Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SMARCB1 (SW1/SNF related, matrix associated, actin dependent regulator of chromatin B1)

Written1999-03Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Other nameshSNF5
SNF5L1
INI1 (integrase interactor 1)
BAF47 (BRG1-associated factor)
HGNC (Hugo) SMARCB1
LocusID (NCBI) 6598
Atlas_Id 169
Location 22q11.23  [Link to chromosome band 22q11]
Location_base_pair Starts at 24129118 and ends at 24176705 bp from pter ( according to hg19-Feb_2009)  [Mapping SMARCB1.png]
Local_order distal to BCR
Fusion genes
(updated 2016)		CABIN1 (22q11.23) / SMARCB1 (22q11.23)SMARCB1 (22q11.23) / ANKRD28 (3p25.1)SMARCB1 (22q11.23) / MARK3 (14q32.32)
SMARCB1 (22q11.23) / ORM1 (9q32)SMARCB1 (22q11.23) / SMARCB1 (22q11.23)SMARCB1 (22q11.23) / TTC3 (21q22.13)
SMARCB1 (22q11.23) / WASF2 (1p36.11)

DNA/RNA

Description spans over 50 kb; 9 exons
Transcription alternative splicing including/excluding exon 2

Protein

Description 385 amino acids; 47 kDa ; a DNA binding domain and 2 repeat motifs
Localisation nucleus; associated with the chromatin and with the nuclear matrix
Function binds and activates human immunodeficiency virus integrase; member of the SWI/SNF complex, thought to facilitate the transcriptional activation of inducible genes through the remodelling of the chromatin; could be involved in the chromatin organization associated with the nuclear matrix attachment; could also have a role in the cell cycle control, through binding to P105-Rb
Homology with SNF5 (yeast transcription factor)

Mutations

Germinal found in the rhabdoid tumor predisposition syndrome
Somatic mutation and allele loss events in sporadic rhabdoid tumors are consistent with the two-hit model of Knutson; deletion of the entire gene on one allele (sometimes due to translocations involving 22q11), and mutation (frameshift mutations, widely dispersed through the entire gene and leading to stop codons) on the other allele

Implicated in

Note
Entity rhabdoid tumor
Disease tumor of uncertain origin, occuring in early childhood
Prognosis highly aggressive; 80% mortality rate
Cytogenetics normal karyotype or t(Var; 22)(-;q11.2)
Hybrid/Mutated Gene no hybrid gene but inactivation of both alleles
  
Entity rhabdoid tumor predisposition syndrome
Hybrid/Mutated Gene germline mutation on one allele, predisposing to a rabdoid tumor (and perhaps to tumors of the central nervous system) when the other allele is also inactivated
  

Bibliography

Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors.
Biegel JA, Zhou JY, Rorke LB, Stenstrom C, Wainwright LM, Fogelgren B
Cancer research. 1999 ; 59 (1) : 74-79.
PMID 9892189
 
Paravertebral malignant rhabdoid tumor in infancy. In vitro studies of a familial tumor.
Lynch HT, Shurin SB, Dahms BB, Izant RJ Jr, Lynch J, Danes BS
Cancer. 1983 ; 52 (2) : 290-296.
PMID 6861072
 
Structure-function analysis of integrase interactor 1/hSNF5L1 reveals differential properties of two repeat motifs present in the highly conserved region.
Morozov A, Yung E, Kalpana GV
Proceedings of the National Academy of Sciences of the United States of America. 1998 ; 95 (3) : 1120-1125.
PMID 9448295
 
Components of the human SWI/SNF complex are enriched in active chromatin and are associated with the nuclear matrix.
Reyes JC, Muchardt C, Yaniv M
The Journal of cell biology. 1997 ; 137 (2) : 263-274.
PMID 9128241
 
Cytogenetic and molecular analysis of a t(1;22)(p36;q11.2) in a rhabdoid tumor with a putative homozygous deletion of chromosome 22.
Rosty C, Peter M, Zucman J, Validire P, Delattre O, Aurias A
Genes, chromosomes & cancer. 1998 ; 21 (2) : 82-89.
PMID 9491318
 
Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer.
Versteege I, Sévenet N, Lange J, Rousseau-Merck MF, Ambros P, Handgretinger R, Aurias A, Delattre O
Nature. 1998 ; 394 (6689) : 203-206.
PMID 9671307
 
Rhabdoid tumor of kidney. A report of 111 cases from the National Wilms' Tumor Study Pathology Center.
Weeks DA, Beckwith JB, Mierau GW, Luckey DW
The American journal of surgical pathology. 1989 ; 13 (6) : 439-458.
PMID 2543225
 
Malignant rhabdoid tumors: a clinicopathologic review and conceptual discussion.
Wick MR, Ritter JH, Dehner LP
Seminars in diagnostic pathology. 1995 ; 12 (3) : 233-248.
PMID 8545590
 

