H2AX H2A.X variant histone [Homo sapiens (human)] - Gene

Summary

Official Symbol: H2AXprovided by HGNC
Official Full Name: H2A.X variant histoneprovided by HGNC
Primary source: HGNC:HGNC:4739
See related: Ensembl:ENSG00000188486 MIM:601772; AllianceGenome:HGNC:4739
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: H2A.X; H2A/X; H2AFX
Summary: Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene encodes a replication-independent histone that is a member of the histone H2A family, and generates two transcripts through the use of the conserved stem-loop termination motif, and the polyA addition motif. [provided by RefSeq, Oct 2015]
Orthologs: mouse all
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Genomic context

Location:: 11q23.3

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (119093874..119095465, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (119114257..119115848, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (118964584..118966175, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Overexpression of H2AFX gene in neuroblastoma is associated with worse prognosis.
Title: Overexpression of H2AFX gene in neuroblastoma is associated with worse prognosis.
H2AX promotes replication fork degradation and chemosensitivity in BRCA-deficient tumours.
Title: H2AX promotes replication fork degradation and chemosensitivity in BRCA-deficient tumours.
Hypoxia-responsive lncRNA G077640 promotes ESCC tumorigenesis via the H2AX-HIF1alpha-glycolysis axis.
Title: Hypoxia-responsive lncRNA G077640 promotes ESCC tumorigenesis via the H2AX-HIF1α-glycolysis axis.
Machine learning extracts oncogenic-specific gamma-H2AX foci formation pattern upon genotoxic stress.
Title: Machine learning extracts oncogenic-specific γ-H2AX foci formation pattern upon genotoxic stress.
USP49 is a novel deubiquitylating enzyme for gamma H2AX in DNA double-strand break repair.
Title: USP49 is a novel deubiquitylating enzyme for γ H2AX in DNA double-strand break repair.
Genetic variations in ATM and H2AX loci contribute to risk of hematological abnormalities in individuals exposed to BTEX chemicals.
Title: Genetic variations in ATM and H2AX loci contribute to risk of hematological abnormalities in individuals exposed to BTEX chemicals.
Pyruvate Facilitates FACT-Mediated gammaH2AX Loading to Chromatin and Promotes the Radiation Resistance of Glioblastoma.
Title: Pyruvate Facilitates FACT-Mediated γH2AX Loading to Chromatin and Promotes the Radiation Resistance of Glioblastoma.
Phosphorylation state of the histone variant H2A.X controls human stem and progenitor cell fate decisions.
Title: Phosphorylation state of the histone variant H2A.X controls human stem and progenitor cell fate decisions.
Cleavage-embryo genes and transposable elements are regulated by histone variant H2A.X.
Title: Cleavage-embryo genes and transposable elements are regulated by histone variant H2A.X.
Human mesenchymal stromal cells maintain their stem cell traits after high-LET particle irradiation - Potential implications for particle radiotherapy and manned space missions.
Title: Human mesenchymal stromal cells maintain their stem cell traits after high-LET particle irradiation - Potential implications for particle radiotherapy and manned space missions.

Submit: New GeneRIF Correction See all GeneRIFs (322)

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

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	HIV-1 Tat peptides bind core histones H2A, H2B, H3 and H4, and Tat protein recruits histone acetyltransferases to the HIV-1 LTR promoter leading to acetylation of histones H3 and H4, derepressing chromatin structure and increasing NFkappaB responsiveness	PubMed
Vpr	vpr	Soluble HIV-1 Vpr induces a DNA damage response by forming H2AX- and 53BP1-containing DNA repair foci	PubMed
	vpr	HIV-1 Vpr expression in HeLa cells and human primary CD4+ lymphocytes induces phosphorylation of H2AFX and formation of nuclear foci containing H2AFX and BRCA1	PubMed
	vpr	Recruitment of a catalytically active CRL4A (VPRBP) complex is required to observe HIV-1 Vpr-interacting unknown cellular ubiquitinated proteins. Phosphorylation of H2AX requires Vpr-induced K48 residue polyubiquitination	PubMed
	vpr	HIV-1 Vpr binds DCAF1 and activates the DNA damage response in renal tubule epithelial cells, in which gamma H2AX-positive nuclei are abundant compared to the control	PubMed
integrase	gag-pol	HIV-1 IN-mediated proviral DNA integration triggers cell death during HIV-1 infection. The mechanism of killing during viral integration involves activation of DNA-PK, which causes phosphorylation of p53 and histone gammaH2AX	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

D11S4378 (e-PCR)
- UniSTS:80395

STS-R55620 (e-PCR)
- UniSTS:28434

RH70756 (e-PCR)
- UniSTS:87342

H2AFX_1240 (e-PCR)
- UniSTS:277303

A004Z11 (e-PCR)
- UniSTS:66234

STS-M95623 (e-PCR)
- UniSTS:2280

RH80367 (e-PCR)
- UniSTS:87530

G15876 (e-PCR)
- UniSTS:8697

H2AFX (e-PCR)
- UniSTS:266494

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	NAS Non-traceable Author Statement more info	PubMed
enables chromatin-protein adaptor activity	IDA Inferred from Direct Assay more info	PubMed
enables damaged DNA binding	IEA Inferred from Electronic Annotation more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables structural constituent of chromatin	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of chromatin	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA damage checkpoint signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA damage response	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA damage response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to gamma radiation	IEA Inferred from Electronic Annotation more info
involved_in cellular senescence	IEA Inferred from Electronic Annotation more info
involved_in cerebral cortex development	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair	NAS Non-traceable Author Statement more info	PubMed
involved_in double-strand break repair via homologous recombination	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in meiotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in nucleosome assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of DNA repair	NAS Non-traceable Author Statement more info	PubMed
involved_in protein localization to site of double-strand break	IDA Inferred from Direct Assay more info	PubMed
involved_in response to ionizing radiation	NAS Non-traceable Author Statement more info	PubMed
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in XY body	IEA Inferred from Electronic Annotation more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in condensed nuclear chromosome	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in male germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
part_of nucleosome	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	HDA more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
located_in replication fork	IEA Inferred from Electronic Annotation more info
located_in site of DNA damage	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in site of double-strand break	IDA Inferred from Direct Assay more info	PubMed
located_in site of double-strand break	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone H2AX

Names: H2A histone family member X; H2AX histone; histone H2A.x

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.