H3-3B (H3.3 histone B)

Gene

• Entrez ID: 3021
• Gene name: H3.3 histone B
• Gene symbol: H3-3B
• Synonyms (NCBI Gene): BRYLIB2, H3-3A, H3.3B, H3F3B
• Chromosome: 17
• Chromosome location: 17q25.1
• 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)

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: 601058
• HGNC: 4765
• e!Ensembl: ENSG00000132475

Interactions View interactions

Pathways

KEGG:

Neutrophil extracellular trap formation
Alcoholism
Shigellosis
Transcriptional misregulation in cancer
Systemic lupus erythematosus

Reactome:

Formation of the beta-catenin:TCF transactivating complex
PRC2 methylates histones and DNA
Condensation of Prophase Chromosomes
Oxidative Stress Induced Senescence
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
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Brain imaging abnormality	Likely pathogenic; Pathogenic	rs2143629918, rs2143630846, rs2143631320, rs2143631415	RCV001541920 RCV001541919 RCV001541918 RCV001541917	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Bryant-Li-Bhoj neurodevelopmental syndrome 2	Likely pathogenic; Pathogenic	rs2143630846, rs2143631293, rs2143629995, rs2143629984, rs2143631320, rs2545911185, rs2545910776, rs2545911172	RCV001823781 RCV001823805 RCV001823806 RCV001823807 RCV002267589 RCV002287214 RCV003315190 RCV003479647	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Delayed speech and language development	Likely pathogenic; Pathogenic	rs2143629918, rs2143630846, rs2143631320, rs2143631415	RCV001541920 RCV001541919 RCV001541918 RCV001541917	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Likely pathogenic; Pathogenic	rs2143629918, rs2143630846, rs2143631320, rs2143631415	RCV001541920 RCV001541919 RCV001541918 RCV001541917	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
H3-3B-related disorder	Likely pathogenic; Pathogenic	rs2143629984	RCV003407831	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Likely pathogenic; Pathogenic	rs2143629918, rs2143630846, rs2143631320, rs2143631415	RCV001541920 RCV001541919 RCV001541918 RCV001541917	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Likely pathogenic; Pathogenic	rs2143631260	RCV004785535	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Short stature	Likely pathogenic; Pathogenic	rs2143629918, rs2143630846, rs2143631320, rs2143631415	RCV001541920 RCV001541919 RCV001541918 RCV001541917	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHONDROBLASTOMA	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEMIPARKINSONISM HEMIATROPHY SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hemiparkinsonism-hemiatrophy syndrome	Uncertain significance	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
Adrenocortical carcinoma	Adrenocortical carcinoma	CLINVAR_DG	26619011		★☆☆☆☆ Found in Text Mining only
Adult Oligodendroglioma	Oligodendroglioma	BEFREE	26493382		★☆☆☆☆ Found in Text Mining only
ALPHA-THALASSEMIA/MENTAL RETARDATION SYNDROME, NONDELETION TYPE, X-LINKED	alpha-Thalassemia Mental Retardation Syndrome, X-Linked	BEFREE	22886134		★☆☆☆☆ Found in Text Mining only
Anaplastic astrocytoma	Anaplastic Astrocytoma	BEFREE	23595628, 27392443		★☆☆☆☆ Found in Text Mining only
Astigmatism	Astigmatism	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Astrocytoma	Astrocytoma	BEFREE	23429371, 24285547, 26493382, 27311324, 28032389, 30358620		★☆☆☆☆ Found in Text Mining only
Astrocytoma	Astrocytoma	CLINVAR_DG	26619011		★☆☆☆☆ Found in Text Mining only
Bilateral camptodactyly	Camptodactyly	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain Neoplasms	BEFREE	23429371, 28416018, 30943283		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain Neoplasms	CLINVAR_DG	26619011		★☆☆☆☆ Found in Text Mining only
Brain Stem Glioma	Brain Stem Glioma	CLINVAR_DG	26619011		★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	15870878		★☆☆☆☆ Found in Text Mining only
Central Nervous System Neoplasms	Central Nervous System Neoplasms	BEFREE	23429371		★☆☆☆☆ Found in Text Mining only
Childhood Oligodendroglioma	Oligodendroglioma	BEFREE	26493382		★☆☆☆☆ Found in Text Mining only
Chondroblastoma	Chondroblastoma	BEFREE	24162739, 26457357, 26844533, 28059095, 28129023, 28211081, 28899740, 29757500, 30582658		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chondroblastoma	Chondroblastoma	CTD_human_DG	24162739		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chondromyxoid fibroma	Chondromyxoid Fibroma	BEFREE	30582658		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	21716316		★☆☆☆☆ Found in Text Mining only
Congenital chromosomal disease	Congenital Chromosomal Disease	BEFREE	29944971		★☆☆☆☆ Found in Text Mining only
Craniosynostosis	Craniosynostosis	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	BEFREE	25807424		★☆☆☆☆ Found in Text Mining only
