H3-3A (H3.3 histone A)

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Gene Gene ontology Other IDs Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 3020
• Gene name: H3.3 histone A
• Gene symbol: H3-3A
• Synonyms (NCBI Gene): BRYLIB1, H3-3B, H3.3A, H3F3, H3F3A
• Chromosome: 1
• Chromosome location: 1q42.12
• 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

Gene ontology (GO) Show/Hide all (48)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000775	Component	Chromosome, centromeric region	IEA
GO:0000781	Component	Chromosome, telomeric region	IDA	20110566
GO:0000785	Component	Chromatin	IEA
GO:0000786	Component	Nucleosome	IDA	14718166, 19633671, 21636898, 25615412
GO:0000786	Component	Nucleosome	IEA
GO:0000939	Component	Inner kinetochore	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	19633671
GO:0000979	Function	RNA polymerase II core promoter sequence-specific DNA binding	IDA	19633671
GO:0001556	Process	Oocyte maturation	IEA
GO:0001649	Process	Osteoblast differentiation	IEA
GO:0001740	Component	Barr body	IEA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	19494831, 19834512, 20110566, 20211137, 20448663, 20504901, 20651253, 20953165, 23075851, 23142979, 24183680, 24209620, 24590075, 24981860, 25416956, 26167883, 26439302, 32296183, 33857403, 33961781
GO:0005576	Component	Extracellular region	TAS
GO:0005634	Component	Nucleus	HDA	21630459
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	21636898
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	IMP	34876591
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005694	Component	Chromosome	IEA
GO:0006334	Process	Nucleosome assembly	IDA	21636898
GO:0006334	Process	Nucleosome assembly	IMP	25615412
GO:0006997	Process	Nucleus organization	IEA
GO:0007283	Process	Spermatogenesis	IEA
GO:0007286	Process	Spermatid development	IEA
GO:0007338	Process	Single fertilization	IEA
GO:0007566	Process	Embryo implantation	IEA
GO:0008283	Process	Cell population proliferation	IEA
GO:0008584	Process	Male gonad development	IEA
GO:0030307	Process	Positive regulation of cell growth	IMP	21274551
GO:0030527	Function	Structural constituent of chromatin	IDA	14718166
GO:0030527	Function	Structural constituent of chromatin	IEA
GO:0031492	Function	Nucleosomal DNA binding	IDA	19633671
GO:0031508	Process	Pericentric heterochromatin formation	IEA
GO:0031509	Process	Subtelomeric heterochromatin formation	IEA
GO:0032200	Process	Telomere organization	TAS	17675446
GO:0032991	Component	Protein-containing complex	IDA	14718166
GO:0035264	Process	Multicellular organism growth	IEA
GO:0042692	Process	Muscle cell differentiation	IEA
GO:0046982	Function	Protein heterodimerization activity	IEA
GO:0048477	Process	Oogenesis	IEA
GO:0070062	Component	Extracellular exosome	HDA	20458337
GO:0090230	Process	Regulation of centromere complex assembly	IEA
GO:1902340	Process	Negative regulation of chromosome condensation	IEA

Other IDs

• MIM: 601128
• HGNC: 4764
• e!Ensembl: ENSG00000163041

Interactions View interactions

Pathways

KEGG Pathway	Reactome Pathway
Neutrophil extracellular trap formation	Formation of the beta-catenin:TCF transactivating complex
Alcoholism	PRC2 methylates histones and DNA
Shigellosis	Condensation of Prophase Chromosomes
Transcriptional misregulation in cancer	Oxidative Stress Induced Senescence
Systemic lupus erythematosus	Senescence-Associated Secretory Phenotype (SASP)
	SIRT1 negatively regulates rRNA expression
	NoRC negatively regulates rRNA expression
	B-WICH complex positively regulates rRNA expression
	Transcriptional regulation by small RNAs
	Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
	RNA Polymerase I Promoter Opening
	RNA Polymerase I Promoter Escape
	RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
	Estrogen-dependent gene expression
	Amyloid fiber formation
	Factors involved in megakaryocyte development and platelet production

