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    SMARCA2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 [ Homo sapiens (human) ]

    Gene ID: 6595, updated on 23-Nov-2017
    Official Symbol
    SMARCA2provided by HGNC
    Official Full Name
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2provided by HGNC
    Primary source
    HGNC:HGNC:11098
    See related
    Ensembl:ENSG00000080503 MIM:600014; Vega:OTTHUMG00000019445
    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
    BRM; SNF2; SWI2; hBRM; NCBRS; Sth1p; BAF190; SNF2L2; SNF2LA; hSNF2a
    Summary
    The protein encoded by this gene is a member of the SWI/SNF family of proteins and is highly similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, which contains a trinucleotide repeat (CAG) length polymorphism. [provided by RefSeq, Jan 2014]
    Expression
    Ubiquitous expression in ovary (RPKM 42.5), testis (RPKM 29.4) and 25 other tissues See more
    Orthologs
    Location:
    9p24.3
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 9 NC_000009.12 (2015219..2193624)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (2015342..2193624)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375951 Neighboring gene uncharacterized LOC105375953 Neighboring gene uncharacterized LOC105375952 Neighboring gene uncharacterized LOC107987043 Neighboring gene RNA, U2 small nuclear 25, pseudogene Neighboring gene RNA, 7SL, cytoplasmic 592, pseudogene Neighboring gene uncharacterized LOC105375955

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Nicolaides-Baraitser syndrome
    MedGen: C1303073 OMIM: 601358 GeneReviews: Nicolaides-Baraitser Syndrome
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated (2013-03-27)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated (2013-03-27)

    ClinGen Genome Curation Page

    NHGRI GWAS Catalog

    Description
    A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients.
    NHGRI GWA Catalog
    Common variants at 1p36 are associated with superior frontal gyrus volume.
    NHGRI GWA Catalog
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    NHGRI GWA Catalog
    Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Brm-type SWI/SNF chromatin remodeling complex is required for the occasional transcriptional elongation of the HIV-1 provirus in the absence of Tat and for the reactivation of proviral expression from HIV-1 latently infected cells PubMed
    tat HIV-1 Tat interacts directly with BRM, a DNA-dependent ATPase subunit of the SWI/SNF chromatin-remodeling complex, to activate the HIV-1 LTR, and this interaction is regulated by Tat lysine 50 acetylation PubMed
    retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2) at amino acid residues 616-617 by the HIV-1 protease PubMed

    Go to the HIV-1, Human Interaction Database

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ36757, MGC74511

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-dependent ATPase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    RNA polymerase II transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    helicase activity IEA
    Inferred from Electronic Annotation
    more info
     
    histone binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription coactivator activity TAS
    Traceable Author Statement
    more info
    PubMed 
    transcription regulatory region DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intermediate filament cytoskeleton IDA
    Inferred from Direct Assay
    more info
     
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    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 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    probable global transcription activator SNF2L2
    Names
    ATP-dependent helicase SMARCA2
    BAF190B
    BRG1-associated factor 190B
    SNF2-alpha
    SNF2/SWI2-like protein 2
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a2
    brahma homolog
    global transcription activator homologous sequence
    protein brahma homolog
    sucrose nonfermenting 2-like protein 2

    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_032162.2 RefSeqGene

      Range
      39930..218335
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001289396.1NP_001276325.1  probable global transcription activator SNF2L2 isoform a

      See identical proteins and their annotated locations for NP_001276325.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same protein (isoform a).
      Source sequence(s)
      AK094076, AK299683, AL359076, BC066596, BC068252, X72889
      Consensus CDS
      CCDS34977.1
      UniProtKB/Swiss-Prot
      P51531
      UniProtKB/TrEMBL
      B4DSC8, Q8N9Q1
      Related
      ENSP00000371638.1, OTTHUMP00000020970, ENST00000382203.5, OTTHUMT00000051505
      Conserved Domains (10) summary
      cd05516
      Location:13821506
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      smart00592
      Location:590632
      BRK; domain in transcription and CHROMO domain helicases
      smart00573
      Location:436508
      HSA; domain in helicases and associated with SANT domains
      cd00046
      Location:744883
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam08430
      Location:40174
      Forkhead_N; Forkhead N-terminal region
      pfam00176
      Location:7271022
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10491164
      Helicase_C; Helicase conserved C-terminal domain
      pfam08880
      Location:173207
      QLQ; QLQ
      pfam14619
      Location:12591326
      SnAC; Snf2-ATP coupling, chromatin remodelling complex
      cl02556
      Location:13331419
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    2. NM_001289397.1NP_001276326.1  probable global transcription activator SNF2L2 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded protein (isoform c) is shorter, compared to isoform a.
      Source sequence(s)
      BC068252, CA313181, D26155
      Consensus CDS
      CCDS83338.1
      UniProtKB/Swiss-Prot
      P51531
      UniProtKB/TrEMBL
      F6VDE0
      Related
      ENSP00000392081.2, OTTHUMP00000020974, ENST00000450198.6, OTTHUMT00000051510
      Conserved Domains (10) summary
      cd05516
      Location:13241430
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      smart00592
      Location:590632
      BRK; domain in transcription and CHROMO domain helicases
      smart00573
      Location:436508
      HSA; domain in helicases and associated with SANT domains
      cd00046
      Location:744872
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam08430
      Location:40174
      Forkhead_N; Forkhead N-terminal region
      pfam00176
      Location:727964
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:9911106
      Helicase_C; Helicase conserved C-terminal domain
      pfam08880
      Location:173207
      QLQ; QLQ
      pfam14619
      Location:12011268
      SnAC; Snf2-ATP coupling, chromatin remodelling complex
      cl02556
      Location:12751337
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    3. NM_001289398.1NP_001276327.1  probable global transcription activator SNF2L2 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded protein (isoform d) has a shorter and distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AL138755, BI758293, CA313181, CD107405, CD513892, DA084762, DA823500
      Consensus CDS
      CCDS75807.1
      UniProtKB/TrEMBL
      F6T8Q0
      Related
      ENSP00000324770.6, OTTHUMP00000281409, ENST00000324954.10, OTTHUMT00000488360
      Conserved Domains (2) summary
      cd05516
      Location:58164
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      cl02556
      Location:971
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    4. NM_001289399.1NP_001276328.1  probable global transcription activator SNF2L2 isoform e precursor

