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FLASH GENE
Symbol SMARCB1 contributors: mct/pgu - updated : 10-05-2019
HGNC name SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
HGNC id 11103
Corresponding disease
CSSSB1 Coffin-siris syndrome
MRBDT malignant rhabdoid tumors
SCWT schwannomatosis
Location 22q11.23      Physical location : 24.129.149 - 24.176.704
Synonym name
  • BRG1 (brm/SWI2-related gene 1) associated factor 47
  • integrase interactor 1
  • malignant rhabdoid tumor suppressor
  • sucrose nonfermenting, yeast, homolog-like 1
  • protein phosphatase 1, regulatory subunit 144
  • sucrose nonfermenting, yeast, homolog-like 1
    • Synonym symbol(s) BAF47, SNF5, INI1, RDT, SNF5L1, Snr1, Sfh1p, hSNF5, CSS3, MRD15, PPP1R144, RDT, RTPS1, SWNTS1, hSNFS
    DNA
    TYPE functioning gene
    STRUCTURE 47.59 kb     9 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    MAPPING cloned Y linked N status confirmed
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    9 - 1717 - 385 - 2006 16772295
  • isoform a
  • a compensatory effect exists between SNF5 isoforms, possibly to maintain a proper level of SNF5 proteins, suggesting that SNF5 is necessary for cell survival
  • SNF5a and SNF5b can functionally compensate each other and that lack of both isoforms impairs cell proliferation
    • 9 - 1690 - 376 - 2006 16772295
  • isoform b
  • a compensatory effect exists between SNF5 isoforms, possibly to maintain a proper level of SNF5 proteins, suggesting that SNF5 is necessary for cell survival
  • SNF5a and SNF5b can functionally compensate each other and that lack of both isoforms impairs cell proliferation
    • 9 - 1776 - 394 - 2006 16772295
    9 - 1803 - 403 - 2006 16772295
    EXPRESSION
    Type widely
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    blood / hematopoieticthymus   highly
    Cardiovascularheart   highly
    Digestiveliver   moderately
    Endocrinepancreas   highly
    Nervousbrain   moderately
    Reproductivemale systemprostate  highly
    Respiratorylung   highly
    Urinarykidney   moderately
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Muscularstriatumskeletal  
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • two highly conserved imperfect repeats (Rpt1, Rpt2) important for interaction with HIV integrase one with MYC
  • a C terminal coiled coil region
    • HOMOLOGY
    interspecies ortholog to murine Smarcb1 (100.00pc)
    ortholog to rattus Smarcb1 (100.00pc)
    Homologene
    FAMILY
  • SNF5 family
    • CATEGORY DNA associated , transcription factor , tumor suppressor
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,nucleus,nucleoplasm
    intracellular,nucleus,chromatin/chromosome
    intracellular,nucleus,nucleolus
    basic FUNCTION
  • actin-dependent regulator of chromatin
  • involved in cell cycle control pathway
  • involved in the oncogenesis of tumors with a completely different histology and prognosis
  • required for upregulation of BNIP3L by IGFBP7
  • promotes nucleotide excision repair by influencing ATM recruitment and downstream H2AFX phosphorylation
  • exerts ploidy control through a pathway that includes CDKN2A, cyclin D, CDK4, RB and E2F
  • role in hereditary forms of schwannomas, but not in solitary, sporadic schwannomas
  • has a protective role in the DNA damage response
  • key mediator of HH signaling and aberrant activation of GLI1 is a previously undescribed targetable mechanism contributing to the growth of malignant rhabdoid tumors cells
  • loss of SMARCB1 drives cancer formation through simultaneous epigenetic perturbation of GLI1 and other key cancer-promoting pathways, several of which may thus constitute viable therapeutic targets
  • represses Aurora A transcription in a cell-type-specific manner
  • loss dramatically alters SWI/SNF complex composition and prevents formation of complexes required for cellular differentiation
  • differential roles for SWI/SNF subunits in muscle differentiation, with SMARCB1 playing a dual role both in the permanent cell cycle exit and in the regulation of muscle-specific genes
  • antagonistic roles of the SMARCB1 and MYC transcriptional regulators in mediating cellular and oncogenic functions
  • is required for the integrity of SWI/SNF complexes and its loss alters enhancer targeting-markedly impairing SWI/SNF binding to typical enhancers, particularly those required for differentiation, while maintaining SWI/SNF binding at super-enhancers
  • SMARCB1, SMARCD1 and SMARCE1 might act as novel pro-senescence factors in both normal and tumor human skin cells
