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

1999-03-01 Jean-Loup Huret Affiliation

Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

Identity

HGNC

SMARCB1

LOCATION

22q11.23

LOCUSID

6598

ALIAS

BAF47,CSS3,INI1,MRD15,PPP1R144,RDT,RTPS1,SNF5,SNF5L1,SWNTS1,Sfh1p,Snr1,hSNFS

FUSION GENES

Show Gene Fusions

DNA/RNA

Description

spans over 50 kb; 9 exons

Transcription

alternative splicing including/excluding exon 2

Proteins

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

Entity name

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 gene

no hybrid gene but inactivation of both alleles

Entity name

rhabdoid tumor predisposition syndrome

Hybrid 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

Pubmed ID	Last Year	Title	Authors
9892189	1999	Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors.	Biegel JA et al
6861072	1983	Paravertebral malignant rhabdoid tumor in infancy. In vitro studies of a familial tumor.	Lynch HT et al
9448295	1998	Structure-function analysis of integrase interactor 1/hSNF5L1 reveals differential properties of two repeat motifs present in the highly conserved region.	Morozov A et al
9128241	1997	Components of the human SWI/SNF complex are enriched in active chromatin and are associated with the nuclear matrix.	Reyes JC et al
9491318	1998	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 et al
9671307	1998	Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer.	Versteege I et al
2543225	1989	Rhabdoid tumor of kidney. A report of 111 cases from the National Wilms' Tumor Study Pathology Center.	Weeks DA et al
8545590	1995	Malignant rhabdoid tumors: a clinicopathologic review and conceptual discussion.	Wick MR et al

Other Information

Locus ID:

NCBI: 6598
MIM: 601607
HGNC: 11103
Ensembl: ENSG00000099956

Variants:

dbSNP: 6598
ClinVar: 6598
TCGA: ENSG00000099956
COSMIC: SMARCB1

RNA/Proteins

Gene ID	Transcript ID	Uniprot
ENSG00000099956	ENST00000263121	A0A0G2JRV3
ENSG00000099956	ENST00000344921	G5E975
ENSG00000099956	ENST00000407082	B5MCL5
ENSG00000099956	ENST00000407422	Q12824
ENSG00000099956	ENST00000417137	C9JTA6
ENSG00000099956	ENST00000634926	A0A0U1RRB8
ENSG00000099956	ENST00000635578	A0A0U1RQQ2
ENSG00000099956	ENST00000642727	A0A2R8Y5Z2
ENSG00000099956	ENST00000644036	Q12824
ENSG00000099956	ENST00000644462	A0A2R8YEE8
ENSG00000099956	ENST00000644619	A0A2R8Y5N5
ENSG00000099956	ENST00000647057	A0A2R8YDN6

Expression (GTEx)

100

150

Adipose - Subcutaneous

Adipose - Visceral

Adrenal Gland

Artery - Aorta

Artery - Tibial

Bladder

Brain - Amygdala

Brain - Anterior cingulate cortex

Brain - Caudate

Brain - Cerebellar Hemisphere

Brain - Cerebellum

Brain - Cortex

Brain - Frontal Cortex

Brain - Hippocampus

Brain - Hypothalamus

Brain - Nucleus accumbens

Brain - Putamen

Brain - Spinal cord

Brain - Substantia nigra

Breast - Mammary Tissue

Cells - Cultured fibroblasts

Cells - EBV - transformed lymphocytes

Cervix - Ectocervix

Cervix - Endocervix

Colon - Sigmoid

Colon - Transverse

Esophagus - Gastroesophageal Junction

Esophagus - Mucosa

Esophagus - Muscularis

Fallopian Tube

Heart - Atrial Appendage

Heart - Left Ventricle

Kidney - Cortex

Kidney - Medulla

Liver

Lung

Minor Salivary Gland

Muscle - Skeletal

Nerve - Tibial

Ovary

Pancreas

Pituitary

Prostate

Skin - Not Sun Exposed

Skin - Sun Exposed

Small Intestine - Terminal Ileum

Spleen

Stomach

Testis

Thyroid

Uterus

Vagina

Whole Blood

Pathways

Pathway	Source	External ID
Chromatin organization	REACTOME	R-HSA-4839726
Chromatin modifying enzymes	REACTOME	R-HSA-3247509
RMTs methylate histone arginines	REACTOME	R-HSA-3214858

Protein levels (Protein atlas)

Not detected

Low

Medium

High

References

Pubmed ID	Year	Title	Citations
24285714	2013	Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation.	156
22797305	2012	A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers.	116
17357086	2007	Germline mutation of INI1/SMARCB1 in familial schwannomatosis.	85
19913121	2009	Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.	85
12138206	2002	Cell cycle arrest and repression of cyclin D1 transcription by INI1/hSNF5.	84
11950834	2002	SWI/SNF complex interacts with tumor suppressor p53 and is necessary for the activation of p53-mediated transcription.	73
19033866	2009	Loss of INI1 expression is characteristic of both conventional and proximal-type epithelioid sarcoma.	63
27941797	2017	SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation.	63
21108436	2011	Spectrum of SMARCB1/INI1 mutations in familial and sporadic rhabdoid tumors.	61
14604992	2004	P16INK4a is required for hSNF5 chromatin remodeler-induced cellular senescence in malignant rhabdoid tumor cells.	58

Citation

Jean-Loup Huret

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

Atlas Genet Cytogenet Oncol Haematol. 1999-03-01

Online version: http://atlasgeneticsoncology.org/gene/169/smarcb1-(sw1-snf-related-matrix-associated-actin-dependent-regulator-of-chromatin-b1)