SMARCC2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCC2provided by HGNC
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2provided 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: mouse all
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Genomic context

Location:: 12q13.2

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (56162359..56189483, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (56129971..56157086, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (56556143..56583267, complement)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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.
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.
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.
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.
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.
Results identified phosphosites in SMARCC2 and provide evidence for its role in neuronal differentiation.
Title: The functional landscape of the human phosphoproteome.
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.
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.
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.
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	Compare labs

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-T64879 (e-PCR)
- UniSTS:71534

A005R19 (e-PCR)
- UniSTS:5496

G32279 (e-PCR)
- UniSTS:116877

G64806 (e-PCR)
- UniSTS:164750

STS-U66616 (e-PCR)
- UniSTS:11710

RH47781 (e-PCR)
- UniSTS:28650

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 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 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
part_of chromatin	HDA more info	PubMed
part_of 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 more info	PubMed

General protein information

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Preferred Names: SWI/SNF complex subunit SMARCC2

Names: SWI/SNF complex 170 kDa subunit; 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

NG_047081.1 RefSeqGene

Range

5085..32209

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

56162359..56189483 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047429448.1 → XP_047285404.1 SWI/SNF complex subunit SMARCC2 isoform X8
XM_047429447.1 → XP_047285403.1 SWI/SNF complex subunit SMARCC2 isoform X6
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
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
XM_017019885.2 → XP_016875374.1 SWI/SNF complex subunit SMARCC2 isoform X5

UniProtKB/TrEMBL

Q59G16
XM_017019884.2 → XP_016875373.1 SWI/SNF complex subunit SMARCC2 isoform X4

UniProtKB/TrEMBL

Q59G16
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
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
XM_047429449.1 → XP_047285405.1 SWI/SNF complex subunit SMARCC2 isoform X9