  • SMARCB1 represses bivalent genes in human embryonic stem cells (hESCs) and antagonizes chromatin accessibility at super-enhancers
    • CELLULAR PROCESS nucleotide, chromatin organization, remodeling
    nucleotide, transcription
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling
    a component
  • component of the chromatin remodeling complex
  • component of SWI/SNF chromatin remodeling enzymes that contain SNF2 family ATPases BRM (Brahma) or BRG1 (Brahma Related Gene 1)
  • component of the WINAC complex, at least composed of SMARCA2, SMARCA4, SMARCB1, SMARCC1, SMARCC2, SMARCD1, SMARCE1, ACTL6A, BAZ1B/WSTF, ARID1A, SUPT16H, CHAF1A and TOP2B
    • INTERACTION
    DNA binding to double-strand DNA
    RNA
    small molecule
    protein
  • previously shown to interact with HIV integrase
  • part of a pathway in which IGFBP7 increases expression of SMARCB1, which in turn leads to increased expression of BNIP3L culminating in apoptosis
  • interacting with MYK and MAEL
  • interacting with PPP1R15A
  • HIV-1 integrase and SMARCB1 bind SAP18 and selectively recruit components of SIN3a-HDAC1 complex into HIV-1 virions
  • required for TP53 transcriptional activity, and induction of prosurvival TP53 targets, including CDKN1A and MDM2, may have a role in SMARCB1 prosurvival activity
  • interacts with GLI1 (localizes to GLI1-regulated promoters and loss of SMARCB1 leads to activation of the HH-GLI pathway)
  • RB1CC1 essentially requires binding with SMARCB1, a chromatin-remodeling factor) to activate the CDKN2A promoter, in order to enhance the RB1 pathway and acts as a tumor suppressor
  • CHFR interacts with SMARCA4, SMARCB1, and SMARCD1 of the SWI/SNF-like BAF complex and ubiquitinates them to target for degradation through a proteasome-mediated pathway, and SMARCC1 stabilizes these components by blocking their interaction with CHFR
  • SMARCA4, SMARCB1, and SMARCD1, but not SMARCC1, are the substrates of CHFR for ubiquitination
  • interacts with CHFR through its RPT2 region
  • SMARCB1 is indispensable for GADD45GIP1-enhanced TP53 activity and its function in the suppression of cell cycle arrest in human cancer cells
  • is a modular domain involved in SMARCB1 interaction, which is functionally distinct from other characterized SWIRM domains that possess DNA binding activity
  • BICRA and BICRAL each exclusively associate with BRD9, but not with SMARCB1 (PMID;
  • SMARCB1 also interacts with the oncoprotein transcription factor MYC and is proposed to stimulate MYC activity
    • cell & other
  • matrix associated
    • REGULATION
    Other phosphorylated upon DNA damage
    ASSOCIATED DISORDERS
    corresponding disease(s) MRBDT , SCWT , CSSSB1
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    tumoral   deletion    
    in chromic myeloid leukemia
    tumoral   LOH    
    in meningiomas
    tumoral   deletion    
    or mutated in malignant rhabdoid tumor or atypical teratoid tumor
    tumoral somatic mutation      
    in plexus carcinoma
    tumoral       loss of function
    stimulates cell cycle progression and cooperates with p53 loss in oncogenic transformation, in infantile malignant rhabdoid tumors, and epithelioid sarcomas
    tumoral germinal mutation     loss of function
    mutation loss of functio in familial schwannomatosis
    tumoral   deletion    
    predisposing to malignant rhabdoid tumor
    tumoral   LOH    
    in schwannomatosis
    tumoral germinal mutation      
    associated with somatic NF2 mutations in familial multiple meningiomas
    constitutional germinal mutation     loss of function
    ID via EHMT1-associated chromatin modification module
    tumoral     --low  
    is associated with poor prognosis in skull base chordoma
    tumoral germinal mutation      
    predispose to rhabdoid tumors and schwannomas
    tumoral        
    complete absence of SMARCB1 immunoreactivity seen in malignant rhabdoid tumor
    tumoral     --low  
    decreased SMARCB1 immunoreactivity with a high specificity (100 p100) for synovial sarcoma and particular sensitivity for poorly differentiated subtypes of synovial sarcoma
    constitutional   amplification    
    microduplication in region with SMARCB1 and SNRPD3 genes in patient presented healed cleft lip, mild facial dysmorphism, cognitive deficit, and delayed language development associated with severe behavioral problems including learning difficulties and aggressive behavior
    Susceptibility
  • to familial schwannomatosis
  • to malignant rhabdoid tumor
    • Variant & Polymorphism insertion/deletion deletion in malignant rhabdoid tumor
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS