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SMARCC1 SWI/SNF related BAF chromatin remodeling complex subunit C1 [ Homo sapiens (human) ]

Gene ID: 6599, updated on 2-Nov-2024

Summary

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Official Symbol
SMARCC1provided by HGNC
Official Full Name
SWI/SNF related BAF chromatin remodeling complex subunit C1provided by HGNC
Primary source
HGNC:HGNC:11104
See related
Ensembl:ENSG00000173473 MIM:601732; AllianceGenome:HGNC:11104
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HYC5; Rsc8; SRG3; SWI3; BAF155; CRACC1
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 contains a predicted leucine zipper motif typical of many transcription factors. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 18.4), endometrium (RPKM 15.8) and 25 other tissues See more
Orthologs
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Genomic context

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See SMARCC1 in Genome Data Viewer
Location:
3p21.31
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (47585269..47781893, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (47604348..47801082, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (47626759..47823383, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47613774-47614274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47614275-47614775 Neighboring gene Sharpr-MPRA regulatory region 12920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14310 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14311 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47620980-47621684 Neighboring gene RNA, 7SL, cytoplasmic 870, pseudogene Neighboring gene uncharacterized LOC124906234 Neighboring gene chondroitin sulfate proteoglycan 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:47710070-47710273 Neighboring gene small nucleolar RNA, C/D box 146 Neighboring gene HIGD2A pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19819 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14313 Neighboring gene Sharpr-MPRA regulatory region 56 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14316 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:47844773-47845298 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:47846226-47846422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47859072-47859572 Neighboring gene MPRA-validated peak4635 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47879089-47879907 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47883235-47883741 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:47888661-47888762 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47893749-47894266 Neighboring gene DExH-box helicase 30 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47912431-47912931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19820 Neighboring gene microRNA 1226 Neighboring gene microtubule associated protein 4 Neighboring gene MPRA-validated peak4636 silencer Neighboring gene VPS26B pseudogene 1

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. SMARCC1 expression is upregulated in prostate cancer and positively correlated with tumour recurrence and dedifferentiation. Heebøll S, et al. Histol Histopathol, 2008 Sep. PMID 18581278
  2. 1H, 15N, and 13C resonance assignments and secondary structure of the SWIRM domain of human BAF155, a chromatin remodeling complex component. Moon S, et al. Mol Cells, 2013 Oct. PMID 23996527, Free PMC Article
  3. A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus. Singh AK, et al. Brain, 2024 Apr 4. PMID 38128548,
  4. SWI/SNF subunit BAF155 N-terminus structure informs the impact of cancer-associated mutations and reveals a potential drug binding site. Allen MD, et al. Commun Biol, 2021 May 5. PMID 33953332, Free PMC Article
  5. SMARCC1 is a susceptibility gene for congenital hydrocephalus with an autosomal dominant inheritance mode and incomplete penetrance. Hourvitz N, et al. Prenat Diagn, 2023 Sep. PMID 37639281

See all (276) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus.
    Title: A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus.
  2. RNF138 inhibits late inflammatory gene transcription through degradation of SMARCC1 of the SWI/SNF complex.
    Title: RNF138 inhibits late inflammatory gene transcription through degradation of SMARCC1 of the SWI/SNF complex.
  3. SMARCC1 is a susceptibility gene for congenital hydrocephalus with an autosomal dominant inheritance mode and incomplete penetrance.
    Title: SMARCC1 is a susceptibility gene for congenital hydrocephalus with an autosomal dominant inheritance mode and incomplete penetrance.
  4. First reports of fetal SMARCC1 related hydrocephalus.
    Title: First reports of fetal SMARCC1 related hydrocephalus.
  5. 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.
  6. Multiple interactions of the oncoprotein transcription factor MYC with the SWI/SNF chromatin remodeler.
    Title: Multiple interactions of the oncoprotein transcription factor MYC with the SWI/SNF chromatin remodeler.
  7. SWI/SNF subunit BAF155 N-terminus structure informs the impact of cancer-associated mutations and reveals a potential drug binding site.
    Title: SWI/SNF subunit BAF155 N-terminus structure informs the impact of cancer-associated mutations and reveals a potential drug binding site.
  8. A Coil-to-Helix Transition Serves as a Binding Motif for hSNF5 and BAF155 Interaction.
    Title: A Coil-to-Helix Transition Serves as a Binding Motif for hSNF5 and BAF155 Interaction.
  9. BAF155 plays important roles in ubiquitin-independent degradation of hepatitis B virus X protein
    Title: Chromatin remodelling factor BAF155 protects hepatitis B virus X protein (HBx) from ubiquitin-independent proteasomal degradation.
  10. Study found SMARCC1 as a direct target of miR-202-5p and promoted the growth and metastasis of colorectal carcinoma (CRC) cells. Furthermore, SMARCC1 could reverse the inhibitory effect of miR-202-5p on growth and metastasis of CRC cells.
    Title: MicroRNA-202-5p functions as a tumor suppressor in colorectal carcinoma by directly targeting SMARCC1.
Submit: New GeneRIF Correction See all GeneRIFs (26)

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
Hydrocephalus, congenital, 5, susceptibility to
MedGen: C5830272 OMIM: 620241 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 HIV-1 Tat induces phosphorylation of BRG1 and BAF155 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 histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
Process Evidence Code Pubs
involved_in animal organ morphogenesis IEA
Inferred from Electronic Annotation
more info
  
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 insulin receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
  
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
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 positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in prostate gland development IEA
Inferred from Electronic Annotation
more info
  
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 NAS
Non-traceable Author Statement
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 
located_in XY body IEA
Inferred from Electronic Annotation
more info
  
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 cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in kinetochore NAS
Non-traceable Author Statement
more info
 PubMed 
located_in male germ cell nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of nBAF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of protein-containing complex HDA PubMed 

General protein information

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Preferred Names
SWI/SNF complex subunit SMARCC1
Names
BRG1-associated factor 155
SWI/SNF complex 155 kDa subunit
SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1
chromatin remodeling complex BAF155 subunit
mammalian chromatin remodeling complex BRG1-associated factor 155

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.

mRNA and Protein(s)

  1. NM_003074.4 → NP_003065.3  SWI/SNF complex subunit SMARCC1

    See identical proteins and their annotated locations for NP_003065.3

    Status: VALIDATED

    Source sequence(s)
    AC112512, BC012101, BC040242, BC050564
    Consensus CDS
    CCDS2758.1
    UniProtKB/Swiss-Prot
    Q17RS0, Q6P172, Q8IWH2, Q92922
    UniProtKB/TrEMBL
    Q58EY4
    Related
    ENSP00000254480.5, ENST00000254480.10
    Conserved Domains (5) summary
    COG5259
    Location:444 → 710
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam04433
    Location:452 → 537
    SWIRM; SWIRM domain
    pfam16495
    Location:883 → 954
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:32 → 445
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:706 → 770
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    47585269..47781893 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    47604348..47801082 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92922.3 GenPept UniProtKB/Swiss-Prot:Q92922

Gene LinkOut

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