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

1999-03-01   Jean-Loup Huret  

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 IDLast YearTitleAuthors
98921891999Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors.Biegel JA et al
68610721983Paravertebral malignant rhabdoid tumor in infancy. In vitro studies of a familial tumor.Lynch HT et al
94482951998Structure-function analysis of integrase interactor 1/hSNF5L1 reveals differential properties of two repeat motifs present in the highly conserved region.Morozov A et al
91282411997Components of the human SWI/SNF complex are enriched in active chromatin and are associated with the nuclear matrix.Reyes JC et al
94913181998Cytogenetic 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
96713071998Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer.Versteege I et al
25432251989Rhabdoid tumor of kidney. A report of 111 cases from the National Wilms' Tumor Study Pathology Center.Weeks DA et al
85455901995Malignant 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 IDTranscript IDUniprot
ENSG00000099956ENST00000263121A0A0G2JRV3
ENSG00000099956ENST00000344921G5E975
ENSG00000099956ENST00000407082B5MCL5
ENSG00000099956ENST00000407422Q12824
ENSG00000099956ENST00000417137C9JTA6
ENSG00000099956ENST00000634926A0A0U1RRB8
ENSG00000099956ENST00000635578A0A0U1RQQ2
ENSG00000099956ENST00000642727A0A2R8Y5Z2
ENSG00000099956ENST00000644036Q12824
ENSG00000099956ENST00000644462A0A2R8YEE8
ENSG00000099956ENST00000644619A0A2R8Y5N5
ENSG00000099956ENST00000647057A0A2R8YDN6

Expression (GTEx)

0
50
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

PathwaySourceExternal ID
Chromatin organizationREACTOMER-HSA-4839726
Chromatin modifying enzymesREACTOMER-HSA-3247509
RMTs methylate histone argininesREACTOMER-HSA-3214858

Protein levels (Protein atlas)

Not detected
Low
Medium
High
cerebral cortex
cerebellum
hippocampus
caudate
thyroid gland
parathyroid gland
adrenal gland
nasopharynx
bronchus
lung
oral mucosa
salivary gland
esophagus
stomach 1
stomach 2
duodenum
small intestine
colon
rectum
liver
gallbladder
pancreas
kidney
urinary bladder
testis
epididymis
seminal vesicle
prostate
vagina
ovary
fallopian tube
endometrium 1
endometrium 2
cervix, uterine
placenta
breast
heart muscle
smooth muscle
skeletal muscle
soft tissue 1
soft tissue 2
adipose tissue
skin 1
skin 2
appendix
spleen
lymph node
tonsil
bone marrow

References

Pubmed IDYearTitleCitations
375482712024Constitutional balanced translocations involving SMARCB1: A rare cause of rhabdoid tumor predisposition syndrome.0
380396172024SMARCB1/INI1-deficient epithelioid and myxoid neoplasms in paratesticular region: Expanding the clinicopathologic and molecular spectrum.0
380884612024SMARCB1 (INI1)-deficient sinonasal carcinoma manifesting as oral lesions: A report of two cases.1
383555602024The IL6/JAK/STAT3 signaling axis is a therapeutic vulnerability in SMARCB1-deficient bladder cancer.0
385387982024Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF.1
386398532024Central nervous system embryonal tumors with EWSR1-PLAGL1 rearrangements reclassified as INI-1 deficient tumors at relapse.0
375482712024Constitutional balanced translocations involving SMARCB1: A rare cause of rhabdoid tumor predisposition syndrome.0
380396172024SMARCB1/INI1-deficient epithelioid and myxoid neoplasms in paratesticular region: Expanding the clinicopathologic and molecular spectrum.0
380884612024SMARCB1 (INI1)-deficient sinonasal carcinoma manifesting as oral lesions: A report of two cases.1
383555602024The IL6/JAK/STAT3 signaling axis is a therapeutic vulnerability in SMARCB1-deficient bladder cancer.0
385387982024Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF.1
386398532024Central nervous system embryonal tumors with EWSR1-PLAGL1 rearrangements reclassified as INI-1 deficient tumors at relapse.0
366562302023SMARCB1 deficient sinonasal carcinoma: An emerging entity with a diagnostic challenge.0
366577182023SMARCB1 Loss in Poorly Differentiated Chordomas Drives Tumor Progression.3
371868442023SMARCB1 regulates the hypoxic stress response in sickle cell trait.6

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/css/cancer-prone-explorer/gene-explorer/