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal Show/Hide Causal Diseases (9)
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Brain imaging abnormality	Likely pathogenic; Pathogenic	rs2102735801, rs2102736976, rs2102742562, rs1658121882	RCV001541909 RCV001541910 RCV001541912 RCV001541914	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bryant-Li-Bhoj neurodevelopmental syndrome 1	Likely pathogenic; Pathogenic	rs2102735801, rs2102742562, rs1658121882, rs2102735576, rs1276519904, rs1657904113, rs1657901999, rs1658118461	RCV001823778 RCV003314008 RCV001823780 RCV001823808 RCV001823740 RCV003493835 RCV001823766 RCV002226429	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Delayed speech and language development	Likely pathogenic; Pathogenic	rs2102735801, rs2102736976, rs2102742562, rs1658121882	RCV001541909 RCV001541910 RCV001541912 RCV001541914	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Likely pathogenic; Pathogenic	rs2102735801, rs2102736976, rs2102742562, rs1658121882	RCV001541909 RCV001541910 RCV001541912 RCV001541914	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
H3-3A-related disorder	Likely pathogenic	rs1657903750	RCV003393935	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
H3F3A-related disorder	Likely pathogenic; Pathogenic	rs1276519904, rs1576203003	RCV004555590 RCV003336364	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Likely pathogenic; Pathogenic	rs2102735801, rs2102736976, rs2102742562, rs1658121882	RCV001541909 RCV001541910 RCV001541912 RCV001541914	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Likely pathogenic	rs1657904113	RCV001262997	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Short stature	Likely pathogenic; Pathogenic	rs2102735801, rs2102736976, rs2102742562, rs1658121882	RCV001541909 RCV001541910 RCV001541912 RCV001541914	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations Show/Hide Unknown Diseases (10)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
BRYANT-LI-BHOJ NEURODEVELOPMENTAL SYNDROME 2	—	Disgenet	31942419,33057194,33268356	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diffuse glioma, H3 G34 mutant	other	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diffuse midline glioma, H3 K27M-mutant	-	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ganglioglioma	-	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GIANT CELL TUMOR OF BONE	—	CTD	24162739	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glioblastoma	other	ClinVar CTD	22286216, 23817572	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
GLIOMA	—	CTD	22286216, 23583981	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	35835914	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neoplasm	-	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Central Nervous System Neoplasms	Central nervous system neoplasm	Pubtator	22829774	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	22829774	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	22829774	Associate	★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

