SMARCC1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCC1provided by HGNC
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1provided 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: mouse all
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Genomic context

Location:: 3p21.31

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (47585269..47781893, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (47604348..47801082, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (47626759..47823383, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
First reports of fetal SMARCC1 related hydrocephalus.
Title: First reports of fetal SMARCC1 related hydrocephalus.
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.
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.
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.
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.
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.
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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-53111 (e-PCR)
- UniSTS:63260

SHGC-30198 (e-PCR)
- UniSTS:80452

WI-11317 (e-PCR)
- UniSTS:58444

SHGC-146379 (e-PCR)
- UniSTS:175186

SHGC-146380 (e-PCR)
- UniSTS:175187

WI-17963 (e-PCR)
- UniSTS:55896

SHGC-76924 (e-PCR)
- UniSTS:64361

HSC11A082 (e-PCR)
- UniSTS:2155

G22291 (e-PCR)
- UniSTS:45171

D3S3441 (e-PCR)
- UniSTS:22657

D3S2944E (e-PCR)
- UniSTS:150928

G42248 (e-PCR)
- UniSTS:93351

SMARCC1_2308 (e-PCR)
- UniSTS:281021

RH91777 (e-PCR)
- UniSTS:85983

G20574 (e-PCR)
- UniSTS:1787

A005X26 (e-PCR)
- UniSTS:1788

D3S3284 (e-PCR)
- UniSTS:40957

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 more info	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 more info	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
part_of chromatin	HDA more info	PubMed
part_of 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 more info	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; 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)

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