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SMARCC2 SWI/SNF related BAF chromatin remodeling complex subunit C2 [ Homo sapiens (human) ]

Gene ID: 6601, updated on 27-Nov-2024

Summary

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Official Symbol
SMARCC2provided by HGNC
Official Full Name
SWI/SNF related BAF chromatin remodeling complex subunit C2provided by HGNC
Primary source
HGNC:HGNC:11105
See related
Ensembl:ENSG00000139613 MIM:601734; AllianceGenome:HGNC:11105
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
CSS8; Rsc8; BAF170; CRACC2
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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 28.0), ovary (RPKM 22.4) and 25 other tissues See more
Orthologs
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Genomic context

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See SMARCC2 in Genome Data Viewer
Location:
12q13.2
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (56162359..56189483, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (56129971..56157086, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (56556143..56583267, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902943 Neighboring gene uncharacterized LOC124902942 Neighboring gene MYL6B antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6477 Neighboring gene myosin light chain 6B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4546 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6479 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56554412-56555034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56555035-56555655 Neighboring gene myosin light chain 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4548 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6480 Neighboring gene uncharacterized LOC107984468 Neighboring gene tRNA-Ser (anticodon CGA) 4-1

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
  • 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. SMARCC2 combined with c‑Myc inhibits the migration and invasion of glioma cells via modulation of the Wnt/β‑catenin signaling pathway. Li C, et al. Mol Med Rep, 2021 Aug. PMID 34080022, Free PMC Article
  2. Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals. Bosch E, et al. Genet Med, 2023 Nov. PMID 37551667
  3. The functional landscape of the human phosphoproteome. Ochoa D, et al. Nat Biotechnol, 2020 Mar. PMID 31819260, Free PMC Article
  4. Frameshift mutations of a chromatin-remodeling gene SMARCC2 in gastric and colorectal cancers with microsatellite instability. Kim SS, et al. APMIS, 2013 Feb. PMID 23030715
  5. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Machol K, et al. Am J Hum Genet, 2019 Jan 3. PMID 30580808, Free PMC Article

See all (232) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals.
    Title: Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals.
  2. FBXO28 promotes proliferation, invasion, and metastasis of pancreatic cancer cells through regulation of SMARCC2 ubiquitination.
    Title: FBXO28 promotes proliferation, invasion, and metastasis of pancreatic cancer cells through regulation of SMARCC2 ubiquitination.
  3. SMARCC2 mediates the regulation of DKK1 by the transcription factor EGR1 through chromatin remodeling to reduce the proliferative capacity of glioblastoma.
    Title: SMARCC2 mediates the regulation of DKK1 by the transcription factor EGR1 through chromatin remodeling to reduce the proliferative capacity of glioblastoma.
  4. Further supporting SMARCC2-related neurodevelopmental disorder through exome analysis and reanalysis in two patients.
    Title: Further supporting SMARCC2-related neurodevelopmental disorder through exome analysis and reanalysis in two patients.
  5. SMARCC2 combined with cMyc inhibits the migration and invasion of glioma cells via modulation of the Wnt/betacatenin signaling pathway.
    Title: SMARCC2 combined with c‑Myc inhibits the migration and invasion of glioma cells via modulation of the Wnt/β‑catenin signaling pathway.
  6. Results identified phosphosites in SMARCC2 and provide evidence for its role in neuronal differentiation.
    Title: The functional landscape of the human phosphoproteome.
  7. findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits
    Title: Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay.
  8. our data showed that Swi3 strongly affects haem/oxygen-dependent activation of respiration gene promoters whereas Swi2 affects only the basal, haem-independent activities of these promoters. using computational analysis and RNAi knockdown, we showed that the mammalian Swi3 BAF155 and BAF170 regulate respiration in HeLa cells.
    Title: The Swi3 protein plays a unique role in regulating respiration in eukaryotes.
  9. BAF170 is important for neurogenesis in embryonic olfactory epithelium.
    Title: mSWI/SNF (BAF) Complexes Are Indispensable for the Neurogenesis and Development of Embryonic Olfactory Epithelium.
  10. Identification of frameshift mutations in the SMARCC2 gene in gastric and colorectal cancers with microsatellite instability.
    Title: Frameshift mutations of a chromatin-remodeling gene SMARCC2 in gastric and colorectal cancers with microsatellite instability.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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 8
MedGen: C5193054 OMIM: 618362 GeneReviews: Coffin-Siris Syndrome
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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)

