Selected-GenAtlas references SOURCE GeneCards NCBI Gene Swiss-Prot Ensembl
HGNC UniGene Nucleotide OMIM UCSC
Home Page
Symbol H2AFX contributors: mct/pgu - updated : 07-04-2016
HGNC name H2A histone family, member X
HGNC id 4739
Location 11q23.3      Physical location : 118.964.586 - 118.966.177
Synonym name H2AX histone
Synonym symbol(s) H2AX, H2A.X, H2A/X
TYPE functioning gene
SPECIAL FEATURE opposite orientation, tail to tail
STRUCTURE 1.59 kb     1 Exon(s)
10 Kb 5' upstream gene genomic sequence study
regulatory sequence Promoter (CAAT box)
text structure 2CCAAT boxes, H2AFX and AIP are tail to tail in opposite orientation with less 34 out separating their 3-prime ends
MAPPING cloned Y linked N status confirmed
Map cen - HMBS - H2AFX - CBL - qter
Physical map
DDX6 11q23.3 DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 LOC338656 11q23.3 similar to protein phosphatase 2A inhibitor-2 I-2PP2A BLR1 11q23.3 Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5) BCL9L 11q23.3 B-cell CLL/lymphoma 9-like UPK2 11q23 uroplakin 2 LOC283150 11q23.3 hypothetical protein LOC283150 DLNB14 11q23.3 similar to DLNB14 RPS25 11q23.3 ribosomal protein S25 TRAPPC4 11q23.3 trafficking protein particle complex 4 SLC37A4 11q23.3 solute carrier family 37 (glycerol-6-phosphate transporter), member 4 HYOU1 11q23.1-q23.3 hypoxia up-regulated 1 VPS11 11q23 vacuolar protein sorting 11 (yeast) HMBS 11q23.3 hydroxymethylbilane synthase H2AFX 11q23.3 H2A histone family, member X DPAGT1 11q23.3 dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase) KIAA0285 11q23.3 dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase) MIZF 11q23.3 MBD2 (methyl-CpG-binding protein)-interacting zinc finger protein ABCG4 11q23.3 ATP-binding cassette, sub-family G (WHITE), member 4 NOD9 11q23.3 NOD9 protein PDZK2 11q23.3 PDZ domain containing 2 LOC387812 11 LOC387812 CBL 11q23.3 Cas-Br-M (murine) ecotropic retroviral transforming sequence MCAM 11q23.3 melanoma cell adhesion molecule RNF26 11q23 ring finger protein 26 C1QTNF5 11q23.3 C1q and tumor necrosis factor related protein 5 MFRP 11q23 membrane frizzled-related protein USP2 11q23.3 ubiquitin specific protease 2 LOC94105 11q22.3-q23 Thy-1 co-transcribed THY1 11q23.3 Thy-1 cell surface antigen
TRANSCRIPTS type messenger
identificationnb exonstypebpproduct
ProteinkDaAAspecific expressionYearPubmed
1 - 1651 - 143 - 1998 9488723
Type ubiquitous
constitutive of
   expressed in (based on citations)
SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
Endocrinepancreas   highly
Lymphoid/Immunelymph node   highly
 tonsils   highly
Nervousbrain   lowly
Reproductivefemale systemovary  highly
 male systemprostate  lowly
Urinarykidney   lowly
SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
Blood / Hematopoieticbone marrow   
cell lineage
cell lines
cell cycle     cell cycle, G1, S
  • C-terminal SQE motif
  • conjugated PhosphoP
    mono polymer octamer
    interspecies homolog to S. cerevisiae HTA2 (77.05 pc)
    homolog to murine H2afx (97.20 pc)
  • histone H2A family
  • CATEGORY DNA associated , transcription factor , tumor suppressor
    SUBCELLULAR LOCALIZATION     intracellular
    basic FUNCTION
  • playing a role in the compaction of DNA into nucleosomes
  • basal histone, maybe functioning as a dosage-dependent suppressor of genomic instability and tumors
  • involved in the FA/BRCA pathway, and functionally connected to the FA/BRCA pathway to resolve stalled
  • replication forks and prevent chromosome instability
  • have post-replication repair functions distinct from those of ATM, but likely have independent functions that theoretically could synergize in DNA repair and maintenance of genomic integrity
  • functioning as an active determinant of repair/survival upon dephosphorylation
  • play a facilitative role in homologous recombination
  • plays an important role in replication fork stability as part of a salvage pathway to reinitiate replication following collapse
  • has important role for effective DSB-dependent activation of ATM-related damage responses via NBS1
  • role in the TP53/CDKN1A pathway and indicate that it is required for CDKN1A-induced cell cycle arrest after replication stalling
  • required for increasing CDKN1A levels after replication inhibition and that this subsequently results in checkpoint activation and cell cycle arrest
  • participates in the DNA damage response and mediates DNA repair
  • like ATM, is essential for viability in a PARP1-deficient background
  • roles of H2AFX and PARP1, PARP2 in the DNA damage response
  • NHEJ1, ATM and H2AFX all have fundamental roles in processing and joining DNA ends during V(D)J recombination, but these roles have been masked by unanticipated functional redundancies
  • preserves the structural integrity of broken DNA ends in G1-phase lymphocytes, thereby preventing these DNA ends from accessing repair pathways that promote genomic instability
  • maintains the structural integrity of broken DNA ends generated during V(D)J recombination in G1-phase lymphocytes
  • CELLULAR PROCESS cell cycle
    nucleotide, chromatin organization, remodeling
    nucleotide, transcription, regulation
    text involved in spermatogenesis
    pathway involving H2AFX–MDC1–WHSC1 regulates the induction of H4K20 methylation on histones around DSBs, which, in turn, facilitates TP53BP1 recruitment
    a component core histone H2A/H3B/H3/H4
    DNA approximatively 0.146 kb
    small molecule
  • H2A, H2B, H3, H4
  • interaction with KAT5 (regulates the ubiquitination of H2AFX via the ubiquitin-conjugating enzyme UBE2N, which is induced by DNA damage, and sequential acetylation and ubiquitination of H2AFX by KAT5/UBE2N promote enhanced histone dynamics, which in turn stimulate a DNA damage response
  • interacting with ATR (ATR and H2AFX provide cooperative safeguards to ensure genome stability during DNA replication)
  • cooperates with both NBS1 and ATM for regulation of ATM-dependent cell cycle checkpoint in response to DNA damage
  • H2AFX is a substrate of STK4, which functions to induce apoptotic chromatin condensation and DNA fragmentation
  • PPP2R5E is responsible for the dephosphorylation of H2AFX
  • cell & other
    induced by oxydative stress in human spermatozoa
    Other phosphorylated by ATM
    phosphorylated by BAZ1B
    gamma-H2AFX is dephosphorylated directly by PPM1D to silence the checkpoint and restore chromatin structure
    corresponding disease(s)
    Variant & Polymorphism
    Candidate gene
    Therapy target
    vascular-targeted inhibitors of H2AFX may provide a new strategy for preventing hypoxia-induced pathological neovascularization in conditions such as in tumor growth
    vascular-targeted inhibitors of H2AFX may provide a new strategy for preventing hypoxia-induced pathological neovascularization in conditions such as retinopathy of prematurity or diabetic retinopathy
    H2AX-/- mice