      See identical proteins and their annotated locations for NP_001276328.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded protein (isoform e) has a shorter and distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AK298045, CA313181
      Consensus CDS
      CCDS83339.1
      UniProtKB/TrEMBL
      B4DNT1
      Related
      ENSP00000371620.2, OTTHUMP00000281412, ENST00000382185.6, OTTHUMT00000488367
      Conserved Domains (2) summary
      cd05516
      Location:86192
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      cl02556
      Location:3799
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    5. NM_001289400.1NP_001276329.1  probable global transcription activator SNF2L2 isoform f precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded protein (isoform f) has a shorter and distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AK094076, AK298045, CA313181, CD702931
      Consensus CDS
      CCDS75808.1
      UniProtKB/TrEMBL
      B1ALF6, B4DNT1, Q8N9Q1
      Related
      ENSP00000305411.3, OTTHUMP00000020968, ENST00000302401.8, OTTHUMT00000051503
      Conserved Domains (2) summary
      cd05516
      Location:88194
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      cl02556
      Location:39101
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    6. NM_003070.4NP_003061.3  probable global transcription activator SNF2L2 isoform a

      See identical proteins and their annotated locations for NP_003061.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 3 encode the same protein (isoform a).
      Source sequence(s)
      AK094076, AL359076, AL558829, BC040029, BC066596, BC068252, X72889
      Consensus CDS
      CCDS34977.1
      UniProtKB/Swiss-Prot
      P51531
      UniProtKB/TrEMBL
      Q56A76, Q8N9Q1
      Related
      ENSP00000265773.5, OTTHUMP00000281406, ENST00000349721.7, OTTHUMT00000488355
      Conserved Domains (10) summary
      cd05516
      Location:13821506
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      smart00592
      Location:590632
      BRK; domain in transcription and CHROMO domain helicases
      smart00573
      Location:436508
      HSA; domain in helicases and associated with SANT domains
      cd00046
      Location:744883
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam08430
      Location:40174
      Forkhead_N; Forkhead N-terminal region
      pfam00176
      Location:7271022
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10491164
      Helicase_C; Helicase conserved C-terminal domain
      pfam08880
      Location:173207
      QLQ; QLQ
      pfam14619
      Location:12591326
      SnAC; Snf2-ATP coupling, chromatin remodelling complex
      cl02556
      Location:13331419
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.
    7. NM_139045.3NP_620614.2  probable global transcription activator SNF2L2 isoform b

      See identical proteins and their annotated locations for NP_620614.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1, resulting in a shorter protein (isoform a).
      Source sequence(s)
      AK094076, AL359076, BC040029, BC066596, BC068252, X72889
      Consensus CDS
      CCDS34978.1
      UniProtKB/Swiss-Prot
      P51531
      UniProtKB/TrEMBL
      Q56A76, Q8N9Q1
      Related
      ENSP00000349788.2, OTTHUMP00000281407, ENST00000357248.8, OTTHUMT00000488357
      Conserved Domains (10) summary
      cd05516
      Location:13821488
      Bromo_SNF2L2; Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone ...
      smart00592
      Location:590632
      BRK; domain in transcription and CHROMO domain helicases
      smart00573
      Location:436508
      HSA; domain in helicases and associated with SANT domains
      cd00046
      Location:744883
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam08430
      Location:40174
      Forkhead_N; Forkhead N-terminal region
      pfam00176
      Location:7271022
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:10491164
      Helicase_C; Helicase conserved C-terminal domain
      pfam08880
      Location:173207
      QLQ; QLQ
      pfam14619
      Location:12591326
      SnAC; Snf2-ATP coupling, chromatin remodelling complex
      cl02556
      Location:13331395
      Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p7 Primary Assembly

      Range
      2015219..2193624
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      2015344..2193714
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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