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Aliases for H3F3A Gene

Aliases for H3F3A Gene

  • H3 Histone Family Member 3A 2 3 5
  • H3 Histone, Family 3A 2 3
  • H3.3A 3 4
  • H3F3 3 4
  • Histone H3.3 3
  • H3F3A H3F3B 4
  • H3.3B 4

External Ids for H3F3A Gene

Previous HGNC Symbols for H3F3A Gene

  • H3F3

Previous GeneCards Identifiers for H3F3A Gene

  • GC01P224732
  • GC01P222067
  • GC01P222656
  • GC01P223225
  • GC01P222557
  • GC01P224316
  • GC01P226249
  • GC01P196767

Summaries for H3F3A Gene

Entrez Gene Summary for H3F3A Gene

  • 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 contains introns and its mRNA is polyadenylated, unlike most histone genes. The protein encoded is a replication-independent member of the histone H3 family. [provided by RefSeq, Jul 2008]

GeneCards Summary for H3F3A Gene

H3F3A (H3 Histone Family Member 3A) is a Protein Coding gene. Diseases associated with H3F3A include Glioma Susceptibility 1 and Chondroblastoma. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and Mitotic Prophase. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity and RNA polymerase II distal enhancer sequence-specific DNA binding. An important paralog of this gene is H3F3B.

UniProtKB/Swiss-Prot for H3F3A Gene

  • Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Gene Wiki entry for H3F3A Gene

Additional gene information for H3F3A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for H3F3A Gene

Genomics for H3F3A Gene

GeneHancer (GH) Regulatory Elements for H3F3A Gene

Promoters and enhancers for H3F3A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I226060 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 574.1 +1.5 1450 5.6 DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF263 SP3 NFYC ZNF610 GLIS1 H3F3A ENSG00000272562 ACBD3-AS1 SDE2 LOC105373110 LINC01703 ENAH MIXL1 ACBD3 LBR
GH01I226082 Promoter/Enhancer 1.5 Ensembl ENCODE 55.6 +21.6 21635 1.5 HDGF ARNT ZFP64 ARID4B SIN3A ZNF2 ZBTB7B POLR2B KLF13 SP3 LINC01703 H3F3A ACBD3-AS1 ACBD3 SDE2 GC01P226072
GH01I225995 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 26.3 -61.6 -61553 8.8 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF548 SP3 SDE2 ACBD3 ACBD3-AS1 H3F3A LINC01703 ENAH LOC105373110 TMEM63A GC01M225948
GH01I226307 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23 +247.6 247583 3.3 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B GC01M226306 LIN9 ACBD3-AS1 H3F3A LOC105373110 ENAH LINC01703 ACBD3
GH01I226033 Enhancer 1.2 FANTOM5 Ensembl ENCODE 38.6 -26.9 -26905 3.5 CTCF MEIS2 SAP130 MAX ZNF384 YY1 TCF12 ZNF316 NCOR1 POLR2A H3F3A SDE2 GC01M225948
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around H3F3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the H3F3A gene promoter:

Genomic Locations for H3F3A Gene

Genomic Locations for H3F3A Gene
chr1:226,061,851-226,072,002
(GRCh38/hg38)
Size:
10,152 bases
Orientation:
Plus strand
chr1:226,249,552-226,259,703
(GRCh37/hg19)

Genomic View for H3F3A Gene

Genes around H3F3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
H3F3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for H3F3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for H3F3A Gene

Proteins for H3F3A Gene

  • Protein details for H3F3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P84243-H33_HUMAN
    Recommended name:
    Histone H3.3
    Protein Accession:
    P84243
    Secondary Accessions:
    • P06351
    • P33155
    • Q5VV55
    • Q5VV56
    • Q66I33
    • Q9V3W4

