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    SMARCD2 SWI/SNF related BAF chromatin remodeling complex subunit D2 [ Homo sapiens (human) ]

    Gene ID: 6603, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SMARCD2provided by HGNC
    Official Full Name
    SWI/SNF related BAF chromatin remodeling complex subunit D2provided by HGNC
    Primary source
    HGNC:HGNC:11107
    See related
    Ensembl:ENSG00000108604 MIM:601736; AllianceGenome:HGNC:11107
    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
    SGD2; Rsc6p; BAF60B; CRACD2; PRO2451
    Summary
    The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which 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 and has sequence similarity to the yeast Swp73 protein. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in skin (RPKM 24.5), esophagus (RPKM 18.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMARCD2 in Genome Data Viewer
    Location:
    17q23.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (63832081..63842685, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64702930..64713532, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (61909441..61920045, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61850832-61851416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8831 Neighboring gene DEAD-box helicase 42 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:61897185-61898384 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:61904136-61905335 Neighboring gene FtsJ RNA 2'-O-methyltransferase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12563 Neighboring gene proteasome 26S subunit, ATPase 5 Neighboring gene Sharpr-MPRA regulatory region 8123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8833 Neighboring gene CRISPRi-validated cis-regulatory element chr17.4273 Neighboring gene Sharpr-MPRA regulatory region 5702 Neighboring gene testicular cell adhesion molecule 1, pseudogene Neighboring gene chorionic somatomammotropin hormone 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Evidence for evolutionary conservation of a physical linkage between the human BAF60b, a subunit of SWI/SNF complex, and thyroid hormone receptor interacting protein-1 genes on chromosome 17. Surabhi RM, et al. Genome, 1999 Jun. PMID 10382302
    2. Defective neutrophil development and specific granule deficiency caused by a homozygous splice-site mutation in SMARCD2. Schim van der Loeff I, et al. J Allergy Clin Immunol, 2021 Jun. PMID 33279574, Free PMC Article
    3. Novel Frameshift Autosomal Recessive Loss-of-Function Mutation in SMARCD2 Encoding a Chromatin Remodeling Factor Mediates Granulopoiesis. Yucel E, et al. J Clin Immunol, 2021 Jan. PMID 33025377
    4. SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism. Priam P, et al. Nat Genet, 2017 May. PMID 28369034
    5. The SWI/SNF protein BAF60b is ubiquitinated through a signalling process involving Rac GTPase and the RING finger protein Unkempt. Lorès P, et al. FEBS J, 2010 Mar. PMID 20148946

    See all (121) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel Frameshift Autosomal Recessive Loss-of-Function Mutation in SMARCD2 Encoding a Chromatin Remodeling Factor Mediates Granulopoiesis.
      Title: Novel Frameshift Autosomal Recessive Loss-of-Function Mutation in SMARCD2 Encoding a Chromatin Remodeling Factor Mediates Granulopoiesis.
    2. Defective neutrophil development and specific granule deficiency caused by a homozygous splice-site mutation in SMARCD2.
      Title: Defective neutrophil development and specific granule deficiency caused by a homozygous splice-site mutation in SMARCD2.
    3. Defective expression of SMARCD2 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily D, member 2) leads to transcriptional and chromatin changes in acute myeloid leukemia (AML) promyelocytic cells, suggesting SMARCD2 is a key factor controlling myelopoiesis and is a potential tumor suppressor in leukemia.
      Title: Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes.
    4. Data show that both CEBPE and SMARCD2 loss-of-function mutations identified in patients with neutrophil-specific granule deficiency (SGD) abolish the interaction with SWI/SNF and secondary granule gene expression, thus providing a molecular basis for this disease.
      Title: SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism.
    5. the role of SMARCA4 and the two SWI/SNF subunits SMARCD2/BAF60B and DPF2/BAF45D in leukaemia, was investigated.
      Title: SWI/SNF Subunits SMARCA4, SMARCD2 and DPF2 Collaborate in MLL-Rearranged Leukaemia Maintenance.
    6. the Rac- and Unkempt-dependent process leading to BAF60b ubiquitination takes place in the nuclear compartment
      Title: The SWI/SNF protein BAF60b is ubiquitinated through a signalling process involving Rac GTPase and the RING finger protein Unkempt.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Specific granule deficiency 2
    MedGen: C4479548 OMIM: 617475 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to nucleosomal DNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling HDA PubMed 
    involved_in chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in nucleosome disassembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 myoblast differentiation NAS
    Non-traceable Author Statement
    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 
    Component Evidence Code Pubs
    part_of RSC-type complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of SWI/SNF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 
    part_of bBAF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of brahma complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in chromatin HDA PubMed 
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in kinetochore NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nuclear matrix NAS
    Non-traceable Author Statement
    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
    		  
    part_of protein-containing complex HDA PubMed 

    General protein information

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    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2
    Names
    60 kDa BRG-1/Brm-associated factor subunit B
    BRG1-associated factor 60B
    SWI/SNF complex 60 kDa subunit B
    SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2
    Swp73-like protein
    chromatin remodeling complex BAF60B subunit
    mammalian chromatin remodeling complex BRG1-associated factor 60B

    NCBI Reference Sequences (RefSeq)

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    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_053004.1 RefSeqGene

      Range
      5307..15911
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001098426.2 → NP_001091896.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 1

      See identical proteins and their annotated locations for NP_001091896.1

      Status: REVIEWED

      Source sequence(s)
      AC015651
      Consensus CDS
      CCDS45756.1
      UniProtKB/Swiss-Prot
      A5PLL5, A6NNQ7, B4DV56, B4E1R6, Q7L2I6, Q92925, Q9UHZ1
      UniProtKB/TrEMBL
      A0A8V8TLC9
      Related
      ENSP00000392617.2, ENST00000448276.7
      Conserved Domains (2) summary
      PHA03201
      Location:61 → 148
      PHA03201; uracil DNA glycosylase; Provisional
      cd17675
      Location:307 → 386
      SWIB_BAF60B; SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins

    2. NM_001330439.1 → NP_001317368.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AK307944, AW375602, BQ670607
      Consensus CDS
      CCDS82187.1
      UniProtKB/TrEMBL
      A0A8V8TLC9, J3KMX2
      Related
      ENSP00000225742.9, ENST00000225742.13
      Conserved Domains (1) summary
      cd17675
      Location:232 → 311
      SWIB_BAF60B; SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins

    3. NM_001330440.2 → NP_001317369.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AK303951, AW375602, BQ670607
      Consensus CDS
      CCDS82188.1
      UniProtKB/TrEMBL
      A0A8V8TLC9
      Related
      ENSP00000318451.10, ENST00000323347.14
      Conserved Domains (2) summary
      PHA03201
      Location:10 → 100
      PHA03201; uracil DNA glycosylase; Provisional
      cd17675
      Location:259 → 338
      SWIB_BAF60B; SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      63832081..63842685 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      64702930..64713532 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_003077.3: Suppressed sequence

      Description
      NM_003077.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which aligns with non-consensus splice sites.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92925.3 GenPept UniProtKB/Swiss-Prot:Q92925

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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