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 (NCBI)	hSNF5
	SNF5L1
	INI1 (integrase interactor 1)
	BAF47 (BRG1-associated factor)
HGNC (Hugo)	SMARCB1
HGNC Alias symb	BAF47
	Ini1
	Snr1
	hSNFS
	Sfh1p
	RDT
	PPP1R144
	SNF5
HGNC Alias name	"sucrose nonfermenting, yeast, homolog-like 1
	integrase interactor 1
	malignant rhabdoid tumor suppressor
	protein phosphatase 1, regulatory subunit 144"
HGNC Previous name	SNF5L1
LocusID (NCBI)	6598
Atlas_Id	169
Location	22q11.23 [Link to chromosome band 22q11]
Location_base_pair	Starts at 23786966 and ends at 23838009 bp from pter ( according to GRCh38/hg38-Dec_2013) [Mapping SMARCB1.png]
Local_order	distal to BCR

Fusion genes
(updated 2017)

Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

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 ]

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 7 ]

Bone: Chordoma
Nervous system: Ependymomas
Soft Tissues: Extraskeletal myxoid chondrosarcoma
Rhabdoid tumor del(22)(q11)
Soft tissue tumors: an overview
t(14;22)(q32;q11) SMARCB1/MARK3
CABIN1/SMARCB1 (22q11)