    Protein attributes for H3F3A Gene

    Size:
    136 amino acids
    Molecular mass:
    15328 Da
    Quaternary structure:
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Interacts with HIRA, a chaperone required for its incorporation into nucleosomes. Interacts with ZMYND11; when trimethylated at Lys-36 (H3.3K36me3).
    • The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Interacts with HIRA, a chaperone required for its incorporation into nucleosomes. Interacts with ZMYND11; when trimethylated at Lys-36 (H3.3K36me3).
    SequenceCaution:
    • Sequence=CAH73371.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for H3F3A Gene

neXtProt entry for H3F3A Gene

Post-translational modifications for H3F3A Gene

  • Acetylation is generally linked to gene activation. Acetylation on Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me). Acetylation at Lys-123 (H3K122ac) by EP300/p300 plays a central role in chromatin structure: localizes at the surface of the histone octamer and stimulates transcription, possibly by promoting nucleosome instability.
  • Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) by PRMT5 is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3 of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters.
  • Butyrylation of histones marks active promoters and competes with histone acetylation. It is present during late spermatogenesis.
  • Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.
  • Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.
  • Lysine deamination at Lys-5 (H3K4all) to form allysine is mediated by LOXL2. Allysine formation by LOXL2 only takes place on H3K4me3 and results in gene repression (PubMed:22483618).
  • Phosphorylated at Thr-4 (H3T3ph) by HASPIN during prophase and dephosphorylated during anaphase. Phosphorylation at Ser-11 (H3S10ph) by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 (H3S10ph) by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 (H3S28ph) by MAP3K20 isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation. Phosphorylation at Thr-7 (H3T6ph) by PRKCB is a specific tag for epigenetic transcriptional activation that prevents demethylation of Lys-5 (H3K4me) by LSD1/KDM1A. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, by DAPK3 and PKN1. Phosphorylation at Thr-12 (H3T11ph) by PKN1 is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me) by KDM4C/JMJD2C. Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin. Phosphorylation on Ser-32 (H3S31ph) is specific to regions bordering centromeres in metaphase chromosomes.
  • Specifically enriched in modifications associated with active chromatin such as methylation at Lys-5 (H3K4me), Lys-37 and Lys-80. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me), which are linked to gene repression, are underrepresented. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at Lys-120. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are enriched in inactive X chromosome chromatin. Monomethylation at Lys-57 (H3K56me1) by EHMT2/G9A in G1 phase promotes interaction with PCNA and is required for DNA replication.
  • Ubiquitinated. Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination (By similarity).
  • Ubiquitination at posLast=116116

Other Protein References for H3F3A Gene

No data available for DME Specific Peptides for H3F3A Gene

Domains & Families for H3F3A Gene

Gene Families for H3F3A Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for H3F3A Gene

Suggested Antigen Peptide Sequences for H3F3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P84243

UniProtKB/Swiss-Prot:

H33_HUMAN :
  • Specific interaction of trimethylated form at Lys-36 (H3.3K36me3) with ZMYND11 is mediated by the encapsulation of Ser-32 residue with a composite pocket formed by the tandem bromo-PWWP domains.
  • Belongs to the histone H3 family.
Domain:
  • Specific interaction of trimethylated form at Lys-36 (H3.3K36me3) with ZMYND11 is mediated by the encapsulation of Ser-32 residue with a composite pocket formed by the tandem bromo-PWWP domains.
Family:
  • Belongs to the histone H3 family.
genes like me logo Genes that share domains with H3F3A: view

Function for H3F3A Gene

Molecular function for H3F3A Gene

GENATLAS Biochemistry:
histone family 3,replacement subtype,replication independent protein,species H3.3A
UniProtKB/Swiss-Prot Function:
Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes. Constitutes the predominant form of histone H3 in non-dividing cells and is incorporated into chromatin independently of DNA synthesis. Deposited at sites of nucleosomal displacement throughout transcribed genes, suggesting that it represents an epigenetic imprint of transcriptionally active chromatin. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Phenotypes From GWAS Catalog for H3F3A Gene

Gene Ontology (GO) - Molecular Function for H3F3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000979 RNA polymerase II core promoter sequence-specific DNA binding IDA 19633671
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IDA 19633671
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 19494831
GO:0031492 nucleosomal DNA binding IDA 19633671
genes like me logo Genes that share ontologies with H3F3A: view

Phenotypes for H3F3A Gene

genes like me logo Genes that share phenotypes with H3F3A: view

Animal Model Products

Clone Products

  • Addgene plasmids for H3F3A

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for H3F3A Gene

Localization for H3F3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for H3F3A Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for H3F3A gene
Compartment Confidence
extracellular 5
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for H3F3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 nuclear chromosome IDA 14718166
GO:0000784 nuclear chromosome, telomeric region IDA 20110566
GO:0000786 nucleosome IDA 21636898
GO:0000788 nuclear nucleosome IDA 19633671
GO:0005576 extracellular region TAS --
genes like me logo Genes that share ontologies with H3F3A: view

