SMARCA1 Gene

HGNC Family	SANT/Myb domain containing
Name	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1
Description	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]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nSMARCA1, which encodes the ATP‐dependent chromatin remodeler SNF2L, plays multifaceted roles in cancer biology. In several studies, reduced or aberrant SMARCA1 activity has been linked to tumorigenesis. For instance, epigenetic silencing by aberrant methylation in gastric tissues leads to loss of SMARCA1 expression, and experimental depletion in cancer cell lines results in increased proliferation, migration, and activation of oncogenic signaling such as the Wnt pathway. A pan‐cancer analysis further revealed that SMARCA1 expression and post‐translational modifications (e.g., S116 phosphorylation) vary across tumors and correlate with the degree of stromal and immune cell infiltration. In colorectal cancer, a long noncoding RNA (MIR99AHG) modulates the alternative splicing of SMARCA1 pre‐mRNA, promoting expression of an isoform that is less effective at counteracting invasive phenotypes."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "5"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn developmental and neural contexts, SMARCA1 is fundamental for promoting the transition of cells from a progenitor state to a differentiated phenotype. A novel splice variant of SNF2L, which lacks enzymatic activity, underscores the importance of alternative splicing in fine‐tuning its function in neurogenesis. Moreover, the basal transcription of the SNF2L gene is regulated by critical cis-elements—including a cAMP-response element (CRE) and an Sp1-binding site—and its expression is modulated by protein kinase A signaling in neural and gonadal cells."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "6", "end_ref": "8"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its roles in cancer and development, rare genetic variants in SMARCA1 have been implicated in neuropsychiatric disorders, including familial psychotic conditions and X-linked mental retardation, highlighting its significance in cognitive function. Additionally, the dynamic recruitment of SMARCA1 to sites of DNA damage—a rapid accumulation at UV-induced lesions—points to its involvement in chromatin remodeling required for DNA replication and repair."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "9", "end_ref": "11"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Yin Ye, Yi Xiao, Wenting Wang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Inhibition of expression of the chromatin remodeling gene, SNF2L, selectively leads to DNA damage, growth inhibition, and cancer cell death."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cancer Res (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1158/1541-7786.MCR-09-0119"}], "href": "https://doi.org/10.1158/1541-7786.MCR-09-0119"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19996304"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19996304"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Maren Eckey, Silke Kuphal, Tobias Straub, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Nucleosome remodeler SNF2L suppresses cell proliferation and migration and attenuates Wnt signaling."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.06619-11"}], "href": "https://doi.org/10.1128/MCB.06619-11"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22508985"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22508985"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Hideyuki Takeshima, Tohru Niwa, Takamasa Takahashi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Frequent involvement of chromatin remodeler alterations in gastric field cancerization."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Lett (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.canlet.2014.11.038"}], "href": "https://doi.org/10.1016/j.canlet.2014.11.038"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25462860"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25462860"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Lei Dai, Joseph Mugaanyi, Tongyue Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A pan-cancer bioinformatic analysis of the carcinogenic role of SMARCA1 in human carcinomas."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS One (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pone.0274823"}], "href": "https://doi.org/10.1371/journal.pone.0274823"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36126083"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36126083"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Danxiu Li, Xin Wang, Hui Miao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The lncRNA MIR99AHG directs alternative splicing of "}, {"type": "a", "children": [{"type": "t", "text": "i"}], "href": "i"}, {"type": "t", "text": "SMARCA1"}, {"type": "a", "children": [{"type": "t", "text": "/i"}], "href": "/i"}, {"type": "t", "text": " by PTBP1 to enable invadopodia formation in colorectal cancer cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Signal (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/scisignal.adh4210"}], "href": "https://doi.org/10.1126/scisignal.adh4210"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "37725664"}], "href": "https://pubmed.ncbi.nlm.nih.gov/37725664"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Orr Barak, Maribeth A Lazzaro, Neil S Cooch, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A tissue-specific, naturally occurring human SNF2L variant inactivates chromatin remodeling."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M406212200"}], "href": "https://doi.org/10.1074/jbc.M406212200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15310751"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15310751"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Yu Xia, Baichun Jiang, Yongxin Zou, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Sp1 and CREB regulate basal transcription of the human SNF2L gene."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Biophys Res Commun (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbrc.2008.01.111"}], "href": "https://doi.org/10.1016/j.bbrc.2008.01.111"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18243132"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18243132"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Yu Xia, Laicheng Wang, Chunyan Ma, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Human SNF2L gene is regulated constitutively and inducibly in neural cells via a cAMP-response element."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Yonsei Med J (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3349/ymj.2013.54.3.772"}], "href": "https://doi.org/10.3349/ymj.2013.54.3.772"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23549828"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23549828"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Maribeth A Lazzaro, Matthew A M Todd, Paul Lavigne, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "BMC Med Genet (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/1471-2350-9-11"}], "href": "https://doi.org/10.1186/1471-2350-9-11"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18302774"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18302774"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Fabian Erdel, Karsten Rippe "}, {"type": "b", "children": [{"type": "t", "text": "Binding kinetics of human ISWI chromatin-remodelers to DNA repair sites elucidate their target location mechanism."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleus (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.4161/nucl.2.2.15209"}], "href": "https://doi.org/10.4161/nucl.2.2.15209"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21738833"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21738833"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "O R Homann, K Misura, E Lamas, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Whole-genome sequencing in multiplex families with psychoses reveals mutations in the SHANK2 and SMARCA1 genes segregating with illness."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Psychiatry (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/mp.2016.24"}], "href": "https://doi.org/10.1038/mp.2016.24"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27001614"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27001614"}]}]}]}
Synonyms	hSNF2L, SNF2L, SNF2LB, ISWI, SWI2, NURF140, SWI, SNF2L1, SNF2LT
Proteins	SMCA1_HUMAN
NCBI Gene ID	6594
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

SMARCA1 has 7,257 functional associations with biological entities spanning 9 categories (molecular profile, organism, disease, phenotype or trait, functional term, phrase or reference, chemical, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 119 datasets.

Click the + buttons to view associations for SMARCA1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

SMARCA1 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by SMARCA1 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SMARCA1 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of SMARCA1 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of SMARCA1 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of SMARCA1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of SMARCA1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SMARCA1 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of SMARCA1 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SMARCA1 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SMARCA1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of SMARCA1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of SMARCA1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with SMARCA1 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with SMARCA1 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SMARCA1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of SMARCA1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of SMARCA1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with SMARCA1 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing SMARCA1 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of SMARCA1 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing SMARCA1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing SMARCA1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with SMARCA1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with SMARCA1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing SMARCA1 protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of SMARCA1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with SMARCA1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with SMARCA1 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with SMARCA1 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of SMARCA1 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by SMARCA1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with SMARCA1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with SMARCA1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with SMARCA1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with SMARCA1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at SMARCA1 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SMARCA1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of SMARCA1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing SMARCA1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of SMARCA1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.