Citation

This paper should be referenced as such :
Huret, JL
SMARCB1 (SW1/SNF related, matrix associated, actin dependent regulator of chromatin B1)
Atlas Genet Cytogenet Oncol Haematol. 1999;3(2):71-72.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SMARCB1ID169.html

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  Nervous system: Ependymomas
Rhabdoid tumor
Soft tissue tumors: an overview

Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 2 ]
  Rhabdoid predisposition syndrome Schwannomatosis

External links

Nomenclature
HGNC (Hugo)SMARCB1   11103
Cards
AtlasSMARCB1ID169
Entrez_Gene (NCBI)SMARCB1  6598  SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
AliasesBAF47; INI1; MRD15; PPP1R144; 
RDT; RTPS1; SNF5; SNF5L1; SWNTS1; Sfh1p; Snr1; hSNFS
GeneCards (Weizmann)SMARCB1
Ensembl hg19 (Hinxton)ENSG00000099956 [Gene_View]  chr22:24129118-24176705 [Contig_View]  SMARCB1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000099956 [Gene_View]  chr22:24129118-24176705 [Contig_View]  SMARCB1 [Vega]
ICGC DataPortalENSG00000099956
TCGA cBioPortalSMARCB1
AceView (NCBI)SMARCB1
Genatlas (Paris)SMARCB1
WikiGenes6598
SOURCE (Princeton)SMARCB1
Genomic and cartography
GoldenPath hg19 (UCSC)SMARCB1  -     chr22:24129118-24176705 +  22q11.23   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SMARCB1  -     22q11.23   [Description]    (hg38-Dec_2013)
EnsemblSMARCB1 - 22q11.23 [CytoView hg19]  SMARCB1 - 22q11.23 [CytoView hg38]
Mapping of homologs : NCBISMARCB1 [Mapview hg19]  SMARCB1 [Mapview hg38]
OMIM162091   601607   609322   614608   
Gene and transcription
Genbank (Entrez)AB017523 AJ011737 AJ011738 AK021419 AK024025
RefSeq transcript (Entrez)NM_001007468 NM_001317946 NM_003073
RefSeq genomic (Entrez)NC_000022 NC_018933 NG_009303 NT_011520 NT_187633 NW_004929430
Consensus coding sequences : CCDS (NCBI)SMARCB1
Cluster EST : UnigeneHs.534350 [ NCBI ]
CGAP (NCI)Hs.534350
Alternative Splicing GalleryENSG00000099956
Gene ExpressionSMARCB1 [ NCBI-GEO ]   SMARCB1 [ EBI - ARRAY_EXPRESS ]   SMARCB1 [ SEEK ]   SMARCB1 [ MEM ]
Gene Expression Viewer (FireBrowse)SMARCB1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6598
GTEX Portal (Tissue expression)SMARCB1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ12824 (Uniprot)
NextProtQ12824  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ12824
Splice isoforms : SwissVarQ12824 (Swissvar)
PhosPhoSitePlusQ12824
Domains : Interpro (EBI)SNF5    SWI_SNF_chromatin_remodel_cplx   
Domain families : Pfam (Sanger)SNF5 (PF04855)   
Domain families : Pfam (NCBI)pfam04855   
DMDM Disease mutations6598
Blocks (Seattle)SMARCB1
PDB (SRS)5AJ1   
PDB (PDBSum)5AJ1   
PDB (IMB)5AJ1   
PDB (RSDB)5AJ1   
Structural Biology KnowledgeBase5AJ1   
SCOP (Structural Classification of Proteins)5AJ1   
CATH (Classification of proteins structures)5AJ1   
SuperfamilyQ12824
Human Protein AtlasENSG00000099956
Peptide AtlasQ12824
HPRD03364
IPIIPI00029695   IPI00745019   IPI01010351   IPI00879096   IPI00303439   IPI00879156   
Protein Interaction databases
DIP (DOE-UCLA)Q12824
IntAct (EBI)Q12824
FunCoupENSG00000099956
BioGRIDSMARCB1
STRING (EMBL)SMARCB1
ZODIACSMARCB1
Ontologies - Pathways
QuickGOQ12824
Ontology : AmiGOnuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II distal enhancer sequence-specific DNA binding  RNA polymerase I CORE element sequence-specific DNA binding  XY body  blastocyst hatching  p53 binding  DNA binding  transcription coactivator activity  transcription coactivator activity  protein binding  nucleus  nucleoplasm  nucleoplasm  nucleolus  DNA repair  nucleosome disassembly  chromatin remodeling  chromatin remodeling  transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  cell cycle  nervous system development  negative regulation of cell proliferation  DNA integration  SWI/SNF complex  cell differentiation  Tat protein binding  nucleosomal DNA binding  single stranded viral RNA replication via double stranded DNA intermediate  ATP-dependent chromatin remodeling  protein complex  positive regulation by host of viral transcription  positive regulation of transcription from RNA polymerase II promoter  positive regulation of sequence-specific DNA binding transcription factor activity  npBAF complex  nBAF complex  positive regulation of histone H4 acetylation  negative regulation of histone H3-K9 dimethylation  negative regulation of histone H3-K9 trimethylation  positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter  positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter  positive regulation of glucose mediated signaling pathway  positive regulation of histone H3-K9 acetylation  regulation of histone H4-K16 acetylation  