Pathways & Interactions for H3F3A Gene

SuperPathways for H3F3A Gene

SuperPathway Contained pathways
1 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
2 Cellular Senescence (REACTOME)
3 Cell Cycle, Mitotic
.60
4 Mitotic Prophase
5 Development NOTCH1-mediated pathway for NF-KB activity modulation
genes like me logo Genes that share pathways with H3F3A: view

Interacting Proteins for H3F3A Gene

SIGNOR curated interactions for H3F3A Gene

Gene Ontology (GO) - Biological Process for H3F3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000183 chromatin silencing at rDNA TAS --
GO:0006334 nucleosome assembly IMP 25615412
GO:0006336 DNA replication-independent nucleosome assembly IDA 14718166
GO:0007420 brain development IEA --
GO:0007596 blood coagulation TAS --
genes like me logo Genes that share ontologies with H3F3A: view

Drugs & Compounds for H3F3A Gene

No Compound Related Data Available

Transcripts for H3F3A Gene

Unigene Clusters for H3F3A Gene

H3 histone, family 3A:
Representative Sequences:

Clone Products

  • Addgene plasmids for H3F3A

Alternative Splicing Database (ASD) splice patterns (SP) for H3F3A Gene

No ASD Table

Relevant External Links for H3F3A Gene

GeneLoc Exon Structure for
H3F3A
ECgene alternative splicing isoforms for
H3F3A

Expression for H3F3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for H3F3A Gene

mRNA differential expression in normal tissues according to GTEx for H3F3A Gene

This gene is overexpressed in Whole Blood (x11.1).

Protein differential expression in normal tissues from HIPED for H3F3A Gene

This gene is overexpressed in Frontal cortex (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for H3F3A Gene



Protein tissue co-expression partners for H3F3A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of H3F3A Gene:

H3F3A

SOURCE GeneReport for Unigene cluster for H3F3A Gene:

Hs.533624

Evidence on tissue expression from TISSUES for H3F3A Gene

  • Liver(4.8)
  • Nervous system(4.8)
  • Eye(4.7)
  • Lung(4.2)
  • Pancreas(4.2)
  • Stomach(4.2)
  • Blood(3.9)
  • Intestine(3.8)
  • Bone(3.1)
  • Muscle(3)
  • Adrenal gland(2.6)
  • Bone marrow(2.6)
  • Gall bladder(2.6)
  • Heart(2.6)
  • Kidney(2.6)
  • Lymph node(2.6)
  • Skin(2.6)
  • Spleen(2.6)
  • Thyroid gland(2.6)
genes like me logo Genes that share expression patterns with H3F3A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for H3F3A Gene

Orthologs for H3F3A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for H3F3A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia H3F3A 33
  • 100 (n)
H3F3C 34
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia H3F3A 33
  • 98.28 (n)
H3F3C 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia H3F3B 33
  • 97.55 (n)
-- 34
  • 95 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia H3f3a 33
  • 96.08 (n)
rat
(Rattus norvegicus)
Mammalia LOC100361558 33
  • 95.59 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 94 (a)
ManyToMany
chicken
(Gallus gallus)
Aves H3-IX 34
  • 100 (a)
OneToOne
LOC100859629 33
  • 79.17 (n)
lizard
(Anolis carolinensis)
Reptilia H3F3A 34
  • 100 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101730642 33
  • 77.21 (n)
Str.6553 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8034 33
zebrafish
(Danio rerio)
Actinopterygii H3F3A 34
  • 99 (a)
OneToOne
LOC565028 33
  • 79.66 (n)
fruit fly
(Drosophila melanogaster)
Insecta His3.3B 35
  • 100 (a)
His3.3A 35
  • 100 (a)
His3:CG33857 33
  • 79.17 (n)
worm
(Caenorhabditis elegans)
Secernentea his-71 35 34
  • 99 (a)
his-72 35
  • 98 (a)
W05B10.1 35
  • 93 (a)
his-69 35
  • 88 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HHT1 34
  • 90 (a)
ManyToMany
HHT2 34
  • 90 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1064 34
  • 100 (a)
OneToMany
Species where no ortholog for H3F3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for H3F3A Gene

ENSEMBL:
Gene Tree for H3F3A (if available)
TreeFam:
Gene Tree for H3F3A (if available)

