H2BC11
H2B clustered histone 11, the group of H2B histones
Basic information
Region (hg38): 6:27122657-27132795
Previous symbols: [ "H2BFR", "HIST1H2BJ" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2BC11 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in H2BC11
This is a list of pathogenic ClinVar variants found in the H2BC11 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-27132459-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 6-27132462-T-A | not specified | Uncertain significance (Oct 04, 2024) | ||
| 6-27132506-G-A | not specified | Uncertain significance (Mar 05, 2025) | ||
| 6-27132512-C-T | not specified | Uncertain significance (May 31, 2023) | ||
| 6-27132599-G-T | not specified | Uncertain significance (Apr 12, 2023) | ||
| 6-27132614-A-T | not specified | Uncertain significance (Feb 28, 2023) | ||
| 6-27132659-T-C | not specified | Uncertain significance (Aug 30, 2021) | ||
| 6-27132662-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
| 6-27132672-C-A | not specified | Uncertain significance (Dec 21, 2022) | ||
| 6-27132672-C-T | not specified | Uncertain significance (Jan 15, 2025) | ||
| 6-27132692-G-A | not specified | Uncertain significance (May 03, 2023) | ||
| 6-27132696-C-T | not specified | Uncertain significance (Aug 05, 2024) | ||
| 6-27132699-C-T | not specified | Uncertain significance (Jun 29, 2023) | ||
| 6-27132704-T-A | not specified | Uncertain significance (Mar 20, 2024) | ||
| 6-27132740-G-A | not specified | Uncertain significance (Oct 09, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| H2BC11 | protein_coding | protein_coding | ENST00000607124 | 1 | 6866 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0313 | 0.618 | 125724 | 0 | 24 | 125748 | 0.0000954 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.55 | 107 | 70.4 | 1.52 | 0.00000338 | 810 |
| Missense in Polyphen | 22 | 18.795 | 1.1705 | 272 | ||
| Synonymous | -7.85 | 83 | 29.1 | 2.85 | 0.00000151 | 255 |
| Loss of Function | 0.234 | 2 | 2.39 | 0.837 | 1.02e-7 | 43 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000879 | 0.0000879 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.000229 | 0.000229 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Core component of nucleosome. 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.;
- Pathway
- Systemic lupus erythematosus - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Alcoholism - Homo sapiens (human);HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);B-WICH complex positively regulates rRNA expression;ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;SIRT1 negatively regulates rRNA expression;DNA Repair;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Signaling by WNT;Signal Transduction;DNA methylation;Epigenetic regulation of gene expression;Gene expression (Transcription);Nonhomologous End-Joining (NHEJ);DNA Double-Strand Break Repair;Generic Transcription Pathway;Oxidative Stress Induced Senescence;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Homology Directed Repair;Cellular responses to stress;Post-translational protein modification;HDACs deacetylate histones;Metabolism of proteins;Reproduction;RNA Polymerase I Promoter Clearance;RNA Polymerase I Promoter Opening;RNA Polymerase II Transcription;G2/M DNA damage checkpoint;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Chromatin modifying enzymes;G2/M Checkpoints;Cell Cycle Checkpoints;RNA Polymerase I Transcription;Amyloid fiber formation;RNA Polymerase I Chain Elongation;Meiotic recombination;Meiotic synapsis;Meiosis;Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3;RHO GTPases activate PKNs;HATs acetylate histones;Cellular responses to external stimuli;RHO GTPase Effectors;Signaling by Rho GTPases;Packaging Of Telomere Ends;Telomere Maintenance;Chromosome Maintenance;Ub-specific processing proteases;Condensation of Prophase Chromosomes;Deubiquitination;Signaling by Nuclear Receptors;Chromatin organization;Mitotic Prophase;M Phase;Protein ubiquitination;Estrogen-dependent gene expression;Transcriptional regulation by small RNAs;RUNX1 regulates transcription of genes involved in differentiation of HSCs;Cell Cycle;Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks;DNA Double Strand Break Response;Cell Cycle, Mitotic;ESR-mediated signaling;Transcriptional regulation by RUNX1;E3 ubiquitin ligases ubiquitinate target proteins;Processing of DNA double-strand break ends;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT;Gene Silencing by RNA;PRC2 methylates histones and DNA
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.529
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.42
Haploinsufficiency Scores
- pHI
- 0.971
- hipred
- N
- hipred_score
- 0.339
- ghis
- 0.586
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hist2h2be
- Phenotype
- taste/olfaction phenotype; growth/size/body region phenotype; cellular phenotype; craniofacial phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); respiratory system phenotype;
Gene ontology
- Biological process
- innate immune response in mucosa;nucleosome assembly;negative regulation of tumor necrosis factor-mediated signaling pathway;protein ubiquitination;antibacterial humoral response;killing of cells of other organism;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;antimicrobial humoral immune response mediated by antimicrobial peptide
- Cellular component
- nucleosome;extracellular space;nucleus;nucleoplasm;cytosol;plasma membrane
- Molecular function
- lipopolysaccharide binding;DNA binding;protein binding;protein heterodimerization activity