SMARCB1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCB1provided by HGNC
Official Full Name: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1provided by HGNC
Primary source: HGNC:HGNC:11103
See related: Ensembl:ENSG00000099956 MIM:601607; AllianceGenome:HGNC:11103
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: RDT; CSS3; INI1; SNF5; Snr1; BAF47; INI-1; MRD15; RTPS1; Sfh1p; hSNFS; SNF5L1; SWNTS1; PPP1R144
Summary: The protein encoded by this gene is part of a complex that relieves repressive chromatin structures, allowing the transcriptional machinery to access its targets more effectively. The encoded nuclear protein may also bind to and enhance the DNA joining activity of HIV-1 integrase. This gene has been found to be a tumor suppressor, and mutations in it have been associated with malignant rhabdoid tumors. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]
Expression: Ubiquitous expression in testis (RPKM 42.3), ovary (RPKM 34.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q11.23; 22q11

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (23786966..23838009)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (24234168..24285193)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (24129153..24180196)

Chromosome 22 - NC_000022.11 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?

The IL6/JAK/STAT3 signaling axis is a therapeutic vulnerability in SMARCB1-deficient bladder cancer.
Title: The IL6/JAK/STAT3 signaling axis is a therapeutic vulnerability in SMARCB1-deficient bladder cancer.
SMARCB1 (INI1)-deficient sinonasal carcinoma manifesting as oral lesions: A report of two cases.
Title: SMARCB1 (INI1)-deficient sinonasal carcinoma manifesting as oral lesions: A report of two cases.
SMARCB1/INI1-deficient epithelioid and myxoid neoplasms in paratesticular region: Expanding the clinicopathologic and molecular spectrum.
Title: SMARCB1/INI1-deficient epithelioid and myxoid neoplasms in paratesticular region: Expanding the clinicopathologic and molecular spectrum.
Constitutional balanced translocations involving SMARCB1: A rare cause of rhabdoid tumor predisposition syndrome.
Title: Constitutional balanced translocations involving SMARCB1: A rare cause of rhabdoid tumor predisposition syndrome.
SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors.
Title: SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors.
Recent insights into the SWI/SNF complex and the molecular mechanism of hSNF5 deficiency in rhabdoid tumors.
Title: Recent insights into the SWI/SNF complex and the molecular mechanism of hSNF5 deficiency in rhabdoid tumors.
SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance.
Title: SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance.
SMARCB1 regulates the hypoxic stress response in sickle cell trait.
Title: SMARCB1 regulates the hypoxic stress response in sickle cell trait.
SMARCB1 Loss in Poorly Differentiated Chordomas Drives Tumor Progression.
Title: SMARCB1 Loss in Poorly Differentiated Chordomas Drives Tumor Progression.
SMARCB1 deficient sinonasal carcinoma: An emerging entity with a diagnostic challenge.
Title: SMARCB1 deficient sinonasal carcinoma: An emerging entity with a diagnostic challenge.

Submit: New GeneRIF Correction See all GeneRIFs (288)

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
Intellectual disability, autosomal dominant 15 MedGen: C3553248 OMIM: 614608 GeneReviews: Not available	Compare labs
Rhabdoid tumor predisposition syndrome 1 MedGen: C1836327 OMIM: 609322 GeneReviews: Not available	Compare labs
Schwannomatosis MedGen: C1335929 GeneReviews: LZTR1- and SMARCB1-Related Schwannomatosis	Compare labs
Schwannomatosis 1 MedGen: C4048809 OMIM: 162091 GeneReviews: LZTR1- and SMARCB1-Related Schwannomatosis	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-04-22) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-04-22) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Replication interactions