Ontology : EGO-EBInuclear chromatin  RNA polymerase II core promoter proximal region sequence-specific DNA binding  RNA polymerase II distal enhancer sequence-specific DNA binding  RNA polymerase I CORE element sequence-specific DNA binding  XY body  blastocyst hatching  p53 binding  DNA binding  transcription coactivator activity  transcription coactivator activity  protein binding  nucleus  nucleoplasm  nucleoplasm  nucleolus  DNA repair  nucleosome disassembly  chromatin remodeling  chromatin remodeling  transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  cell cycle  nervous system development  negative regulation of cell proliferation  DNA integration  SWI/SNF complex  cell differentiation  Tat protein binding  nucleosomal DNA binding  single stranded viral RNA replication via double stranded DNA intermediate  ATP-dependent chromatin remodeling  protein complex  positive regulation by host of viral transcription  positive regulation of transcription from RNA polymerase II promoter  positive regulation of sequence-specific DNA binding transcription factor activity  npBAF complex  nBAF complex  positive regulation of histone H4 acetylation  negative regulation of histone H3-K9 dimethylation  negative regulation of histone H3-K9 trimethylation  positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter  positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter  positive regulation of glucose mediated signaling pathway  positive regulation of histone H3-K9 acetylation  regulation of histone H4-K16 acetylation  
Pathways : BIOCARTAChromatin Remodeling by hSWI/SNF ATP-dependent Complexes [Genes]   
REACTOMEQ12824 [protein]
REACTOME PathwaysR-HSA-3214858 RMTs methylate histone arginines [pathway]
NDEx NetworkSMARCB1
Atlas of Cancer Signalling NetworkSMARCB1
Wikipedia pathwaysSMARCB1
Orthology - Evolution
OrthoDB6598
GeneTree (enSembl)ENSG00000099956
Phylogenetic Trees/Animal Genes : TreeFamSMARCB1
Homologs : HomoloGeneSMARCB1
Homology/Alignments : Family Browser (UCSC)SMARCB1
Gene fusions - Rearrangements
Fusion : MitelmanCABIN1/SMARCB1 [22q11.23/22q11.23]  [t(22;22)(q11;q11)]  
Fusion : MitelmanSMARCB1/MARK3 [22q11.23/14q32.32]  [t(14;22)(q32;q11)]  
Fusion : MitelmanSMARCB1/WASF2 [22q11.23/1p36.11]  [t(1;22)(p36;q11)]  
Fusion: TCGACABIN1 22q11.23 SMARCB1 22q11.23 OV
Polymorphisms : SNP, variants
NCBI Variation ViewerSMARCB1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMARCB1
dbVarSMARCB1
ClinVarSMARCB1
1000_GenomesSMARCB1 
Exome Variant ServerSMARCB1
ExAC (Exome Aggregation Consortium)SMARCB1 (select the gene name)
Genetic variants : HAPMAP6598
Genomic Variants (DGV)SMARCB1 [DGVbeta]
Mutations
ICGC Data PortalSMARCB1 
TCGA Data PortalSMARCB1 
Broad Tumor PortalSMARCB1
OASIS PortalSMARCB1 [ Somatic mutations - Copy number]
Cancer Gene: CensusSMARCB1 
Somatic Mutations in Cancer : COSMICSMARCB1 
intOGen PortalSMARCB1
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)Mendelian genes
BioMutasearch SMARCB1
DgiDB (Drug Gene Interaction Database)SMARCB1
DoCM (Curated mutations)SMARCB1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMARCB1 (select a term)
intoGenSMARCB1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)22:24129118-24176705  ENSG00000099956
CONAN: Copy Number AnalysisSMARCB1 
Mutations and Diseases : HGMDSMARCB1
OMIM162091    601607    609322    614608   
MedgenSMARCB1
Genetic Testing Registry SMARCB1
NextProtQ12824 [Medical]
TSGene6598
GENETestsSMARCB1
Huge Navigator SMARCB1 [HugePedia]
snp3D : Map Gene to Disease6598
BioCentury BCIQSMARCB1
ClinGenSMARCB1 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6598
Chemical/Pharm GKB GenePA35953
Drug Sensitivity SMARCB1
Clinical trialSMARCB1
Miscellaneous
canSAR (ICR)SMARCB1 (select the gene name)
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=SMARCB1
Probes
Litterature
PubMed285 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMARCB1
EVEXSMARCB1
GoPubMedSMARCB1
iHOPSMARCB1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Sep 28 16:02:45 CEST 2016
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jlhuret@AtlasGeneticsOncology.org.