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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 30-Jun-2015
    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; 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]
    Orthologs
    See SMARCB1 in Epigenomics, MapViewer
    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 (facilitated glucose transporter), 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
    Compare labs
    Rhabdoid tumor predisposition syndrome 1
    MedGen: C1836327 OMIM: 609322 GeneReviews: Not available
    Compare labs
    Schwannomatosis
    MedGen: C1335929 OMIM: 162091 GeneReviews: Not available
    Compare labs

    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

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    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 differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    chromatin organization TAS
    Traceable Author Statement
    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
     
    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_001007468.1NP_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 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
      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 identical proteins and their annotated locations for 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
      SNF5; SNF5 / SMARCB1 / INI1

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

    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  

      See identical proteins and their annotated locations for XP_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  

      See identical proteins and their annotated locations for XP_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)