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Aliases for SMARCB1 Gene

Aliases for SMARCB1 Gene

  • SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1 2 3
  • INI1 3 4 6
  • Malignant Rhabdoid Tumor Suppressor 2 3
  • Integrase Interactor 1 Protein 3 4
  • BRG1-Associated Factor 47 3 4
  • SNF5 Homolog 3 4
  • SNF5L1 3 4
  • SWNTS1 3 6
  • MRD15 3 6
  • RTPS1 3 6
  • BAF47 3 4
  • HSNF5 3 4
  • SNF5 3 6
  • RDT 3 6
  • SWI/SNF-Related Matrix-Associated Actin-Dependent Regulator Of Chromatin Subfamily B Member 1 3
  • Protein Phosphatase 1, Regulatory Subunit 144 3
  • Sucrose Nonfermenting, Yeast, Homolog-Like 1 3
  • SWI/SNF-Related Matrix-Associated Protein 3
  • Integrase Interactor 1 2
  • Regulatory Subunit 144 2
  • Protein Phosphatase 1 2
  • Sucrose Nonfermenting 2
  • Homolog-Like 1 2
  • PPP1R144 3
  • Yeast 2
  • Sfh1p 3
  • HSNFS 3
  • Snr1 3

External Ids for SMARCB1 Gene

Previous Symbols for SMARCB1 Gene

  • SNF5L1

Summaries for SMARCB1 Gene

Entrez Gene Summary for SMARCB1 Gene

  • The protein encoded by this gene is part of a complex that relieves repressive chromatin structures, allowing the transcriptional machinery to access its targets more effectively. The encoded nuclear protein may also bind to and enhance the DNA joining activity of HIV-1 integrase. This gene has been found to be a tumor suppressor, and mutations in it have been associated with malignant rhabdoid tumors. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for SMARCB1 Gene

SMARCB1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily B, Member 1) is a Protein Coding gene. Diseases associated with SMARCB1 include mental retardation, autosomal dominant 15 and chromosome 22q deletion. Among its related pathways are Transcription Ligand-dependent activation of the ESR1/SP pathway and Transcription Ligand-dependent activation of the ESR1/SP pathway. GO annotations related to this gene include transcription coactivator activity and Tat protein binding.

UniProtKB/Swiss-Prot for SMARCB1 Gene

  • Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of tumor formation. The BAF complex is able to create a stable, altered form of chromatin that constrains fewer negative supercoils than normal. This change in supercoiling would be due to the conversion of up to one-half of the nucleosomes on polynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2 histones octamers. Stimulates in vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Plays a key role in cell-cycle control and causes cell cycle arrest in G0/G1.

Gene Wiki entry for SMARCB1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMARCB1 Gene

Genomics for SMARCB1 Gene

Genomic Location for SMARCB1 Gene

Start:
23,786,963 bp from pter
End:
23,834,518 bp from pter
Size:
47,556 bases
Orientation:
Plus strand

Genomic View for SMARCB1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SMARCB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMARCB1 Gene

Regulatory Elements for SMARCB1 Gene

Proteins for SMARCB1 Gene

  • Protein details for SMARCB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q12824-SNF5_HUMAN
    Recommended name:
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
    Protein Accession:
    Q12824
    Secondary Accessions:
    • O75784
    • O95474
    • Q17S11
    • Q38GA1
    • Q76N08
    • Q9UBH2

    Protein attributes for SMARCB1 Gene

    Size:
    385 amino acids
    Molecular mass:
    44141 Da
    Quaternary structure:
    • Component of the BAF (hSWI/SNF) complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57 SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Binds to double-stranded DNA. Interacts with MYK and MAEL. Interacts with PPP1R15A. Binds tightly to the human immunodeficiency virus-type 1 (HIV-1) integrase in vitro and stimulates its DNA-joining activity. Interacts with human papillomavirus 18 E1 protein to stimulate its viral replication. Interacts with Epstein-Barr virus protein EBNA-2. Component of neural progenitors-specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin (By similarity).

    Alternative splice isoforms for SMARCB1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMARCB1 Gene

Proteomics data for SMARCB1 Gene at MOPED

Post-translational modifications for SMARCB1 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys292 and Lys324

Other Protein References for SMARCB1 Gene

No data available for DME Specific Peptides for SMARCB1 Gene

Domains for SMARCB1 Gene

Protein Domains for SMARCB1 Gene

UniProtKB/Swiss-Prot:

SNF5_HUMAN
Family:
  • Belongs to the SNF5 family.:
    • Q12824
genes like me logo Genes that share domains with SMARCB1: view

