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

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

Written	1999-03	Jean-Loup Huret
		Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_names	SNF5L1
Alias_symbol (synonym)	BAF47
	Ini1
	Snr1
	hSNFS
	Sfh1p
	RDT
	PPP1R144
Other alias	hSNF5
	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 23786931 and ends at 23834518 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) [ 4 ]

Nervous system: Ependymomas
Soft Tissues: Extraskeletal myxoid chondrosarcoma
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
LRG (Locus Reference Genomic)	LRG_520
	Cards
Atlas	SMARCB1ID169
Entrez_Gene (NCBI)	SMARCB1 6598 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
Aliases	BAF47; CSS3; INI1; MRD15;
	PPP1R144; RDT; RTPS1; SNF5; SNF5L1; SWNTS1; Sfh1p; Snr1; hSNFS
GeneCards (Weizmann)	SMARCB1
Ensembl hg19 (Hinxton)	ENSG00000099956 [Gene_View]
Ensembl hg38 (Hinxton)	ENSG00000099956 [Gene_View] chr22:23786931-23834518 [Contig_View] SMARCB1 [Vega]
ICGC DataPortal	ENSG00000099956
TCGA cBioPortal	SMARCB1
AceView (NCBI)	SMARCB1
Genatlas (Paris)	SMARCB1
WikiGenes	6598
SOURCE (Princeton)	SMARCB1
Genetics Home Reference (NIH)	SMARCB1
	Genomic and cartography
GoldenPath hg38 (UCSC)	SMARCB1 - chr22:23786931-23834518 + 22q11.23\|22q11 [Description] (hg38-Dec_2013)
GoldenPath hg19 (UCSC)	SMARCB1 - 22q11.23\|22q11 [Description] (hg19-Feb_2009)
Ensembl	SMARCB1 - 22q11.23\|22q11 [CytoView hg19] SMARCB1 - 22q11.23\|22q11 [CytoView hg38]
Mapping of homologs : NCBI	SMARCB1 [Mapview hg19] SMARCB1 [Mapview hg38]
OMIM	162091 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_187633
Consensus coding sequences : CCDS (NCBI)	SMARCB1
Cluster EST : Unigene	Hs.534350 [ NCBI ]
CGAP (NCI)	Hs.534350
Alternative Splicing Gallery	ENSG00000099956
Gene Expression	SMARCB1 [ 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]
Genevisible	Expression in : [tissues] [cell-lines] [cancer] [perturbations]
BioGPS (Tissue expression)	6598
GTEX Portal (Tissue expression)	SMARCB1
	Protein : pattern, domain, 3D structure
UniProt/SwissProt	Q12824 [function] [subcellular_location] [family_and_domains] [pathology_and_biotech] [ptm_processing] [expression] [interaction]
NextProt	Q12824 [Sequence] [Exons] [Medical] [Publications]
With graphics : InterPro	Q12824
Splice isoforms : SwissVar	Q12824
PhosPhoSitePlus	Q12824
Domains : Interpro (EBI)	SNF5 SWI_SNF_chromatin_remodel_cplx
Domain families : Pfam (Sanger)	SNF5 (PF04855)
Domain families : Pfam (NCBI)	pfam04855
Conserved Domain (NCBI)	SMARCB1
DMDM Disease mutations	6598
Blocks (Seattle)	SMARCB1
PDB (SRS)	5AJ1
PDB (PDBSum)	5AJ1
PDB (IMB)	5AJ1
PDB (RSDB)	5AJ1
Structural Biology KnowledgeBase	5AJ1
SCOP (Structural Classification of Proteins)	5AJ1
CATH (Classification of proteins structures)	5AJ1
Superfamily	Q12824
Human Protein Atlas	ENSG00000099956
Peptide Atlas	Q12824
HPRD	03364
IPI	IPI00029695 IPI00745019 IPI01010351 IPI00879096 IPI00303439 IPI00879156
	Protein Interaction databases
DIP (DOE-UCLA)	Q12824
IntAct (EBI)	Q12824
FunCoup	ENSG00000099956
BioGRID	SMARCB1
STRING (EMBL)	SMARCB1
ZODIAC	SMARCB1
	Ontologies - Pathways
QuickGO	Q12824
