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SMARCD1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 [ Homo sapiens (human) ]

Gene ID: 6602, updated on 3-Apr-2024

Summary

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Official Symbol
SMARCD1provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1provided by HGNC
Primary source
HGNC:HGNC:11106
See related
Ensembl:ENSG00000066117 MIM:601735; AllianceGenome:HGNC:11106
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
CSS11; Rsc6p; BAF60A; CRACD1
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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 14.1), testis (RPKM 13.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
12q13.12
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (50085342..50100707)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (50048400..50063789)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50479125..50494490)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Rac GTPase activating protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6338 Neighboring gene Sharpr-MPRA regulatory region 11175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50433443-50434198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50434199-50434954 Neighboring gene CRISPRi-validated cis-regulatory element chr12.1559 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:50444767-50445695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4445 Neighboring gene acid sensing ion channel subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6341 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:50474871-50475040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:50477618-50478350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50479817-50480548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6347 Neighboring gene glycerol-3-phosphate dehydrogenase 1 Neighboring gene cytochrome c oxidase assembly factor COX14

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. Expression of SMARCD1 interacts with age in association with asthma control on inhaled corticosteroid therapy. McGeachie MJ, et al. Respir Res, 2020 Jan 28. PMID 31992292, Free PMC Article
  2. microRNA-99a-5p induces cellular senescence in gemcitabine-resistant bladder cancer by targeting SMARCD1. Tamai M, et al. Mol Oncol, 2022 Mar. PMID 35148461, Free PMC Article
  3. Smarcd1 Inhibits the Malignant Phenotypes of Human Glioblastoma Cells via Crosstalk with Notch1. Zhu Y, et al. Mol Neurobiol, 2021 Apr. PMID 33190170, Free PMC Article
  4. NMR spectroscopy uncovers direct interaction between BAF60A and p53. Han J, et al. Biochem Biophys Res Commun, 2021 Jan 1. PMID 33168186
  5. BAF60a Deficiency in Vascular Smooth Muscle Cells Prevents Abdominal Aortic Aneurysm by Reducing Inflammation and Extracellular Matrix Degradation. Chang Z, et al. Arterioscler Thromb Vasc Biol, 2020 Oct. PMID 32787523, Free PMC Article

See all (150) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Myeloid BAF60a deficiency alters metabolic homeostasis and exacerbates atherosclerosis.
    Title: Myeloid BAF60a deficiency alters metabolic homeostasis and exacerbates atherosclerosis.
  2. Integrated analysis reveals SMARCD1 is a potential biomarker and therapeutic target in skin cutaneous melanoma.
    Title: Integrated analysis reveals SMARCD1 is a potential biomarker and therapeutic target in skin cutaneous melanoma.
  3. microRNA-99a-5p induces cellular senescence in gemcitabine-resistant bladder cancer by targeting SMARCD1.
    Title: microRNA-99a-5p induces cellular senescence in gemcitabine-resistant bladder cancer by targeting SMARCD1.
  4. Assembly and interaction of core subunits of BAF complexes and crystal study of the SMARCC1/SMARCE1 binary complex.
    Title: Assembly and interaction of core subunits of BAF complexes and crystal study of the SMARCC1/SMARCE1 binary complex.
  5. Smarcd1 Inhibits the Malignant Phenotypes of Human Glioblastoma Cells via Crosstalk with Notch1.
    Title: Smarcd1 Inhibits the Malignant Phenotypes of Human Glioblastoma Cells via Crosstalk with Notch1.
  6. NMR spectroscopy uncovers direct interaction between BAF60A and p53.
    Title: NMR spectroscopy uncovers direct interaction between BAF60A and p53.
  7. SMARCD1 is a transcriptional target of specific non-hotspot mutant p53 forms.
    Title: SMARCD1 is a transcriptional target of specific non-hotspot mutant p53 forms.
  8. hsa-miR-100-5p, an overexpressed miRNA in human ovarian endometriotic stromal cells, promotes invasion through attenuation of SMARCD1 expression.
    Title: hsa-miR-100-5p, an overexpressed miRNA in human ovarian endometriotic stromal cells, promotes invasion through attenuation of SMARCD1 expression.
  9. BAF60a Deficiency in Vascular Smooth Muscle Cells Prevents Abdominal Aortic Aneurysm by Reducing Inflammation and Extracellular Matrix Degradation.
    Title: BAF60a Deficiency in Vascular Smooth Muscle Cells Prevents Abdominal Aortic Aneurysm by Reducing Inflammation and Extracellular Matrix Degradation.
  10. Expression of SMARCD1 interacts with age in association with asthma control on inhaled corticosteroid therapy.
    Title: Expression of SMARCD1 interacts with age in association with asthma control on inhaled corticosteroid therapy.
Submit: New GeneRIF Correction See all GeneRIFs (19)