Deglutition Disorders	Dysphagia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Diffuse Intrinsic Pontine Glioma	Diffuse Intrinsic Pontine Glioma	BEFREE	22286216, 26727948, 28339768, 31328874, 31848724		★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	10556297, 16472024, 17220215, 19344873, 19348700, 20976243, 21782046, 21937992, 23415232, 25348405, 26139371, 9441765		★☆☆☆☆ Found in Text Mining only
Exotropia	Exotropia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Giant Cell Glioblastoma	Giant Cell Glioblastoma	CTD_human_DG	22286216, 23817572		★☆☆☆☆ Found in Text Mining only
Giant Cell Tumor of Bone	Giant cell tumor of bone	BEFREE	24162739, 26457357, 27020452, 28059095, 28545165, 28899740, 29048579, 29206281, 29254795, 29356963, 29944971, 30582658, 30742944, 31015476, 31285528, 31728625, 31748824, 31784095		★☆☆☆☆ Found in Text Mining only
Giant Cell Tumor of Bone	Giant cell tumor of bone	CTD_human_DG	24162739		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	CTD_human_DG	22286216, 23817572		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	22886134, 23079654, 23414300, 23429371, 23595628, 23658294, 23817572, 23900077, 23907119, 24285547, 24445767, 24997139, 25200322, 25943888, 26087904, 26376656, 27392443, 28447171, 29063957, 30203362		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	CLINVAR_DG	26619011		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	22286061, 23079654, 23414300, 23595628, 23658294, 23817572, 23907119, 24285547, 24445767, 24997139, 25943888, 26087904, 26376656, 27392443		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	CTD_human_DG	22286216, 23817572		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	CTD_human_DG	22286216, 23583981		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	23595628, 24285547, 24997139, 26376656, 26681766, 27311324, 27392443, 28852847, 29053887, 30864101, 31254135, 31419298		★☆☆☆☆ Found in Text Mining only
gliosarcoma	Gliosarcoma	BEFREE	29809131		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Laryngeal cleft	Laryngeal cleft	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Laryngomalacia	Laryngomalacia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	31633236		★☆☆☆☆ Found in Text Mining only
Long narrow head	Dolichocephaly	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Malignant Glioma	Glioma	CTD_human_DG	22286216, 23583981		★☆☆☆☆ Found in Text Mining only
Malignant Glioma	Glioma	BEFREE	31139567		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	23658294, 26700204, 28129023, 29689253, 29970305		★☆☆☆☆ Found in Text Mining only
Medulloblastoma	Medulloblastoma	BEFREE	30830680		★☆☆☆☆ Found in Text Mining only
Mesenchymal Chondrosarcoma	Mesenchymal Chondrosarcoma	BEFREE	30582658		★☆☆☆☆ Found in Text Mining only
Mesocardia	Mesocardia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Metopic synostosis	Metopic synostosis	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
mixed gliomas	Glioma	CTD_human_DG	22286216, 23583981		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	22286061, 23414300, 23417712, 23429371, 24162739, 24548782, 25231549, 26457357, 27311324, 27392443, 28416018, 28823044, 29053887, 29137285, 29356963, 29532523, 29970305, 30298540, 31015476		★☆☆☆☆ Found in Text Mining only
Neuronal heterotopia	Neuronal Heterotopia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Noninfiltrating Intraductal Carcinoma	Ductal carcinoma	BEFREE	31784095		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
oligodendroglioma	Oligodendroglioma	BEFREE	26493382		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	28211081, 31285528		★☆☆☆☆ Found in Text Mining only
Periventricular gray matter heterotopia	Periventricular gray matter heterotopia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Plagiocephaly	Plagiocephaly	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Pleomorphic Xanthoastrocytoma	Pleomorphic Xanthoastrocytoma	BEFREE	29532523		★☆☆☆☆ Found in Text Mining only
Sagittal craniosynostosis	Sagittal craniosynostosis	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	BEFREE	28211081, 28899740, 29609578, 29970305, 31285528		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	29529098		★☆☆☆☆ Found in Text Mining only
Sleep Apnea, Central	Sleep Apnea	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Sleep Apnea, Obstructive	Sleep Apnea	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Tracheomalacia	Tracheomalacia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Unilateral Cryptorchidism	Cryptorchidism	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Unilateral deafness	Deafness	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Well Differentiated Oligodendroglioma	Oligodendroglioma	BEFREE	26493382		★☆☆☆☆ Found in Text Mining only