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SMARCB1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 [ Homo sapiens (human) ]

Gene ID: 6598, updated on 19-Jul-2014
Official Symbol
SMARCB1provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1provided by HGNC
Primary source
HGNC:11103
See related
Ensembl:ENSG00000099956; HPRD:03364; MIM:601607; Vega:OTTHUMG00000150737
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RDT; INI1; SNF5; Snr1; BAF47; MRD15; RTPS1; Sfh1p; hSNFS; SNF5L1; SWNTS1; PPP1R144
Summary
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]
See SMARCB1 in Epigenomics, MapViewer
Location:
22q11.23; 22q11
Exon count:
9
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 22 NC_000022.11 (23786963..23834518)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (24129150..24176705)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene chromosome 22 open reading frame 15 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 10 Neighboring gene matrix metallopeptidase 11 (stromelysin 3) Neighboring gene derlin 3 Neighboring gene solute carrier family 2 (facilitated glucose transporter), member 11 Neighboring gene uncharacterized LOC284889 Neighboring gene macrophage migration inhibitory factor (glycosylation-inhibiting factor)

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Mental retardation, autosomal dominant 15
MedGen: CN123923 OMIM: 614608 GeneReviews: Not available
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Rhabdoid tumor predisposition syndrome 1
MedGen: C1836327 OMIM: 609322 GeneReviews: Not available
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Schwannomatosis
MedGen: C1335929 OMIM: 162091 GeneReviews: Not available
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2013-06-20)

ISCA Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2013-06-20)

ISCA Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag INI1/hSNF5 transdominant negative mutant S6 inhibits particle production by blocking accumulation of HIV-1 Gag at the membrane and by causing a defect in Gag processing and incorporation into particles PubMed
Tat tat Most of the components of the SWI2/SNF2 chromatin remodeling complex (BRG1/BRM, BAF250, BAF180, BAF170, BAF155, BAF60a, BAF53A, actin and InI1) except BRM, BAF155 and BAF57, are identified to interact with HIV-1 Tat in Jurkat cell PubMed
tat Integrase interactor 1 (INI1)/hSNF5 binds to HIV-1 Tat and co-activates Tat-mediated transcription; both the repeat (Rpt) 1 and Rpt 2 domains of INI1 are required for efficient co-activation PubMed
tat INI-1 and BRG-1 synergize with the p300 acetyltransferase to activate the HIV promoter; this synergism depends on the acetyltransferase activity of p300 and on HIV-1 Tat amino acids Lys(50) and Lys(51), suggesting a regulation of Tat by these proteins PubMed
integrase gag-pol INI1-interaction defective HIV-1 IN mutants (K71R, K111E, Q137R, D202G, and S147G) are defective for 2LTR circle formation, integration, or normal virion morphology as comparing to WT PubMed
gag-pol The integrase binding domain (amino acids 174-289) of INI1 inhibits the HIV-1 IN-mediated 3' processing reaction and decreases the amount of integration events PubMed
gag-pol Mass spectrometry and Fluorescence Correlation Spectroscopy analyses show a stable complex between HIV-1 IN, viral U5 DNA, LEDGF/p75, and the integrase binding domain (amino acids 174-289) of INI1 with a 4/2/2/2 stoichiometry PubMed
gag-pol The specificity in incorporation of INI1/hSNF5 into HIV-1 virions is directly correlated with its ability to exclusively interact with HIV-1 integrase but not with other retroviral integrases such as HIV-2, SIV, HTLV-1, and MuLV IN PubMed
gag-pol HIV-1 IN and INI1/hSNF5 bind SAP18 and selectively recruit components of Sin3a-HDAC1 complex into HIV-1 virions. HIV-1 virion-associated HDAC1 is required for efficient early post-entry events PubMed
gag-pol INI1 binds to the minor groove of DNA and stimulates IN strand transfer reactions PubMed
gag-pol Active INI1 is a multimer and binds to HIV-1 IN. Ile-263 is specifically required for multimerization of INI1, whereas Ile-264 and Ile-268 are involved in both multimerization and IN binding PubMed
gag-pol HIV-1 Integrase E69G and K71R mutants are impaired for SNF5/Ini1 interaction, and inhibition of SNF5/Ini1 expression by RNA interference increases HIV-1 replication PubMed
gag-pol Inactivation of ySNF5, the yeast homolog of integrase interactor 1 (INI1, hSNF5) abolishes the lethal phenotype induced by the expression of HIV-1 integrase in yeast, suggesting an important role for INI1 in HIV-1 integration PubMed
gag-pol HIV-1 preintegration complexes containing HIV-1 integrase induce the cytoplasmic recruitment of integrase interactor 1 (INI1, hSNF5) and PML and associate with these cellular proteins before migrating to the nucleus PubMed
gag-pol Integrase interactor 1 (INI1, hSNF5) is incorporated into HIV-1 virions, presumably through its interaction with HIV-1 integrase PubMed
gag-pol A cytoplasmically localized fragment of integrase interactor 1 (INI1, hSNF5; amino acids 183-294) potently inhibits HIV-1 particle production and replication PubMed
gag-pol Binding of integrase interactor 1 (INI1, hSNF5) to HIV-1 integrase is mediated by amino acids 183-243 of INI1 and the central domain of integrase (amino acids 48-188) PubMed
gag-pol Integrase interactor 1 (INI1, hSNF5) binds to HIV-1 integrase and stimulates integrase DNA end joining activity PubMed