H3-3B 1 shared diseaseBryant-li-bhoj neurodevelopmental syndrome 21 shared pathwaysNeutrophil extracellular trap formation, Alcoholism, Shigellosis, Transcriptional misregulation in cancer, Systemic lupus erythematosus, Factors involved in megakaryocyte development and platelet production, Condensation of Prophase Chromosomes, Oxidative Stress Induced Senescence, Amyloid fiber formation, Senescence-Associated Secretory Phenotype (SASP), RNA Polymerase I Promoter Escape, Estrogen-dependent gene expression +9 more 3 shared evidence sourcesClinVar (Bryant-li-bhoj neurodevelopmental syndrome), Disgenet (Bryant-li-bhoj neurodevelopmental syndrome), HPO (Bryant-li-bhoj neurodevelopmental syndrome) Related via 21 shared pathways including Neutrophil extracellular trap formation, Alcoholism — evidence mostly ClinVar. H3C2 21 shared pathwaysNeutrophil extracellular trap formation, Alcoholism, Shigellosis, Transcriptional misregulation in cancer, Systemic lupus erythematosus, Factors involved in megakaryocyte development and platelet production, Condensation of Prophase Chromosomes, Oxidative Stress Induced Senescence, Amyloid fiber formation, Senescence-Associated Secretory Phenotype (SASP), RNA Polymerase I Promoter Escape, Estrogen-dependent gene expression +9 more 2 shared evidence sourcesCTD (Glioblastoma), CTD (Glioma) Related via 21 shared pathways including Neutrophil extracellular trap formation, Alcoholism — evidence mostly CTD. H3C14 21 shared pathwaysNeutrophil extracellular trap formation, Alcoholism, Shigellosis, Transcriptional misregulation in cancer, Systemic lupus erythematosus, Factors involved in megakaryocyte development and platelet production, Condensation of Prophase Chromosomes, Oxidative Stress Induced Senescence, Amyloid fiber formation, Senescence-Associated Secretory Phenotype (SASP), RNA Polymerase I Promoter Escape, Estrogen-dependent gene expression +9 more Related via 21 shared pathways including Neutrophil extracellular trap formation, Alcoholism. H3C15 21 shared pathwaysNeutrophil extracellular trap formation, Alcoholism, Shigellosis, Transcriptional misregulation in cancer, Systemic lupus erythematosus, Factors involved in megakaryocyte development and platelet production, Condensation of Prophase Chromosomes, Oxidative Stress Induced Senescence, Amyloid fiber formation, Senescence-Associated Secretory Phenotype (SASP), RNA Polymerase I Promoter Escape, Estrogen-dependent gene expression +9 more Related via 21 shared pathways including Neutrophil extracellular trap formation, Alcoholism. H3C13 21 shared pathwaysNeutrophil extracellular trap formation, Alcoholism, Shigellosis, Transcriptional misregulation in cancer, Systemic lupus erythematosus, Factors involved in megakaryocyte development and platelet production, Condensation of Prophase Chromosomes, Oxidative Stress Induced Senescence, Amyloid fiber formation, Senescence-Associated Secretory Phenotype (SASP), RNA Polymerase I Promoter Escape, Estrogen-dependent gene expression +9 more Related via 21 shared pathways including Neutrophil extracellular trap formation, Alcoholism.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
H3-3B	1	["Bryant-li-bhoj neurodevelopmental syndrome"]	21	["Neutrophil extracellular trap formation","Alcoholism","Shigellosis","Transcriptional misregulation in cancer","Systemic lupus erythematosus","Factors involved in megakaryocyte development and platelet production","Condensation of Prophase Chromosomes","Oxidative Stress Induced Senescence","Amyloid fiber formation","Senescence-Associated Secretory Phenotype (SASP)","RNA Polymerase I Promoter Escape","Estrogen-dependent gene expression"]	3	["ClinVar (Bryant-li-bhoj neurodevelopmental syndrome)","Disgenet (Bryant-li-bhoj neurodevelopmental syndrome)","HPO (Bryant-li-bhoj neurodevelopmental syndrome)"]
H3C2	0	[]	21	["Neutrophil extracellular trap formation","Alcoholism","Shigellosis","Transcriptional misregulation in cancer","Systemic lupus erythematosus","Factors involved in megakaryocyte development and platelet production","Condensation of Prophase Chromosomes","Oxidative Stress Induced Senescence","Amyloid fiber formation","Senescence-Associated Secretory Phenotype (SASP)","RNA Polymerase I Promoter Escape","Estrogen-dependent gene expression"]	2	["CTD (Glioblastoma)","CTD (Glioma)"]
H3C14	0	[]	21	["Neutrophil extracellular trap formation","Alcoholism","Shigellosis","Transcriptional misregulation in cancer","Systemic lupus erythematosus","Factors involved in megakaryocyte development and platelet production","Condensation of Prophase Chromosomes","Oxidative Stress Induced Senescence","Amyloid fiber formation","Senescence-Associated Secretory Phenotype (SASP)","RNA Polymerase I Promoter Escape","Estrogen-dependent gene expression"]	0	[]
H3C15	0	[]	21	["Neutrophil extracellular trap formation","Alcoholism","Shigellosis","Transcriptional misregulation in cancer","Systemic lupus erythematosus","Factors involved in megakaryocyte development and platelet production","Condensation of Prophase Chromosomes","Oxidative Stress Induced Senescence","Amyloid fiber formation","Senescence-Associated Secretory Phenotype (SASP)","RNA Polymerase I Promoter Escape","Estrogen-dependent gene expression"]	0	[]
H3C13	0	[]	21	["Neutrophil extracellular trap formation","Alcoholism","Shigellosis","Transcriptional misregulation in cancer","Systemic lupus erythematosus","Factors involved in megakaryocyte development and platelet production","Condensation of Prophase Chromosomes","Oxidative Stress Induced Senescence","Amyloid fiber formation","Senescence-Associated Secretory Phenotype (SASP)","RNA Polymerase I Promoter Escape","Estrogen-dependent gene expression"]	0	[]

Diseases Linked via Similar Genes

Asthma Linked via 1 of 5 related genesH3-3B Chondroblastoma Linked via 1 of 5 related genesH3-3B Hemiparkinsonism hemiatrophy syndrome Linked via 1 of 5 related genesH3-3B Hematologic neoplasms Linked via 1 of 5 related genesH3C2

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Asthma	1	["H3-3B"]
Chondroblastoma	1	["H3-3B"]
Hemiparkinsonism hemiatrophy syndrome	1	["H3-3B"]
Hematologic neoplasms	1	["H3C2"]