Paralogs for H3F3A Gene

Variants for H3F3A Gene

Sequence variations from dbSNP and Humsavar for H3F3A Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1057519902 likely-pathogenic, Brainstem glioma, Adrenocortical carcinoma, Glioblastoma, Neoplasm of brain 226,064,451(+) G/C coding_sequence_variant, missense_variant
rs1057519903 likely-pathogenic, Brainstem glioma, Astrocytoma 226,064,434(+) A/T coding_sequence_variant, missense_variant
VAR_079021 Glioma (GLM) [MIM:137800] p.Lys28Met
VAR_079022 Glioma (GLM) [MIM:137800] p.Gly35Arg
VAR_079023 Glioma (GLM) [MIM:137800] p.Gly35Val

Structural Variations from Database of Genomic Variants (DGV) for H3F3A Gene

Variant ID Type Subtype PubMed ID
esv3589008 CNV gain 21293372
nsv832747 CNV gain 17160897
nsv945330 CNV duplication 23825009
nsv952128 CNV duplication 24416366

Variation tolerance for H3F3A Gene

Residual Variation Intolerance Score: 57.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.04; 0.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for H3F3A Gene

Human Gene Mutation Database (HGMD)
H3F3A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
H3F3A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for H3F3A Gene

Disorders for H3F3A Gene

MalaCards: The human disease database

(14) MalaCards diseases for H3F3A Gene - From: HGMD, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
glioma susceptibility 1
  • glm1
chondroblastoma
  • chondroblastoma of bone
clear cell chondrosarcoma
malignant giant cell tumor
  • malignant giant cell neoplasm
diffuse intrinsic pontine glioma
  • dipg
- elite association - COSMIC cancer census association via MalaCards
Search H3F3A in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

H33_HUMAN
  • Glioma (GLM) [MIM:137800]: Gliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes. {ECO:0000269 PubMed:22286061, ECO:0000269 PubMed:22286216, ECO:0000269 PubMed:23539269}. Note=The gene represented in this entry is involved in disease pathogenesis. H3F3A mutations affecting residues involved in post-translational modifications of histone H3.3 are recurrent in malignant, aggressive gliomas including glioblastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG) (PubMed:22286061, PubMed:22286216). The mechanism through which mutations lead to tumorigenesis involves altered histones methylation, impaired regulation of Polycomb repressive complex 2 (PRC2) activity, and aberrant epigenetic regulation of gene expression (PubMed:23539269, PubMed:23539183, PubMed:23603901). {ECO:0000269 PubMed:22286061, ECO:0000269 PubMed:22286216, ECO:0000269 PubMed:23539183, ECO:0000269 PubMed:23539269, ECO:0000269 PubMed:23603901}.
  • Note=H3F3A and H3F3B mutations affecting residues involved in post-translational modifications of histone H3.3 are implicated in the pathogenesis of some bone and cartilage neoplasms. Mutations have been found with high prevalence in chondroblastoma and giant cell tumors of bone, and with low frequency in osteosarcoma, conventional chondrosarcoma and clear cell chondrosarcoma. Chondroblastoma samples frequently carry a H3F3B mutation affecting residue Lys-37 (H3K36), although H3F3A is mutated in some cases. Most giant cell tumors of bone harbor H3F3A mutations affecting residue Gly-35 (H3G34). {ECO:0000269 PubMed:24162739}.

Additional Disease Information for H3F3A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with H3F3A: view

No data available for Genatlas for H3F3A Gene

Publications for H3F3A Gene

  1. The human replacement histone H3.3B gene (H3F3B). (PMID: 8586426) Albig W … Doenecke D (Genomics 1995) 3 4 22 58
  2. Unusual structure, evolutionary conservation of non-coding sequences and numerous pseudogenes characterize the human H3.3 histone multigene family. (PMID: 3031613) Wells D … Kedes L (Nucleic acids research 1987) 2 3 4 58
  3. Serine ADP-Ribosylation Depends on HPF1. (PMID: 28190768) Bonfiglio JJ … Matic I (Molecular cell 2017) 3 4 58
  4. ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. (PMID: 24590075) Wen H … Shi X (Nature 2014) 3 4 58
  5. Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma. (PMID: 23539183) Lewis PW … Allis CD (Science (New York, N.Y.) 2013) 3 4 58

Products for H3F3A Gene

  • Addgene plasmids for H3F3A