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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 22-May-2016
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: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; CSS3; 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. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]
Orthologs
Location:
22q11.23; 22q11
Exon count:
9
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 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 Neighboring gene derlin 3 Neighboring gene solute carrier family 2 member 11 Neighboring gene MIF antisense RNA 1 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: C3553248 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)

ClinGen Genome Curation Page
Haploinsufficency

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

ClinGen 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
Nef nef Interaction of SIV Nef with INI1 enhances proviral DNA integration into the target host chromosomes, while interaction of HIV-1 Nef with INI1 cannot PubMed
nef HIV-1 and SIV Nef proteins directly bind to INI1 in both mammalian and yeast cells PubMed
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 Interaction Database

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • RMTs methylate histone arginines, organism-specific biosystem (from REACTOME)
    RMTs methylate histone arginines, organism-specific biosystemArginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways...
  • Regulation of retinoblastoma protein, organism-specific biosystem (from Pathway Interaction Database)
    Regulation of retinoblastoma protein, organism-specific biosystem
    Regulation of retinoblastoma protein
  • TNF-alpha/NF-kB Signaling Pathway, organism-specific biosystem (from WikiPathways)
    TNF-alpha/NF-kB Signaling Pathway, organism-specific biosystem"The Tumor Necrosis Factor alpha is a proinflammatory cytokine belonging to the TNF superfamily. It signals through 2 separate receptors - TNFRSF1A and TNFRSF1B, both members of the TNF receptor supe...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
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 cycle 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 
chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell proliferation IBA
Inferred from Biological aspect of Ancestor
more info
 
negative regulation of histone H3-K9 dimethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of histone H3-K9 trimethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 glucose mediated signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of histone H3-K9 acetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of histone H4 acetylation 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 
positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT regulation of histone H4-K16 acetylation IMP
Inferred from Mutant Phenotype
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
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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
BRG1-associated factor 47
SNF5 homolog
SWI/SNF-related matrix-associated protein
hSNF5
integrase interactor 1 protein
malignant rhabdoid tumor suppressor
protein phosphatase 1, regulatory subunit 144
sucrose nonfermenting, yeast, homolog-like 1

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 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001007468.2NP_001007469.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform b

    See identical proteins and their annotated locations for NP_001007469.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame donor splice site in the 5' coding region compared to variant 1. The resulting isoform (b) has the same N- and C-termini but lacks a 9 aa protein segment compared to isoform a.
    Source sequence(s)
    AJ011738, HY013730, R37717
    Consensus CDS
    CCDS46671.1
    UniProtKB/Swiss-Prot
    Q12824
    Related
    ENSP00000383984, OTTHUMP00000198411, ENST00000407422, OTTHUMT00000319873
    Conserved Domains (1) summary
    pfam04855
    Location:169364
    SNF5; SNF5 / SMARCB1 / INI1
  2. NM_001317946.1NP_001304875.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses alternate in-frame donor splice sites at two internal coding exons compared to variant 1. The resulting isoform (c) is longer than isoform a.
    Source sequence(s)
    AK024025, CB161660, HY013730, R37717
    UniProtKB/TrEMBL
    G5E975, Q9H836
    Conserved Domains (1) summary
    pfam04855
    Location:187382
    SNF5; SNF5 / SMARCB1 / INI1
  3. NM_003073.4NP_003064.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform a

    See identical proteins and their annotated locations for NP_003064.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a.
    Source sequence(s)
    AJ011737, HY013730, R37717
    Consensus CDS
    CCDS13817.1
    UniProtKB/Swiss-Prot
    Q12824
    Related
    ENSP00000263121, OTTHUMP00000198410, ENST00000263121, OTTHUMT00000319872
    Conserved Domains (1) summary
    pfam04855
    Location:178373
    SNF5; SNF5 / SMARCB1 / INI1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p2 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011530345.1XP_011528647.1  

    See identical proteins and their annotated locations for XP_011528647.1

    Conserved Domains (1) summary
    pfam04855
    Location:196391
    SNF5; SNF5 / SMARCB1 / INI1
  2. XM_011530346.1XP_011528648.1  

    Related
    ENSP00000340883, OTTHUMP00000198413, ENST00000344921, OTTHUMT00000319876
    Conserved Domains (1) summary
    pfam04855
    Location:187382
    SNF5; SNF5 / SMARCB1 / INI1

Reference GRCh38.p2 ALT_REF_LOCI_1

Genomic

  1. NT_187633.1 Reference GRCh38.p2 ALT_REF_LOCI_1

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

mRNA and Protein(s)

  1. XM_011546908.1XP_011545210.1  

    See identical proteins and their annotated locations for XP_011545210.1

    Conserved Domains (1) summary
    pfam04855
    Location:196391
    SNF5; SNF5 / SMARCB1 / INI1
  2. XM_011546909.1XP_011545211.1  

    Conserved Domains (1) summary
    pfam04855
    Location:187382
    SNF5; SNF5 / SMARCB1 / INI1

Alternate CHM1_1.1

Genomic

  1. NC_018933.2 Alternate CHM1_1.1

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