SMARCA1 SNF2 related chromatin remodeling ATPase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMARCA1provided by HGNC
Official Full Name: SNF2 related chromatin remodeling ATPase 1provided by HGNC
Primary source: HGNC:HGNC:11097
See related: Ensembl:ENSG00000102038 MIM:300012; AllianceGenome:HGNC:11097
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: SWI; ISWI; SWI2; SNF2L; SNF2L1; SNF2LB; SNF2LT; hSNF2L; NURF140
Summary: This gene encodes a member of the SWI/SNF family of proteins. The encoded protein is an ATPase which is expressed in diverse tissues and contributes to the chromatin remodeling complex that is involved in transcription. The protein may also play a role in DNA damage, growth inhibition and apoptosis of cancer cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
Expression: Broad expression in adrenal (RPKM 46.7), testis (RPKM 43.0) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xq25-q26.1

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (129446506..129523490, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (127765288..127842272, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (128580483..128657467, complement)

Chromosome X - NC_000023.11 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 lncRNA MIR99AHG directs alternative splicing of SMARCA1 by PTBP1 to enable invadopodia formation in colorectal cancer cells.
Title: The lncRNA MIR99AHG directs alternative splicing of SMARCA1 by PTBP1 to enable invadopodia formation in colorectal cancer cells.
A pan-cancer bioinformatic analysis of the carcinogenic role of SMARCA1 in human carcinomas.
Title: A pan-cancer bioinformatic analysis of the carcinogenic role of SMARCA1 in human carcinomas.
This is the first report of an interstitial deletion encompassing OCRL and SMARCA1 gene in Lowe syndrome.
Title: Whole-genome sequencing revealed an interstitial deletion encompassing OCRL and SMARCA1 gene in a patient with Lowe syndrome.
High SNF2L expression is associated with gastric cancer growth and invasion.
Title: Circular RNA circ-DONSON facilitates gastric cancer growth and invasion via NURF complex dependent activation of transcription factor SOX4.
Data identified SMARCA1 as an interactive protein of DLEU1 in colorectal cancer to regulate cancer cell proliferation.
Title: LncRNA DLEU1 contributes to colorectal cancer progression via activation of KPNA3.
In one family, four siblings with a psychotic illness and their unaffected mother each carry a novel private missense variant in the SMARCA1 gene on the X chromosome.
Title: Whole-genome sequencing in multiplex families with psychoses reveals mutations in the SHANK2 and SMARCA1 genes segregating with illness.
Depletion of a chromatin remodeler, SMARCA1, in cancer cell lines promoted their growth.
Title: Frequent involvement of chromatin remodeler alterations in gastric field cancerization.
The results suggest that the cAMP-response element consensus sequence in the SNF2L proximal promoter most likely confers constitutive activation and regulation by cAMP in neural cells.
Title: Human SNF2L gene is regulated constitutively and inducibly in neural cells via a cAMP-response element.
The effect of SNF2L depletion on gene expression portray the cell in a state of activated Wnt signaling with increased proliferation and locomotion. High levels of SNF2L expression in normal melanocytes contrast with undetectable expression in melanoma.
Title: Nucleosome remodeler SNF2L suppresses cell proliferation and migration and attenuates Wnt signaling.
expression profiling analyses revealed that SWI/SNF likely antagonizes Polycomb repressive complex 2, implicating this as one possible mechanism of tumor suppression
Title: Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer.

Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

L78006 (e-PCR)
- UniSTS:41026

MARC_12207-12208:1004716010:1 (e-PCR)
- UniSTS:267364

L77638 (e-PCR)
- UniSTS:56164

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent DNA/DNA annealing activity	IDA Inferred from Direct Assay more info	PubMed
contributes_to ATP-dependent activity, acting on DNA	IDA Inferred from Direct Assay more info	PubMed
contributes_to ATP-dependent chromatin remodeler activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent chromatin remodeler activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables nucleosome array spacer activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleosome binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain development	NAS Non-traceable Author Statement more info	PubMed
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of ATPase complex	IDA Inferred from Direct Assay more info	PubMed
part_of CERF complex	IDA Inferred from Direct Assay more info	PubMed
part_of CERF complex	IPI Inferred from Physical Interaction more info	PubMed
part_of NURF complex	IDA Inferred from Direct Assay more info	PubMed
part_of NURF complex	IPI Inferred from Physical Interaction more info	PubMed
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay 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
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: probable global transcription activator SNF2L1

Names: ATP-dependent helicase SMARCA1; SNF2-like 1; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1; global transcription activator homologous sequence; nucleosome-remodeling factor subunit SNF2L; sucrose nonfermenting 2-like protein 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_012526.1 RefSeqGene

Range

4994..81978

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001282874.2 → NP_001269803.1 probable global transcription activator SNF2L1 isoform d

See identical proteins and their annotated locations for NP_001269803.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) encodes the longest isoform (d).

Source sequence(s)

BC143954, BQ006393, HY043725

Consensus CDS

CCDS76019.1

UniProtKB/TrEMBL

B7ZLQ5, Q86UA8

Related

ENSP00000360162.4, ENST00000371121.5

Conserved Domains (1) summary

PLN03142
Location:87 → 1069

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
NM_001282875.2 → NP_001269804.1 probable global transcription activator SNF2L1 isoform c

See identical proteins and their annotated locations for NP_001269804.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region, compared to variant 4. It encodes isoform c, which lacks an internal segment and is shorter, compared to isoform d.

Source sequence(s)

BC117447, BC143955, BQ006393, HY043725

Consensus CDS

CCDS76018.1

UniProtKB/TrEMBL

A0A0A0MRP6, Q86UA8

Related

ENSP00000360164.2, ENST00000371123.5

Conserved Domains (1) summary

PLN03142
Location:87 → 1057

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
NM_001378261.1 → NP_001365190.1 probable global transcription activator SNF2L1 isoform e

Status: REVIEWED

Source sequence(s)

AL022577, AL138745

UniProtKB/TrEMBL

Q86UA8

Conserved Domains (1) summary

PLN03142
Location:87 → 1046

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
NM_001378262.1 → NP_001365191.1 probable global transcription activator SNF2L1 isoform f

Status: REVIEWED

Source sequence(s)

AL022577, AL138745

UniProtKB/TrEMBL

Q86UA8

Related

ENST00000617310.4

Conserved Domains (1) summary

PLN03142
Location:87 → 1034

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
NM_001378263.1 → NP_001365192.1 probable global transcription activator SNF2L1 isoform f

Status: REVIEWED

Source sequence(s)

AL022577, AL138745

UniProtKB/TrEMBL

Q86UA8

Conserved Domains (1) summary

PLN03142
Location:87 → 1034

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
NM_001378264.1 → NP_001365193.1 probable global transcription activator SNF2L1 isoform g

Status: REVIEWED

Source sequence(s)

AL022577, AL138745

UniProtKB/TrEMBL

Q86UA8

Conserved Domains (1) summary

PLN03142
Location:87 → 1034

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
NM_003069.5 → NP_003060.2 probable global transcription activator SNF2L1 isoform a

See identical proteins and their annotated locations for NP_003060.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) differs in the 3' UTR and uses two alternate splice sites in the 3' coding region, resulting in an early stop codon, compared to variant 4. It encodes isoform a, which has a shorter and distinct C-terminus, compared to isoform d.

Source sequence(s)

BC117447, BQ006393, HY043725

Consensus CDS

CCDS14612.1

UniProtKB/Swiss-Prot

P28370, Q5JV41, Q5JV42

UniProtKB/TrEMBL

Q86UA8

Related

ENSP00000360163.4, ENST00000371122.8

Conserved Domains (1) summary

PLN03142
Location:87 → 1046

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

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

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

129446506..129523490 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

127765288..127842272 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_139035.2: Suppressed sequence

Description

NM_139035.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.