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
Coffin-Siris syndrome 11
MedGen: C5241442 OMIM: 618779 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)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat Most of the components of the SWI2/SNF2 chromatin remodeling complex (BRG1/BRM, BAF250, BAF180, BAF170, BAF155, BAF60a, BAF53A, actin and InI) except BRM, BAF155 and BAF57, are identified to interact with HIV-1 Tat in Jurkat cell PubMed

Go to the HIV-1, Human Interaction Database

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
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular adaptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables signaling receptor binding IEA
Inferred from Electronic Annotation
more info
  
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 cellular response to fatty acid IEA
Inferred from Electronic Annotation
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 negative regulation of cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
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 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 cell population proliferation 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 positive regulation of stem cell population maintenance 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 
involved_in transcription initiation-coupled chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of GBAF complex NAS
Non-traceable Author Statement
more info
 PubMed 
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 brahma complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of chromatin NAS
Non-traceable Author Statement
more info
 PubMed 
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 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 ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of npBAF complex 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
  

General protein information

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Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Names
60 kDa BRG-1/Brm-associated factor subunit A
BRG1-associated factor 60A
SWI/SNF complex 60 kDa subunit A
Swp73-like protein
chromatin remodeling complex BAF60A subunit
mammalian chromatin remodeling complex BRG1-associated factor 60A

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_003076.5 → NP_003067.3  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform a

    See identical proteins and their annotated locations for NP_003067.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is the longer transcript and encodes the full-length isoform (a).
    Source sequence(s)
    AA610093, BC009368
    Consensus CDS
    CCDS8797.2
    UniProtKB/Swiss-Prot
    A6NN27, Q92924, Q96GM5, Q9Y635
    Related
    ENSP00000378414.4, ENST00000394963.9
    Conserved Domains (1) summary
    cd17674
    Location:294 → 370
    SWIB_BAF60A; SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins

  2. NM_139071.3 → NP_620710.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform b

    See identical proteins and their annotated locations for NP_620710.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform b), compared to isoform a.
    Source sequence(s)
    AA610093, AC025154, BE905082, CN272379, DA825057, DB010252, N75126
    Consensus CDS
    CCDS8798.2
    UniProtKB/Swiss-Prot
    Q96GM5
    Related
    ENSP00000370924.4, ENST00000381513.8
    Conserved Domains (1) summary
    cd17674
    Location:294 → 370
    SWIB_BAF60A; SWIB domain found in BRG1-associated factor 60A (BAF60A) 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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    50085342..50100707
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005269107.5 → XP_005269164.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X1

    See identical proteins and their annotated locations for XP_005269164.2

    Conserved Domains (1) summary
    cd17674
    Location:253 → 329
    SWIB_BAF60A; SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins

  2. XM_047429450.1 → XP_047285406.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X2

  3. XM_011538695.3 → XP_011536997.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X3

    UniProtKB/TrEMBL
    B4DF50
    Conserved Domains (1) summary
    pfam02084
    Location:39 → 98
    Bindin; Bindin

RNA

  1. XR_944683.3 RNA Sequence

  2. XR_944684.3 RNA Sequence

  3. XR_007063120.1 RNA Sequence

  4. XR_007063118.1 RNA Sequence

  5. XR_007063119.1 RNA Sequence

  6. XR_007063121.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    50048400..50063789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373048.1 → XP_054229023.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X1

  2. XM_054373049.1 → XP_054229024.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X2

  3. XM_054373050.1 → XP_054229025.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 isoform X3

RNA

  1. XR_008488667.1 RNA Sequence

  2. XR_008488668.1 RNA Sequence

  3. XR_008488671.1 RNA Sequence

  4. XR_008488669.1 RNA Sequence

  5. XR_008488670.1 RNA Sequence

  6. XR_008488672.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96GM5.2 GenPept UniProtKB/Swiss-Prot:Q96GM5

Gene LinkOut

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