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 "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] ENSG00000099956 [Sequence] chr22:23786966-23838009 [Contig_View] SMARCB1 [Vega]
ICGC DataPortal	ENSG00000099956
TCGA cBioPortal	SMARCB1
AceView (NCBI)	SMARCB1
Genatlas (Paris)	SMARCB1
SOURCE (Princeton)	SMARCB1
Genetics Home Reference (NIH)	SMARCB1
	Genomic and cartography
GoldenPath hg38 (UCSC)	SMARCB1 - chr22:23786966-23838009 + 22q11.23\|22q11 [Description] (hg38-Dec_2013)
GoldenPath hg19 (UCSC)	SMARCB1 - 22q11.23\|22q11 [Description] (hg19-Feb_2009)
GoldenPath	SMARCB1 - 22q11.23\|22q11 [CytoView hg19] SMARCB1 - 22q11.23\|22q11 [CytoView hg38]
ImmunoBase	ENSG00000099956
genome Data Viewer NCBI	SMARCB1 [Mapview hg19]
OMIM	162091 601607 609322 614608
	Gene and transcription
Genbank (Entrez)	AB017523 AJ011737 AJ011738 AK021419 AK024025
RefSeq transcript (Entrez)	NM_001007468 NM_001317946 NM_001362877 NM_003073
RefSeq genomic (Entrez)	NC_000022 NG_009303 NT_187633
Consensus coding sequences : CCDS (NCBI)	SMARCB1
Alternative Splicing Gallery	ENSG00000099956
Gene Expression	SMARCB1 [ NCBI-GEO ] SMARCB1 [ EBI - ARRAY_EXPRESS ] SMARCB1 [ SEEK ] SMARCB1 [ MEM ]
Gene Expression Viewer (FireBrowse)	SMARCB1 [ Firebrowse - Broad ]
Genevisible	Expression of SMARCB1 in : [tissues] [cell-lines] [cancer] [perturbations]
BioGPS (Tissue expression)	6598
GTEX Portal (Tissue expression)	SMARCB1
Human Protein Atlas	ENSG00000099956-SMARCB1 [pathology] [cell] [tissue]
	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)	Sfh1/SNF5 SNF5
Domain families : Pfam (Sanger)	SNF5 (PF04855)
Domain families : Pfam (NCBI)	pfam04855
Conserved Domain (NCBI)	SMARCB1
Blocks (Seattle)	SMARCB1
PDB (RSDB)	5AJ1 5GJK 5L7A 5L7B 6AX5 6UCH
PDB Europe	5AJ1 5GJK 5L7A 5L7B 6AX5 6UCH
PDB (PDBSum)	5AJ1 5GJK 5L7A 5L7B 6AX5 6UCH
PDB (IMB)	5AJ1 5GJK 5L7A 5L7B 6AX5 6UCH
Structural Biology KnowledgeBase	5AJ1 5GJK 5L7A 5L7B 6AX5 6UCH
SCOP (Structural Classification of Proteins)	5AJ1 5GJK 5L7A 5L7B 6AX5 6UCH
CATH (Classification of proteins structures)	5AJ1 5GJK 5L7A 5L7B 6AX5 6UCH
Superfamily	Q12824
Human Protein Atlas [tissue]	ENSG00000099956-SMARCB1 [tissue]
Peptide Atlas	Q12824
HPRD	03364
IPI	IPI00029695 IPI00745019 IPI01010351 IPI00879096 IPI00303439 IPI00879156
	Protein Interaction databases
DIP (DOE-UCLA)	Q12824
IntAct (EBI)	Q12824
Complex Portal (EBI)	Q12824 "CPX-1196 Polybromo-associated SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B variant
	Q12824 CPX-1201 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA2 variant
	Q12824 CPX-1194 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA2 variant
	Q12824 CPX-1223 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA2 variant
	Q12824 CPX-1226 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA4 variant
	Q12824 CPX-1202 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA2 variant
	Q12824 CPX-1203 Brain-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA2 variant
	Q12824 CPX-1204 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA4 variant
	Q12824 CPX-1205 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA2 variant
	Q12824 CPX-1207 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA2 variant
	Q12824 CPX-1210 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA2 variant
	Q12824 CPX-1211 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA4 variant
	Q12824 CPX-1213 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA2 variant
	Q12824 CPX-1164 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA2 variant
	Q12824 CPX-1199 Polybromo-associated SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A variant
	Q12824 CPX-1206 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA4 variant
	Q12824 CPX-1219 Brain-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA4 variant
	Q12824 CPX-1225 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA2 variant
	Q12824 CPX-1195 Embryonic stem cell-specific SWI/SNF ATP-dependent chromatin remodeling complex
	Q12824 CPX-1209 SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1A-SMARCA4 variant
	Q12824 CPX-1212 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA4 variant
	Q12824 CPX-1227 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA2 variant
	Q12824 CPX-1228 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6B-ARID1B-SMARCA4 variant
	Q12824 CPX-1215 Neural progenitor-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA4 variant
	Q12824 CPX-1216 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1A-SMARCA4 variant
	Q12824 CPX-1217 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA2 variant
	Q12824 CPX-1218 Neuron-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA4 variant
	Q12824 CPX-1220 Brain-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA2 variant
	Q12824 CPX-1221 Brain-specific SWI/SNF ATP-dependent chromatin remodeling complex, ARID1B-SMARCA4 variant
	Q12824 CPX-1222 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1A-SMARCA4 variant
	Q12824 CPX-1224 Muscle cell-specific SWI/SNF ATP-dependent chromatin remodeling complex, ACTL6A-ARID1B-SMARCA4 variant"
BioGRID	SMARCB1
STRING (EMBL)	SMARCB1
ZODIAC	SMARCB1
