Gene and transcription
Genbank (Entrez)AK094076 AK296373 AK298045 AK299683 AK300093
RefSeq transcript (Entrez)NM_001289396 NM_001289397 NM_001289398 NM_001289399 NM_001289400 NM_003070 NM_139045
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMARCA2
Cluster EST : UnigeneHs.644901 [ NCBI ]
CGAP (NCI)Hs.644901
Alternative Splicing GalleryENSG00000080503
Gene ExpressionSMARCA2 [ NCBI-GEO ]   SMARCA2 [ EBI - ARRAY_EXPRESS ]   SMARCA2 [ SEEK ]   SMARCA2 [ MEM ]
Gene Expression Viewer (FireBrowse)SMARCA2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6595
GTEX Portal (Tissue expression)SMARCA2
Human Protein AtlasENSG00000080503-SMARCA2 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP51531   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP51531  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP51531
Splice isoforms : SwissVarP51531
PhosPhoSitePlusP51531
Domaine pattern : Prosite (Expaxy)BROMODOMAIN_1 (PS00633)    BROMODOMAIN_2 (PS50014)    HELICASE_ATP_BIND_1 (PS51192)    HELICASE_CTER (PS51194)    HSA (PS51204)    QLQ (PS51666)   
Domains : Interpro (EBI)BRK_domain    BRK_sf    Bromodomain    Bromodomain-like_sf    Bromodomain_CS    Gln-Leu-Gln_QLQ    Helicase_ATP-bd    Helicase_C    HSA_dom    P-loop_NTPase    SMARCA2    SnAC    SNF2-like_sf    SNF2_N   
Domain families : Pfam (Sanger)BRK (PF07533)    Bromodomain (PF00439)    Helicase_C (PF00271)    HSA (PF07529)    QLQ (PF08880)    SnAC (PF14619)    SNF2_N (PF00176)   
Domain families : Pfam (NCBI)pfam07533    pfam00439    pfam00271    pfam07529    pfam08880    pfam14619    pfam00176   
Domain families : Smart (EMBL)BRK (SM00592)  BROMO (SM00297)  DEXDc (SM00487)  HELICc (SM00490)  HSA (SM00573)  QLQ (SM00951)  SnAC (SM01314)  
Conserved Domain (NCBI)SMARCA2
DMDM Disease mutations6595
Blocks (Seattle)SMARCA2
PDB (RSDB)2DAT    4QY4    5DKC    5DKH   
PDB Europe2DAT    4QY4    5DKC    5DKH   
PDB (PDBSum)2DAT    4QY4    5DKC    5DKH   
PDB (IMB)2DAT    4QY4    5DKC    5DKH   
Structural Biology KnowledgeBase2DAT    4QY4    5DKC    5DKH   
SCOP (Structural Classification of Proteins)2DAT    4QY4    5DKC    5DKH   
CATH (Classification of proteins structures)2DAT    4QY4    5DKC    5DKH   
SuperfamilyP51531
Human Protein Atlas [tissue]ENSG00000080503-SMARCA2 [tissue]
Peptide AtlasP51531
HPRD02483
IPIIPI00514648   IPI00386718   IPI00647560   IPI00647028   IPI00641350   IPI00641050   IPI00640353   IPI00642503   IPI00103451   IPI00643691   IPI00640994   IPI00644329   IPI00645885   
Protein Interaction databases
DIP (DOE-UCLA)P51531
IntAct (EBI)P51531
FunCoupENSG00000080503
BioGRIDSMARCA2
STRING (EMBL)SMARCA2
ZODIACSMARCA2
Ontologies - Pathways
QuickGOP51531
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  nuclear chromatin  DNA binding  chromatin binding  transcription coactivator activity  helicase activity  protein binding  ATP binding  nucleus  nucleus  nucleoplasm  nucleoplasm  chromatin remodeling  chromatin remodeling  regulation of transcription, DNA-templated  regulation of transcription by RNA polymerase II  spermatid development  nervous system development  DNA-dependent ATPase activity  DNA-dependent ATPase activity  negative regulation of cell proliferation  SWI/SNF complex  negative regulation of cell growth  histone binding  ATP-dependent chromatin remodeling  intracellular membrane-bounded organelle  transcription regulatory region DNA