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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 12-May-2019

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
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]
Expression
Ubiquitous expression in testis (RPKM 42.3), ovary (RPKM 34.2) and 25 other tissues See more
Orthologs

Genomic context

See SMARCB1 in Genome Data Viewer
Location:
22q11.23; 22q11
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 22 NC_000022.11 (23786931..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 uncharacterized LOC107985577 Neighboring gene matrix metallopeptidase 11 Neighboring gene skeletal muscle cis-regulatory module in DERL3 and SLC2A11 intergenic region Neighboring gene derlin 3 Neighboring gene solute carrier family 2 member 11 Neighboring gene RNA, 7SL, cytoplasmic 268, pseudogene

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 FunctionsWhat's a GeneRIF?

Phenotypes

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

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 BioSystems

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
ATP-dependent chromatin remodeling HDA PubMed 
DNA integration TAS
Traceable Author Statement
more info
PubMed 
RNA polymerase I preinitiation complex assembly IEA
Inferred from Electronic Annotation
more info
 
cell cycle IEA
Inferred from Electronic Annotation
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 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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 DNA-binding transcription factor activity IDA
Inferred from Direct Assay
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 transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I 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 by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II 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 
Component Evidence Code Pubs
SWI/SNF complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SWI/SNF complex IDA
Inferred from Direct Assay
more info
PubMed 
brahma complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
fibrillar center IDA
Inferred from Direct Assay
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nBAF complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
npBAF complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
npBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear chromatin HDA 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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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)

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
    ENSP00000383984.3, ENST00000407422.8
    Conserved Domains (1) summary
    pfam04855
    Location:172354
    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
    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_001362877.1NP_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
    Conserved Domains (1) summary
    pfam04855
    Location:199381
    SNF5; SNF5 / SMARCB1 / INI1
  4. 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
    ENSP00000494049.1, ENST00000644036.1
    Conserved Domains (1) summary
    pfam04855
    Location:181363
    SNF5; SNF5 / SMARCB1 / INI1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p12 Primary Assembly

    Range
    23786931..23834518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011530345.2XP_011528647.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform X1

    Conserved Domains (1) summary
    pfam04855
    Location:199381
    SNF5; SNF5 / SMARCB1 / INI1

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NT_187633.1 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    23293..70880
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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