	Ontologies - Pathways
QuickGO	Q12824
Ontology : AmiGO	nuclear chromatin RNA polymerase II proximal promoter sequence-specific DNA binding RNA polymerase I CORE element sequence-specific DNA binding RNA polymerase I preinitiation complex assembly fibrillar center p53 binding DNA binding transcription coactivator activity transcription coactivator activity protein binding nucleus nucleus nucleoplasm nucleoplasm nucleolus DNA repair nucleosome disassembly nucleosome disassembly chromatin remodeling chromatin remodeling regulation of transcription by RNA polymerase II regulation of transcription by RNA polymerase II cell cycle nervous system development DNA integration SWI/SNF complex SWI/SNF complex Tat protein binding nucleosomal DNA binding protein-containing complex brahma complex single stranded viral RNA replication via double stranded DNA intermediate ATP-dependent chromatin remodeling intracellular membrane-bounded organelle positive regulation by host of viral transcription positive regulation of transcription by RNA polymerase II positive regulation of DNA-binding transcription factor activity npBAF complex npBAF complex nBAF 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 nucleolar large rRNA by RNA polymerase I positive regulation of transcription of nucleolar large rRNA by RNA polymerase I 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 proximal promoter sequence-specific DNA binding RNA polymerase I CORE element sequence-specific DNA binding RNA polymerase I preinitiation complex assembly fibrillar center p53 binding DNA binding transcription coactivator activity transcription coactivator activity protein binding nucleus nucleus nucleoplasm nucleoplasm nucleolus DNA repair nucleosome disassembly nucleosome disassembly chromatin remodeling chromatin remodeling regulation of transcription by RNA polymerase II regulation of transcription by RNA polymerase II cell cycle nervous system development DNA integration SWI/SNF complex SWI/SNF complex Tat protein binding nucleosomal DNA binding protein-containing complex brahma complex single stranded viral RNA replication via double stranded DNA intermediate ATP-dependent chromatin remodeling intracellular membrane-bounded organelle positive regulation by host of viral transcription positive regulation of transcription by RNA polymerase II positive regulation of DNA-binding transcription factor activity npBAF complex npBAF complex nBAF 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 nucleolar large rRNA by RNA polymerase I positive regulation of transcription of nucleolar large rRNA by RNA polymerase I positive regulation of glucose mediated signaling pathway positive regulation of histone H3-K9 acetylation regulation of histone H4-K16 acetylation
REACTOME	Q12824 [protein]
REACTOME Pathways	R-HSA-8939243 [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
HOGENOM	Q12824
Homologs : HomoloGene	SMARCB1
Homology/Alignments : Family Browser (UCSC)	SMARCB1
	Gene fusions - Rearrangements
Fusion : Mitelman	CABIN1/SMARCB1 [22q11.23/22q11.23]
Fusion : Mitelman	SMARCB1/MARK3 [22q11.23/14q32.32]
Fusion : Mitelman	SMARCB1/WASF2 [22q11.23/1p36.11]
Fusion Portal	CABIN1 22q11.23 SMARCB1 22q11.23 OV
Fusion : Fusion_Hub	CABIN1--SMARCB1 CAPN2--SMARCB1 CNBP--SMARCB1 EDC3--SMARCB1 EDF1--SMARCB1 MALAT1--SMARCB1 MAML2--SMARCB1 MARK3--SMARCB1 RBBP7--SMARCB1 RBM39--SMARCB1 RORA--SMARCB1 SLC2A11--SMARCB1 SMARCB1--ANKRD28 SMARCB1--FTL SMARCB1--GNL1
	SMARCB1--HRASLS2 SMARCB1--LPCAT4 SMARCB1--ORM1 SMARCB1--SERTAD3 SMARCB1--SHE SMARCB1--SMARCB1 SMARCB1--SNW1 SMARCB1--SYN3 SMARCB1--TTC3 SMARCB1--TTC38 SPECC1L--SMARCB1 TBCB--SMARCB1 ZFP41--SMARCB1
Fusion : Quiver	SMARCB1
	Polymorphisms : SNP and Copy number variants
NCBI Variation Viewer	SMARCB1 [hg38]
dbVar	SMARCB1
ClinVar	SMARCB1
Monarch	SMARCB1
1000_Genomes	SMARCB1
Exome Variant Server	SMARCB1
GNOMAD Browser	ENSG00000099956
Varsome Browser	SMARCB1
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]
Somatic Mutations in Cancer : COSMIC3D	SMARCB1
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
OncoKB	SMARCB1
NCG6 (London)	select SMARCB1
Cancer3D	SMARCB1(select the gene name)
Impact of mutations	[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
	Diseases
OMIM	162091 601607 609322 614608
Orphanet	321 20073 19153 12482 14539
DisGeNET	SMARCB1
Medgen	SMARCB1
Genetic Testing Registry	SMARCB1
NextProt	Q12824 [Medical]
GENETests	SMARCB1
Target Validation	SMARCB1
Huge Navigator	SMARCB1 [HugePedia]
ClinGen	SMARCB1 (curated)
	Clinical trials, drugs, therapy
MyCancerGenome	SMARCB1
Protein Interactions : CTD
Pharm GKB Gene	PA35953
Pharos	Q12824
Drug Sensitivity	SMARCB1
Clinical trial	SMARCB1
	Miscellaneous
canSAR (ICR)	SMARCB1 (select the gene name)
Harmonizome	SMARCB1
DataMed Index	SMARCB1
Other database	http://cancergenome.broadinstitute.org/index.php?tgene=SMARCB1
	Probes
	Litterature
PubMed	396 Pubmed reference(s) in Entrez
GeneRIFs	Gene References Into Functions (Entrez)
EVEX	SMARCB1

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

Search in all EBI NCBI

indexed on : Fri Feb 19 18:00:33 CET 2021

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