binding  intermediate filament cytoskeleton  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  npBAF complex  nBAF complex  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  nuclear chromatin  DNA binding  chromatin binding  transcription coactivator activity  helicase activity  protein binding  ATP binding  nucleus  nucleus  nucleoplasm  nucleoplasm  chromatin remodeling  chromatin remodeling  regulation of transcription, DNA-templated  regulation of transcription by RNA polymerase II  spermatid development  nervous system development  DNA-dependent ATPase activity  DNA-dependent ATPase activity  negative regulation of cell proliferation  SWI/SNF complex  negative regulation of cell growth  histone binding  ATP-dependent chromatin remodeling  intracellular membrane-bounded organelle  transcription regulatory region DNA binding  intermediate filament cytoskeleton  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  npBAF complex  nBAF complex  
NDEx NetworkSMARCA2
Atlas of Cancer Signalling NetworkSMARCA2
Wikipedia pathwaysSMARCA2
Orthology - Evolution
OrthoDB6595
GeneTree (enSembl)ENSG00000080503
Phylogenetic Trees/Animal Genes : TreeFamSMARCA2
HOGENOMP51531
Homologs : HomoloGeneSMARCA2
Homology/Alignments : Family Browser (UCSC)SMARCA2
Gene fusions - Rearrangements
Fusion : MitelmanRFX3/SMARCA2 [9p24.2/9p24.3]  [t(9;9)(p24;p24)]  
Fusion : MitelmanSMARCA2/DMRT1 [9p24.3/9p24.3]  [t(9;9)(p24;p24)]  
Fusion PortalRFX3 9p24.2 SMARCA2 9p24.3 BRCA
Fusion PortalSMARCA2 9p24.3 AC074212.3 SKCM
Fusion PortalSMARCA2 9p24.3 DMRT1 9p24.3 HNSC
Fusion : QuiverSMARCA2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMARCA2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMARCA2
dbVarSMARCA2
ClinVarSMARCA2
1000_GenomesSMARCA2 
Exome Variant ServerSMARCA2
ExAC (Exome Aggregation Consortium)ENSG00000080503
GNOMAD BrowserENSG00000080503
Varsome BrowserSMARCA2
Genetic variants : HAPMAP6595
Genomic Variants (DGV)SMARCA2 [DGVbeta]
DECIPHERSMARCA2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMARCA2 
Mutations
ICGC Data PortalSMARCA2 
TCGA Data PortalSMARCA2 
Broad Tumor PortalSMARCA2
OASIS PortalSMARCA2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMARCA2  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSMARCA2
Mutations and Diseases : HGMDSMARCA2
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)LOVD - Leiden Open Variation Database
BioMutasearch SMARCA2
DgiDB (Drug Gene Interaction Database)SMARCA2
DoCM (Curated mutations)SMARCA2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMARCA2 (select a term)
intoGenSMARCA2
Cancer3DSMARCA2(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600014    601358   
Orphanet3183   
DisGeNETSMARCA2
MedgenSMARCA2
Genetic Testing Registry SMARCA2
NextProtP51531 [Medical]
TSGene6595
GENETestsSMARCA2
Target ValidationSMARCA2
Huge Navigator SMARCA2 [HugePedia]
snp3D : Map Gene to Disease6595
BioCentury BCIQSMARCA2
ClinGenSMARCA2 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6595
Chemical/Pharm GKB GenePA35948
Clinical trialSMARCA2
Miscellaneous
canSAR (ICR)SMARCA2 (select the gene name)
DataMed IndexSMARCA2
Probes
Litterature
PubMed211 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMARCA2
EVEXSMARCA2
GoPubMedSMARCA2
iHOPSMARCA2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Aug 26 18:29:36 CEST 2019
Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.