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

Clone Names

  • DKFZp313D0632

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 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 negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
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 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 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 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 
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
  
part_of protein-containing complex HDA PubMed 

General protein information

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Preferred Names
SWI/SNF complex subunit SMARCC2
Names
SWI/SNF complex 170 kDa subunit
SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2
SWI3-like protein
chromatin remodeling complex BAF170 subunit
mammalian chromatin remodeling complex BRG1-associated factor 170

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_047081.1 RefSeqGene

    Range
    5085..32209
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130420.3 → NP_001123892.1  SWI/SNF complex subunit SMARCC2 isoform c

    See identical proteins and their annotated locations for NP_001123892.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate in-frame exon in the central coding region and contains alternate in-frame segment in the 3' coding region, compared to variant 1. The encoded isoform (c), contains a novel internal segment, lacks a segment near the C-terminus, and is shorter than isoform a.
    Source sequence(s)
    AB209006, BM875330, CX165574
    Consensus CDS
    CCDS55835.1
    UniProtKB/TrEMBL
    Q59G16
    Related
    ENSP00000377591.3, ENST00000394023.7
    Conserved Domains (6) summary
    PTZ00121
    Location:721 → 978
    PTZ00121; MAEBL; Provisional
    COG5259
    Location:379 → 739
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    PRK07003
    Location:1006 → 1141
    PRK07003; DNA polymerase III subunit gamma/tau
    pfam16495
    Location:911 → 977
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:7 → 420
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:715 → 779
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

  2. NM_001330288.2 → NP_001317217.1  SWI/SNF complex subunit SMARCC2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate in-frame exon in the central coding region compared to variant 1. The encoded isoform (d), contains the same N- and C-termini, but is longer than isoform a.
    Source sequence(s)
    AK315153, BC009067, BM875330, CX165574, DA768316, HY118539
    Consensus CDS
    CCDS81698.1
    UniProtKB/TrEMBL
    F8VXC8, Q59G16
    Related
    ENSP00000449396.1, ENST00000550164.6
    Conserved Domains (6) summary
    pfam16495
    Location:911 → 977
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:4 → 420
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:715 → 779
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
    cl26464
    Location:999 → 1234
    Atrophin-1; Atrophin-1 family
    cl26511
    Location:721 → 978
    Neuromodulin_N; Gap junction protein N-terminal region
    cl27154
    Location:379 → 739
    SWIRM; SWIRM domain

  3. NM_003075.5 → NP_003066.2  SWI/SNF complex subunit SMARCC2 isoform a

    See identical proteins and their annotated locations for NP_003066.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a.
    Source sequence(s)
    AK315153, BC009067, BM875330, CX165574, HY118539
    Consensus CDS
    CCDS8907.1
    UniProtKB/Swiss-Prot
    F8VTJ5, Q59GV3, Q8TAQ2, Q92923, Q96E12, Q96GY4
    UniProtKB/TrEMBL
    Q59G16
    Related
    ENSP00000267064.4, ENST00000267064.8
    Conserved Domains (6) summary
    PTZ00121
    Location:690 → 947
    PTZ00121; MAEBL; Provisional
    PHA03247
    Location:968 → 1203
    PHA03247; large tegument protein UL36; Provisional
    COG5259
    Location:379 → 708
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam16495
    Location:880 → 946
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:7 → 420
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:684 → 748
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

  4. NM_139067.4 → NP_620706.1  SWI/SNF complex subunit SMARCC2 isoform b

    See identical proteins and their annotated locations for NP_620706.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate in-frame exon in the central coding region and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (b), contains a novel internal segment, lacks a segment near the C-terminus, and is shorter than isoform a.
    Source sequence(s)
    AB209006, BM875330, CX165574
    Consensus CDS
    CCDS8908.1
    UniProtKB/TrEMBL
    Q59G16
    Related
    ENSP00000302919.4, ENST00000347471.8
    Conserved Domains (5) summary
    PTZ00121
    Location:721 → 978
    PTZ00121; MAEBL; Provisional
    COG5259
    Location:379 → 739
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam16495
    Location:911 → 977
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:7 → 420
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:715 → 779
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    56162359..56189483 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429448.1 → XP_047285404.1  SWI/SNF complex subunit SMARCC2 isoform X8