No data available for Gene Families for SMARCB1 Gene

Function for SMARCB1 Gene

Molecular function for SMARCB1 Gene

GENATLAS Biochemistry: general transcriptional activator,S cerevisiae SWI/SNF2 related protein,matrix associated,actin-dependent regulator of chromatin,subfamily B,member 1,component of the chromatin remodeling complex,preferentially expressed in muscle and pancreas,mutated in atypical teratoid and rhabdoid tumors,tumor suppressor gene (see TSG22D),frequently deleted in chronic myeloid leukemia
UniProtKB/Swiss-Prot Function: Core component of the BAF (hSWI/SNF) complex. This ATP-dependent chromatin-remodeling complex plays important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of tumor formation. The BAF complex is able to create a stable, altered form of chromatin that constrains fewer negative supercoils than normal. This change in supercoiling would be due to the conversion of up to one-half of the nucleosomes on polynucleosomal arrays into asymmetric structures, termed altosomes, each composed of 2 histones octamers. Stimulates in vitro the remodeling activity of SMARCA4/BRG1/BAF190A. Involved in activation of CSF1 promoter. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Plays a key role in cell-cycle control and causes cell cycle arrest in G0/G1.

Gene Ontology (GO) - Molecular Function for SMARCB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 contributes_to RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 16217013
GO:0000980 contributes_to RNA polymerase II distal enhancer sequence-specific DNA binding IDA 16217013
GO:0002039 p53 binding IPI 11950834
GO:0003713 transcription coactivator activity NAS 8804307
GO:0005515 protein binding IPI 10078207
genes like me logo Genes that share ontologies with SMARCB1: view
genes like me logo Genes that share phenotypes with SMARCB1: view

Animal Models for SMARCB1 Gene

MGI Knock Outs for SMARCB1:

miRNA for SMARCB1 Gene

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for SMARCB1 Gene

Localization for SMARCB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMARCB1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMARCB1 Gene COMPARTMENTS Subcellular localization image for SMARCB1 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for SMARCB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome --
GO:0000790 nuclear chromatin IDA 16217013
GO:0001741 XY body IEA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with SMARCB1: view

Pathways for SMARCB1 Gene

genes like me logo Genes that share pathways with SMARCB1: view

Pathways by source for SMARCB1 Gene

Gene Ontology (GO) - Biological Process for SMARCB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001824 blastocyst development --
GO:0001835 blastocyst hatching IEA --
GO:0006281 DNA repair IBA --
GO:0006325 chromatin organization TAS --
GO:0006337 nucleosome disassembly IDA 8895581
genes like me logo Genes that share ontologies with SMARCB1: view

Transcripts for SMARCB1 Gene

Unigene Clusters for SMARCB1 Gene

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SMARCB1 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9
SP1: - - - -
SP2: - - -
SP3: - - -
SP4: -
SP5: -
SP6:
SP7:

Relevant External Links for SMARCB1 Gene

GeneLoc Exon Structure for
SMARCB1
ECgene alternative splicing isoforms for
SMARCB1

Expression for SMARCB1 Gene

mRNA expression in normal human tissues for SMARCB1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for SMARCB1 Gene

SOURCE GeneReport for Unigene cluster for SMARCB1 Gene Hs.534350

genes like me logo Genes that share expressions with SMARCB1: view

Orthologs for SMARCB1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SMARCB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMARCB1 36
  • 99.83 (n)
  • 100 (a)
SMARCB1 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SMARCB1 36
  • 92.55 (n)
  • 99.74 (a)
SMARCB1 37
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMARCB1 36
  • 93.59 (n)
  • 100 (a)
SMARCB1 37
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smarcb1 36
  • 91.26 (n)
  • 100 (a)
Smarcb1 16
Smarcb1 37
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SMARCB1 37
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMARCB1 37
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smarcb1 36
  • 91.4 (n)
  • 100 (a)
chicken
(Gallus gallus)
Aves MMP11 36
  • 84.68 (n)
  • 96.88 (a)
SMARCB1 37
  • 96 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMARCB1 37
  • 92 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.7591 36
tropical clawed frog
(Silurana tropicalis)
Amphibia smarcb1 36
  • 79.81 (n)
  • 97.88 (a)
Str.7159 36
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.455 36
zebrafish
(Danio rerio)
Actinopterygii Dr.16141 36
smarcb1a 36
  • 83.82 (n)
  • 95.98 (a)
smarcb1a 37
  • 95 (a)
OneToMany
smarcb1b 37
  • 95 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001154 36
  • 65.48 (n)
  • 70.68 (a)
fruit fly
(Drosophila melanogaster)
Insecta Snr1 36
  • 66.21 (n)
  • 68.29 (a)
Snr1 37
  • 67 (a)
OneToOne
Snr1 38
  • 65 (a)
worm
(Caenorhabditis elegans)
Secernentea snfc-5 36
  • 54.75 (n)
  • 54.75 (a)
snfc-5 37
  • 50 (a)
OneToOne
R07E5.3 38
  • 49 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SFH1 39
SNF5 37
  • 11 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9854 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.132 37
  • 68 (a)
OneToOne
Species with no ortholog for SMARCB1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMARCB1 Gene

