ATRX Gene

Name	alpha thalassemia/mental retardation syndrome X-linked
Description	The protein encoded by this gene contains an ATPase/helicase domain, and thus it belongs to the SWI/SNF family of chromatin remodeling proteins. This protein is found to undergo cell cycle-dependent phosphorylation, which regulates its nuclear matrix and chromatin association, and suggests its involvement in the gene regulation at interphase and chromosomal segregation in mitosis. Mutations in this gene are associated with X-linked syndromes exhibiting cognitive disabilities as well as alpha-thalassemia (ATRX) syndrome. These mutations have been shown to cause diverse changes in the pattern of DNA methylation, which may provide a link between chromatin remodeling, DNA methylation, and gene expression in developmental processes. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2017]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n ATRX is a member of the SWI/SNF family of chromatin remodelers that plays a critical role in maintaining genomic stability. Functionally, ATRX partners with DAXX to mediate the replication‐independent deposition of the histone variant H3.3 at telomeres and heterochromatic regions, thereby contributing to proper chromatin assembly and the regulation of gene expression."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": " This activity is essential for the maintenance of telomere integrity and for preventing the activation of alternative telomere lengthening mechanisms—a phenomenon that is commonly observed in tumors harboring ATRX loss‐of‐function mutations."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}, {"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": " In various cancers—including lower‐grade gliomas"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ", pediatric glioblastomas"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": ", pancreatic neuroendocrine tumors"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": ", and neuroblastomas"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": "), ATRX mutations are frequently mutually exclusive with other telomere‐maintenance events (for example, TERT promoter alterations) and are generally associated with genomic instability and distinct oncogenic pathways. Moreover, ATRX has been shown to bind tandem repeat sequences and G‑quadruplex structures, thereby influencing the expression of repeat‐associated genes and contributing to allelic expression variability"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": ", while its interaction with other chromatin regulators helps coordinate DNA repair and replication."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "11"}]}, {"type": "t", "text": " Collectively, these studies underscore that ATRX is a multifunctional protein whose roles in chromatin remodeling, telomere stability, and regulation of gene expression are vital for normal cellular function, and whose disruption can drive tumorigenesis by destabilizing the genome and altering transcriptional programs."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}, {"type": "fg_f", "ref": "6"}, {"type": "fg_f", "ref": "4"}, {"type": "fg_f", "ref": "2"}, {"type": "fg_f", "ref": "12"}, {"type": "fg_f", "ref": "9"}, {"type": "fg_f", "ref": "11"}, {"type": "fg_f", "ref": "10"}]}, {"type": "t", "text": "\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Daniel J Brat, Roel G W Verhaak, Kenneth D Aldape, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "N Engl J Med (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1056/NEJMoa1402121"}], "href": "https://doi.org/10.1056/NEJMoa1402121"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26061751"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26061751"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Peter W Lewis, Simon J Elsaesser, Kyung-Min Noh, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Daxx is an H3.3-specific histone chaperone and cooperates with ATRX in replication-independent chromatin assembly at telomeres."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1008850107"}], "href": "https://doi.org/10.1073/pnas.1008850107"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20651253"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20651253"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Pascal Drané, Khalid Ouararhni, Arnaud Depaux, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.566910"}], "href": "https://doi.org/10.1101/gad.566910"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20504901"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20504901"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Patrick J Killela, Zachary J Reitman, Yuchen Jiao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1303607110"}], "href": "https://doi.org/10.1073/pnas.1303607110"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23530248"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23530248"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Christopher M Heaphy, Roeland F de Wilde, Yuchen Jiao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Altered telomeres in tumors with ATRX and DAXX mutations."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.1207313"}], "href": "https://doi.org/10.1126/science.1207313"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21719641"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21719641"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Jeremy Schwartzentruber, Andrey Korshunov, Xiao-Yang Liu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature10833"}], "href": "https://doi.org/10.1038/nature10833"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22286061"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22286061"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Yuchen Jiao, Chanjuan Shi, Barish H Edil, et al. "}, {"type": "b", "children": [{"type": "t", "text": "DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.1200609"}], "href": "https://doi.org/10.1126/science.1200609"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21252315"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21252315"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Linda J Valentijn, Jan Koster, Danny A Zwijnenburg, et al. "}, {"type": "b", "children": [{"type": "t", "text": "TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.3438"}], "href": "https://doi.org/10.1038/ng.3438"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26523776"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26523776"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Martin J Law, Karen M Lower, Hsiao P J Voon, et al. "}, {"type": "b", "children": [{"type": "t", "text": "ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2010.09.023"}], "href": "https://doi.org/10.1016/j.cell.2010.09.023"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21029860"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21029860"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Andrew Dunford, David M Weinstock, Virginia Savova, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.3726"}], "href": "https://doi.org/10.1038/ng.3726"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27869828"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27869828"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Lee H Wong, James D McGhie, Marcus Sim, et al. "}, {"type": "b", "children": [{"type": "t", "text": "ATRX interacts with H3.3 in maintaining telomere structural integrity in pluripotent embryonic stem cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genome Res (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gr.101477.109"}], "href": "https://doi.org/10.1101/gr.101477.109"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20110566"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20110566"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Yutong Xue, Richard Gibbons, Zhijiang Yan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The ATRX syndrome protein forms a chromatin-remodeling complex with Daxx and localizes in promyelocytic leukemia nuclear bodies."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1937626100"}], "href": "https://doi.org/10.1073/pnas.1937626100"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12953102"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12953102"}]}]}]}
Synonyms	RAD54, JMS, RAD54L, ATR2, MRXHF1, SFM1, XH2, ZNF-HX, XNP, MRX52
Proteins	ATRX_HUMAN
NCBI Gene ID	546
API
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

ATRX has 10,372 functional associations with biological entities spanning 8 categories (molecular profile, organism, disease, phenotype or trait, chemical, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 127 datasets.

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

If available, associations are ranked by standardized value

Harmonizome 3.0

ATRX 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 ATRX 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 ATRX 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 ATRX gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of ATRX 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 ATRX 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 ATRX 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 ATRX 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 ATRX 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 ATRX 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 ATRX 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 ATRX gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Gene Mutation Profiles	cell lines with ATRX gene mutations from the CCLE Cell Line Gene Mutation Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with ATRX protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with ATRX 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 ATRX gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of ATRX 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 ATRX gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations	phenotypes associated with ATRX gene from the curated ClinVar Gene-Phenotype Associations dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of ATRX gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing ATRX protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing ATRX protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing ATRX protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing ATRX protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with ATRX 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 ATRX protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing ATRX protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of ATRX gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with ATRX gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with ATRX gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with ATRX gene/protein from the curated CTD Gene-Disease Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by ATRX gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores	diseases involving ATRX gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving ATRX gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with ATRX 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 ATRX 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 ATRX gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with ATRX 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 ATRX 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 ATRX gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of ATRX gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.