Interaction	Pubs
HIV-1 NL4-3 replication is restricted by SMARCB1 as enhanced replication was discovered when SMARCB1 is deleted through CRISPR/Cas9 genome editing in primary CD4+ T cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	Interaction of SIV Nef with INI1 enhances proviral DNA integration into the target host chromosomes, while interaction of HIV-1 Nef with INI1 cannot	PubMed
	nef	HIV-1 and SIV Nef proteins directly bind to INI1 in both mammalian and yeast cells	PubMed
Pr55(Gag)	gag	HIV-1 Gag/Gag-Pol is stabilized for particle release by endogenous SMARCB1 (INI1)-SAP18 interaction	PubMed
	gag	INI1/hSNF5 transdominant negative mutant S6 inhibits particle production by blocking accumulation of HIV-1 Gag at the membrane and by causing a defect in Gag processing and incorporation into particles	PubMed
Tat	tat	Most of the components of the SWI2/SNF2 chromatin remodeling complex (BRG1/BRM, BAF250, BAF180, BAF170, BAF155, BAF60a, BAF53A, actin and InI1) except BRM, BAF155 and BAF57, are identified to interact with HIV-1 Tat in Jurkat cell	PubMed
	tat	Integrase interactor 1 (INI1)/hSNF5 binds to HIV-1 Tat and co-activates Tat-mediated transcription; both the repeat (Rpt) 1 and Rpt 2 domains of INI1 are required for efficient co-activation	PubMed
	tat	INI-1 and BRG-1 synergize with the p300 acetyltransferase to activate the HIV promoter; this synergism depends on the acetyltransferase activity of p300 and on HIV-1 Tat amino acids Lys(50) and Lys(51), suggesting a regulation of Tat by these proteins	PubMed
integrase	gag-pol	INI1-interaction defective HIV-1 IN mutants (K71R, K111E, Q137R, D202G, and S147G) are defective for 2LTR circle formation, integration, or normal virion morphology as comparing to WT	PubMed
	gag-pol	The integrase binding domain (amino acids 174-289) of INI1 inhibits the HIV-1 IN-mediated 3' processing reaction and decreases the amount of integration events	PubMed
	gag-pol	Mass spectrometry and Fluorescence Correlation Spectroscopy analyses show a stable complex between HIV-1 IN, viral U5 DNA, LEDGF/p75, and the integrase binding domain (amino acids 174-289) of INI1 with a 4/2/2/2 stoichiometry	PubMed
	gag-pol	The specificity in incorporation of INI1/hSNF5 into HIV-1 virions is directly correlated with its ability to exclusively interact with HIV-1 integrase but not with other retroviral integrases such as HIV-2, SIV, HTLV-1, and MuLV IN	PubMed
	gag-pol	HIV-1 IN and INI1/hSNF5 bind SAP18 and selectively recruit components of Sin3a-HDAC1 complex into HIV-1 virions. HIV-1 virion-associated HDAC1 is required for efficient early post-entry events	PubMed
	gag-pol	INI1 binds to the minor groove of DNA and stimulates IN strand transfer reactions	PubMed
	gag-pol	Active INI1 is a multimer and binds to HIV-1 IN. Ile-263 is specifically required for multimerization of INI1, whereas Ile-264 and Ile-268 are involved in both multimerization and IN binding	PubMed
	gag-pol	HIV-1 Integrase E69G and K71R mutants are impaired for SNF5/Ini1 interaction, and inhibition of SNF5/Ini1 expression by RNA interference increases HIV-1 replication	PubMed
	gag-pol	Inactivation of ySNF5, the yeast homolog of integrase interactor 1 (INI1, hSNF5) abolishes the lethal phenotype induced by the expression of HIV-1 integrase in yeast, suggesting an important role for INI1 in HIV-1 integration	PubMed
	gag-pol	HIV-1 preintegration complexes containing HIV-1 integrase induce the cytoplasmic recruitment of integrase interactor 1 (INI1, hSNF5) and PML and associate with these cellular proteins before migrating to the nucleus	PubMed
	gag-pol	Integrase interactor 1 (INI1, hSNF5) is incorporated into HIV-1 virions, presumably through its interaction with HIV-1 integrase	PubMed
	gag-pol	A cytoplasmically localized fragment of integrase interactor 1 (INI1, hSNF5; amino acids 183-294) potently inhibits HIV-1 particle production and replication	PubMed
	gag-pol	Binding of integrase interactor 1 (INI1, hSNF5) to HIV-1 integrase is mediated by amino acids 183-243 of INI1 and the central domain of integrase (amino acids 48-188)	PubMed
	gag-pol	Integrase interactor 1 (INI1, hSNF5) binds to HIV-1 integrase and stimulates integrase DNA end joining activity	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-33862 (e-PCR)
- UniSTS:55853