Go to the HIV-1, Human Protein Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
ATP-dependent chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
 
ATP-dependent chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
DNA integration TAS
Traceable Author Statement
more info
PubMed 
DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
 
blastocyst hatching IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
mitotic cell cycle phase transition IBA
Inferred from Biological aspect of Ancestor
more info
 
negative regulation of cell proliferation IBA
Inferred from Biological aspect of Ancestor
more info
 
nervous system development IEA
Inferred from Electronic Annotation
more info
 
nucleosome disassembly IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation by host of viral transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of sequence-specific DNA binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription from RNA polymerase II promoter NAS
Non-traceable Author Statement
more info
PubMed 
single stranded viral RNA replication via double stranded DNA intermediate IDA
Inferred from Direct Assay
more info
PubMed 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
XY body IEA
Inferred from Electronic Annotation
more info
 
nBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
npBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
NOT nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 
protein complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
hSNF5
SNF5 homolog
BRG1-associated factor 47
integrase interactor 1 protein
malignant rhabdoid tumor suppressor
SWI/SNF-related matrix-associated protein
sucrose nonfermenting, yeast, homolog-like 1
protein phosphatase 1, regulatory subunit 144

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009303.1 

    Range
    5001..52556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_520

mRNA and Protein(s)

  1. NM_001007468.1NP_001007469.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform b

    See proteins identical to NP_001007469.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AJ011738, BG705851, R37717
    Consensus CDS
    CCDS46671.1
    UniProtKB/Swiss-Prot
    Q12824
    Related
    ENSP00000383984, OTTHUMP00000198411, ENST00000407422, OTTHUMT00000319873
    Conserved Domains (1) summary
    pfam04855
    Location:169364
    Blast Score: 763
    SNF5; SNF5 / SMARCB1 / INI1
  2. NM_003073.3NP_003064.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform a

    See proteins identical to NP_003064.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AJ011737, AK024025, AU143041, R37717
    Consensus CDS
    CCDS13817.1
    UniProtKB/Swiss-Prot
    Q12824
    UniProtKB/TrEMBL
    Q9H836
    Related
    ENSP00000263121, OTTHUMP00000198410, ENST00000263121, OTTHUMT00000319872
    Conserved Domains (1) summary
    pfam04855
    Location:178373
    Blast Score: 767
    SNF5; SNF5 / SMARCB1 / INI1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 ALT_REF_LOCI_1

Genomic

  1. NT_187633.1 

    Range
    23325..70880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000022.11 

    Range
    23786963..23834518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000154.1 

    Range
    7117207..7164626
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018933.2 

    Range
    24141393..24188920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)