  2. XM_047429447.1 → XP_047285403.1  SWI/SNF complex subunit SMARCC2 isoform X6

  3. XM_005269103.3 → XP_005269160.1  SWI/SNF complex subunit SMARCC2 isoform X2

    See identical proteins and their annotated locations for XP_005269160.1

    UniProtKB/TrEMBL
    Q59G16
    Conserved Domains (5) summary
    COG5259
    Location:379 → 707
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam04433
    Location:427 → 512
    SWIRM; SWIRM domain
    pfam16495
    Location:879 → 945
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:4 → 420
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:683 → 747
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

  4. XM_017019886.2 → XP_016875375.1  SWI/SNF complex subunit SMARCC2 isoform X7

    UniProtKB/TrEMBL
    Q59G16
    Conserved Domains (5) summary
    PTZ00121
    Location:690 → 947
    PTZ00121; MAEBL; Provisional
    COG5259
    Location:379 → 708
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam16495
    Location:880 → 946
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:7 → 420
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:684 → 748
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

  5. XM_017019885.2 → XP_016875374.1  SWI/SNF complex subunit SMARCC2 isoform X5

    UniProtKB/TrEMBL
    Q59G16

  6. XM_017019884.2 → XP_016875373.1  SWI/SNF complex subunit SMARCC2 isoform X4

    UniProtKB/TrEMBL
    Q59G16

  7. XM_005269104.2 → XP_005269161.1  SWI/SNF complex subunit SMARCC2 isoform X3

    See identical proteins and their annotated locations for XP_005269161.1

    UniProtKB/TrEMBL
    Q59G16
    Conserved Domains (6) summary
    PTZ00121
    Location:720 → 977
    PTZ00121; MAEBL; Provisional
    COG5259
    Location:379 → 738
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    PRK07003
    Location:1005 → 1140
    PRK07003; DNA polymerase III subunit gamma/tau
    pfam16495
    Location:910 → 976
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:7 → 420
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:714 → 778
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

  8. XM_005269102.3 → XP_005269159.1  SWI/SNF complex subunit SMARCC2 isoform X1

    See identical proteins and their annotated locations for XP_005269159.1

    UniProtKB/TrEMBL
    Q59G16
    Conserved Domains (5) summary
    COG5259
    Location:379 → 738
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam04433
    Location:427 → 512
    SWIRM; SWIRM domain
    pfam16495
    Location:910 → 976
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:4 → 420
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:714 → 778
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

  9. XM_047429449.1 → XP_047285405.1  SWI/SNF complex subunit SMARCC2 isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    56129971..56157086 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373046.1 → XP_054229021.1  SWI/SNF complex subunit SMARCC2 isoform X8

  2. XM_054373044.1 → XP_054229019.1  SWI/SNF complex subunit SMARCC2 isoform X6

  3. XM_054373040.1 → XP_054229015.1  SWI/SNF complex subunit SMARCC2 isoform X2

  4. XM_054373045.1 → XP_054229020.1  SWI/SNF complex subunit SMARCC2 isoform X7

  5. XM_054373043.1 → XP_054229018.1  SWI/SNF complex subunit SMARCC2 isoform X5

  6. XM_054373042.1 → XP_054229017.1  SWI/SNF complex subunit SMARCC2 isoform X4

  7. XM_054373041.1 → XP_054229016.1  SWI/SNF complex subunit SMARCC2 isoform X3

  8. XM_054373039.1 → XP_054229014.1  SWI/SNF complex subunit SMARCC2 isoform X1

  9. XM_054373047.1 → XP_054229022.1  SWI/SNF complex subunit SMARCC2 isoform X9

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TAQ2.1 GenPept UniProtKB/Swiss-Prot:Q8TAQ2

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