NoName (e-PCR)
- UniSTS:489010

RH80678 (e-PCR)
- UniSTS:86672

RH80266 (e-PCR)
- UniSTS:88214

A006E25 (e-PCR)
- UniSTS:69588

G20745 (e-PCR)
- UniSTS:69589

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to RNA polymerase I core promoter sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables Tat protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
contributes_to nucleosomal DNA binding	HDA more info	PubMed
enables p53 binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coactivator activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA integration	TAS Traceable Author Statement more info	PubMed
involved_in RNA polymerase I preinitiation complex assembly	IEA Inferred from Electronic Annotation more info
involved_in blastocyst hatching	IEA Inferred from Electronic Annotation more info
involved_in cell cycle	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	HDA more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor 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 hepatocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell population proliferation	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 by host of viral transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-binding transcription factor activity	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 glucose mediated signaling pathway	IDA Inferred from Direct Assay 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	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription of nucleolar large rRNA by RNA polymerase I	IMP Inferred from Mutant Phenotype 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
acts_upstream_of_or_within single stranded viral RNA replication via double stranded DNA intermediate	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription initiation-coupled chromatin remodeling	IMP Inferred from Mutant Phenotype 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	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 bBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of brahma complex	IBA Inferred from Biological aspect of Ancestor 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 fibrillar center	IDA Inferred from Direct Assay more info
located_in germ cell nucleus	IEA Inferred from Electronic Annotation more info
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	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 chromosome	IEA Inferred from Electronic Annotation more info
located_in nuclear matrix	NAS Non-traceable Author Statement more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor 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-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

Names: BRG1-associated factor 47; SNF5 homolog; SWI/SNF-related matrix-associated protein; hSNF5; integrase interactor 1 protein; malignant rhabdoid tumor suppressor; protein phosphatase 1, regulatory subunit 144; sucrose nonfermenting, yeast, homolog-like 1

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_009303.1 RefSeqGene

Range

5001..52556

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_520

mRNA and Protein(s)

NM_001007468.3 → NP_001007469.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform b

See identical proteins and their annotated locations for NP_001007469.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame donor splice site in the 5' coding region compared to variant 1. The resulting isoform (b) has the same N- and C-termini but lacks a 9 aa protein segment compared to isoform a.

Source sequence(s)

AJ011738, AP000350, HY013730, R37717

Consensus CDS

CCDS46671.1

UniProtKB/TrEMBL

Q9H836

Related

ENSP00000383984.3, ENST00000407422.8

Conserved Domains (2) summary

pfam04855
Location:172 → 354

SNF5; SNF5 / SMARCB1 / INI1

cd21086
Location:9 → 98

WH_NTD_SMARCB1; N-terminal winged helix DNA-binding domain found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and similar proteins
NM_001317946.2 → NP_001304875.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses alternate in-frame donor splice sites at two internal coding exons compared to variant 1. The resulting isoform (c) is longer than isoform a.

Source sequence(s)

AK024025, AP000350, CB161660, R37717

Consensus CDS

CCDS82699.1

UniProtKB/TrEMBL

G5E975, Q9H836

Related

ENSP00000340883.6, ENST00000344921.11

Conserved Domains (1) summary

pfam04855
Location:190 → 372

SNF5; SNF5 / SMARCB1 / INI1
NM_001362877.2 → NP_001349806.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate in-frame donor splice sites at an internal coding exon compared to variant 1. The resulting isoform (d) is longer than isoform a.

Source sequence(s)

AP000349, AP000350, R37717

UniProtKB/TrEMBL

Q9H836

Conserved Domains (1) summary

pfam04855
Location:199 → 381

SNF5; SNF5 / SMARCB1 / INI1
NM_003073.5 → NP_003064.2 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform a

See identical proteins and their annotated locations for NP_003064.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform a.

Source sequence(s)

AJ011737, AP000350, HY013730, R37717

Consensus CDS

CCDS13817.1

UniProtKB/Swiss-Prot

O75784, O95474, Q12824, Q17S11, Q38GA1, Q76N08, Q9UBH2

UniProtKB/TrEMBL

Q9H836

Related

ENSP00000494049.2, ENST00000644036.2

Conserved Domains (2) summary

pfam04855
Location:181 → 363

SNF5; SNF5 / SMARCB1 / INI1

cd21086
Location:9 → 107

WH_NTD_SMARCB1; N-terminal winged helix DNA-binding domain found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and similar proteins