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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 17-Jun-2024

    Summary

    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 MIM:601607; AllianceGenome:HGNC:11103
    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; INI-1; 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]
    Expression
    Ubiquitous expression in testis (RPKM 42.3), ovary (RPKM 34.2) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SMARCB1 in Genome Data Viewer
    Location:
    22q11.23; 22q11
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (23786966..23838009)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (24234168..24285193)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (24129153..24180196)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24122834-24123832 Neighboring gene matrix metallopeptidase 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24134505-24135005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24145605-24146105 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24158117-24158618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24158619-24159120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24166870-24167403 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24167404-24167938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24168707-24169427 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24181116-24181418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24184397-24184954 Neighboring gene skeletal muscle cis-regulatory module in DERL3 and SLC2A11 intergenic region Neighboring gene derlin 3 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:24189965-24190722 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24190723-24191478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24191479-24192234 Neighboring gene solute carrier family 2 member 11 Neighboring gene RNA, 7SL, cytoplasmic 268, pseudogene Neighboring gene Sharpr-MPRA regulatory region 10281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:24236245-24237052 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24237053-24237860 Neighboring gene MIF antisense RNA 1 Neighboring gene macrophage migration inhibitory factor

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-04-22)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-04-22)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

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

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 NL4-3 replication is restricted by SMARCB1 as enhanced replication was discovered when SMARCB1 is deleted through CRISPR/Cas9 genome editing in primary CD4+ T cells PubMed

    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 HIV-1 Gag/Gag-Pol is stabilized for particle release by endogenous SMARCB1 (INI1)-SAP18 interaction PubMed
    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to RNA polymerase I core promoter sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables Tat protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    contributes_to nucleosomal DNA binding HDA PubMed 
    enables p53 binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transcription coactivator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA integration TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in RNA polymerase I preinitiation complex assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in blastocyst hatching IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling HDA PubMed 
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in hepatocyte differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nucleosome disassembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation by host of viral transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of T cell differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of cell differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of double-strand break repair NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of glucose mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of myoblast differentiation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of G0 to G1 transition NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of G1/S transition of mitotic cell cycle NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of mitotic metaphase/anaphase transition NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of nucleotide-excision repair NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within single stranded viral RNA replication via double stranded DNA intermediate IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in transcription initiation-coupled chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of RSC-type complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of SWI/SNF complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in XY body IEA
    Inferred from Electronic Annotation
    more info
     
    part_of bBAF complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of brahma complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of brahma complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of chromatin HDA PubMed 
    part_of chromatin NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    located_in germ cell nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in kinetochore NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of nBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of nBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of nBAF complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of npBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of npBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of npBAF complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nuclear chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nuclear matrix NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex HDA PubMed 

    General protein information

    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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001007468.3NP_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, AP000350, HY013730, R37717
      Consensus CDS
      CCDS46671.1
      UniProtKB/TrEMBL
      Q9H836
      Related
      ENSP00000383984.3, ENST00000407422.8
      Conserved Domains (2) summary
      pfam04855
      Location:172354
      SNF5; SNF5 / SMARCB1 / INI1
      cd21086
      Location:998
      WH_NTD_SMARCB1; N-terminal winged helix DNA-binding domain found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and similar proteins
    2. NM_001317946.2NP_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, AP000350, CB161660, R37717
      Consensus CDS
      CCDS82699.1
      UniProtKB/TrEMBL
      G5E975, Q9H836
      Related
      ENSP00000340883.6, ENST00000344921.11
      Conserved Domains (1) summary
      pfam04855
      Location:190372
      SNF5; SNF5 / SMARCB1 / INI1
    3. NM_001362877.2NP_001349806.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame donor splice sites at an internal coding exon compared to variant 1. The resulting isoform (d) is longer than isoform a.
      Source sequence(s)
      AP000349, AP000350, R37717
      UniProtKB/TrEMBL
      Q9H836
      Conserved Domains (1) summary
      pfam04855
      Location:199381
      SNF5; SNF5 / SMARCB1 / INI1
    4. NM_003073.5NP_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, AP000350, HY013730, R37717
      Consensus CDS
      CCDS13817.1
      UniProtKB/Swiss-Prot
      O75784, O95474, Q12824, Q17S11, Q38GA1, Q76N08, Q9UBH2
      UniProtKB/TrEMBL
      Q9H836
      Related
      ENSP00000494049.2, ENST00000644036.2
      Conserved Domains (2) summary
      pfam04855
      Location:181363
      SNF5; SNF5 / SMARCB1 / INI1
      cd21086
      Location:9107
      WH_NTD_SMARCB1; N-terminal winged helix DNA-binding domain found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and similar proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      23786966..23838009
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187633.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      23328..74371
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      24234168..24285193
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)