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SMARCD2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 [ Homo sapiens (human) ]

Gene ID: 6603, updated on 5-Mar-2024

Summary

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Official Symbol
SMARCD2provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2provided 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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (63832081..63842685, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64702930..64713532, complement)
105.20220307 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
  • 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. 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
  2. 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
  3. 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
  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 (112) 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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 
part_of chromatin HDA PubMed 
part_of 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
  
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
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_2023_10

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

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