ENSEMBL:
Gene Tree for SMARCB1 (if available)
TreeFam:
Gene Tree for SMARCB1 (if available)

Paralogs for SMARCB1 Gene

No data available for Paralogs for SMARCB1 Gene

Variants for SMARCB1 Gene

Sequence variations from dbSNP and Humsavar for SMARCB1 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type MAF
rs738793 -- 23,785,308(+) acctc(C/T)gtact upstream-variant-2KB
rs738794 -- 23,792,571(+) ACGTG(A/G)CAATG intron-variant
rs738795 -- 23,800,143(+) actct(A/T)gacct intron-variant
rs738796 -- 23,800,336(+) CAACT(C/T)CTACT intron-variant
rs738797 untested 23,801,315(+) TGGCC(C/G)CTCAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SMARCB1 Gene

Variant ID Type Subtype PubMed ID
nsv7350 OTHER Inversion 18451855
esv2724041 CNV Deletion 23290073
nsv526567 CNV Gain 19592680
dgv4906n71 CNV Gain 21882294
nsv914597 CNV Loss 21882294
nsv829103 CNV Gain 20364138
nsv914598 CNV Loss 21882294
nsv914599 CNV Gain 21882294
nsv511075 CNV Complex 20534489
dgv4907n71 CNV Loss 21882294
dgv4908n71 CNV Loss 21882294

Relevant External Links for SMARCB1 Gene

HapMap Linkage Disequilibrium report
SMARCB1
Human Gene Mutation Database (HGMD)
SMARCB1

Disorders for SMARCB1 Gene

(3) OMIM Diseases for SMARCB1 Gene (601607)

UniProtKB/Swiss-Prot

SNF5_HUMAN
  • Rhabdoid tumor predisposition syndrome 1 (RTPS1) [MIM:609322]: A familial cancer syndrome predisposing to renal or extrarenal malignant rhabdoid tumors and to a variety of tumors of the central nervous system, including choroid plexus carcinoma, medulloblastoma, and central primitive neuroectodermal tumors. Rhabdoid tumors are the most aggressive and lethal malignancies occurring in early childhood. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Schwannomatosis 1 (SWNTS1) [MIM:162091]: A cancer syndrome in which patients develop multiple non-vestibular schwannomas, benign neoplasms that arise from Schwann cells of the cranial, peripheral, and autonomic nerves. {ECO:0000269 PubMed:17357086, ECO:0000269 PubMed:18072270}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Mental retardation, autosomal dominant 15 (MRD15) [MIM:614608]: A disease characterized by multiple congenital anomalies and mental retardation. Mental retardation is defined by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD15 patients manifest developmental delay, hypotonia, absent or hypoplastic fifth finger or toenails, a coarse facial appearance, sparse scalp hair, thick eyebrows, and long eyelashes. Additional variable features include microcephaly, small cerebellum, seizures, hearing loss, abnormal delayed dentition, hirsutism. {ECO:0000269 PubMed:22426308}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(27) Novoseek inferred disease relationships for SMARCB1 Gene

Disease -log(P) Hits PubMed IDs
rhabdoid tumor 97 63
sarcoma epithelioid 80.2 14
embryonal tumor 69.1 3
cns tumors 66.9 4
pediatric brain tumor 59.4 3

Relevant External Links for SMARCB1

Genetic Association Database (GAD)
SMARCB1
Human Genome Epidemiology (HuGE) Navigator
SMARCB1
genes like me logo Genes that share disorders with SMARCB1: view

Publications for SMARCB1 Gene

  1. Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5. (PMID: 7801128) Kalpana G.V. … Goff S.P. (Science 1994) 2 3 4 23
  2. Interaction of E1 and hSNF5 proteins stimulates replication of human papillomavirus DNA. (PMID: 10365963) Lee D. … Choe J. (Nature 1999) 2 3 4 23
  3. Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors. (PMID: 9892189) Biegel J.A. … Fogelgren B. (Cancer Res. 1999) 3 4 23
  4. The mouse ortholog of the human SMARCB1 gene encodes two splice forms. (PMID: 10208879) Bruder C.E. … Kedra D. (Biochem. Biophys. Res. Commun. 1999) 3 4 23
  5. P16INK4a is required for hSNF5 chromatin remodeler-induced cellular senescence in malignant rhabdoid tumor cells. (PMID: 14604992) Oruetxebarria I. … Verrijzer C.P. (J. Biol. Chem. 2004) 3 4 23

Products for SMARCB1 Gene

Sources for SMARCB1 Gene

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