Ontology : AmiGO	nuclear 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 fibrillar center 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 covalent chromatin modification cell differentiation Tat protein binding nucleosomal DNA binding single stranded viral RNA replication via double stranded DNA intermediate ATP-dependent chromatin remodeling intracellular membrane-bounded organelle 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-EBI	nuclear 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 fibrillar center 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 covalent chromatin modification cell differentiation Tat protein binding nucleosomal DNA binding single stranded viral RNA replication via double stranded DNA intermediate ATP-dependent chromatin remodeling intracellular membrane-bounded organelle 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 : BIOCARTA	Chromatin Remodeling by hSWI/SNF ATP-dependent Complexes [Genes]
REACTOME	Q12824 [protein]
REACTOME Pathways	R-HSA-3214858 [pathway]
NDEx Network	SMARCB1
Atlas of Cancer Signalling Network	SMARCB1
Wikipedia pathways	SMARCB1
	Orthology - Evolution
OrthoDB	6598
GeneTree (enSembl)	ENSG00000099956
Phylogenetic Trees/Animal Genes : TreeFam	SMARCB1
HOVERGEN	Q12824
HOGENOM	Q12824
Homologs : HomoloGene	SMARCB1
Homology/Alignments : Family Browser (UCSC)	SMARCB1
	Gene fusions - Rearrangements
Fusion : Mitelman	CABIN1/SMARCB1 [22q11.23/22q11.23] [t(22;22)(q11;q11)]
Fusion : Mitelman	SMARCB1/MARK3 [22q11.23/14q32.32] [t(14;22)(q32;q11)]
Fusion : Mitelman	SMARCB1/WASF2 [22q11.23/1p36.11] [t(1;22)(p36;q11)]
Fusion: TCGA	CABIN1 22q11.23 SMARCB1 22q11.23 OV
	Polymorphisms : SNP and Copy number variants
NCBI Variation Viewer	SMARCB1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)	SMARCB1
dbVar	SMARCB1
ClinVar	SMARCB1
1000_Genomes	SMARCB1
Exome Variant Server	SMARCB1
ExAC (Exome Aggregation Consortium)	SMARCB1 (select the gene name)
Genetic variants : HAPMAP	6598
Genomic Variants (DGV)	SMARCB1 [DGVbeta]
DECIPHER	SMARCB1 [patients] [syndromes] [variants] [genes]
CONAN: Copy Number Analysis	SMARCB1
	Mutations
ICGC Data Portal	SMARCB1
TCGA Data Portal	SMARCB1
Broad Tumor Portal	SMARCB1
OASIS Portal	SMARCB1 [ Somatic mutations - Copy number]
Cancer Gene: Census	SMARCB1
Somatic Mutations in Cancer : COSMIC	SMARCB1 [overview] [genome browser] [tissue] [distribution]
Mutations and Diseases : HGMD	SMARCB1
intOGen Portal	SMARCB1
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
BioMuta	search 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)
intoGen	SMARCB1
NCG5 (London)	SMARCB1
Cancer3D	SMARCB1(select the gene name)
Impact of mutations	[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
	Diseases
OMIM	162091 601607 609322 614608
Orphanet	321 20073 19153 12482 14539
Medgen	SMARCB1
Genetic Testing Registry	SMARCB1
NextProt	Q12824 [Medical]
TSGene	6598
GENETests	SMARCB1
Target Validation	SMARCB1
Huge Navigator	SMARCB1 [HugePedia]
snp3D : Map Gene to Disease	6598
BioCentury BCIQ	SMARCB1
ClinGen	SMARCB1 (curated)
	Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD	6598
Chemical/Pharm GKB Gene	PA35953
Drug Sensitivity	SMARCB1
Clinical trial	SMARCB1
	Miscellaneous
canSAR (ICR)	SMARCB1 (select the gene name)
Other database	http://cancergenome.broadinstitute.org/index.php?tgene=SMARCB1
	Probes
	Litterature
PubMed	299 Pubmed reference(s) in Entrez
GeneRIFs	Gene References Into Functions (Entrez)
CoreMine	SMARCB1
EVEX	SMARCB1
GoPubMed	SMARCB1
iHOP	SMARCB1

REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

Search in all EBI NCBI

indexed on : Fri Jun 30 11:18:35 CEST 2017

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.