H2BC5
H2B clustered histone 5, the group of H2B histones
Basic information
Region (hg38): 6:26158122-26171349
Previous symbols: [ "H2BFB", "HIST1H2BD" ]
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 H2BC5 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in H2BC5
This is a list of pathogenic ClinVar variants found in the H2BC5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-26158216-A-G | not specified | Uncertain significance (Oct 25, 2023) | ||
| 6-26158234-C-A | not specified | Uncertain significance (May 25, 2022) | ||
| 6-26158266-A-G | not specified | Uncertain significance (Jan 20, 2025) | ||
| 6-26158272-A-C | not specified | Uncertain significance (Jul 09, 2021) | ||
| 6-26158408-G-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 6-26158426-A-G | not specified | Uncertain significance (Jul 07, 2022) | ||
| 6-26158440-A-T | not specified | Uncertain significance (Mar 06, 2023) | ||
| 6-26158441-C-T | not specified | Uncertain significance (May 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| H2BC5 | protein_coding | protein_coding | ENST00000289316 | 1 | 13229 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000421 | 0.0666 | 125727 | 0 | 21 | 125748 | 0.0000835 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0138 | 69 | 69.3 | 0.995 | 0.00000332 | 808 |
| Missense in Polyphen | 12 | 12.289 | 0.97648 | 173 | ||
| Synonymous | -6.43 | 76 | 30.7 | 2.48 | 0.00000152 | 268 |
| Loss of Function | -2.43 | 6 | 2.15 | 2.79 | 9.08e-8 | 38 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000214 | 0.000213 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000392 | 0.000392 |
| Other | 0.00 | 0.00 |
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
- 0.113
Intolerance Scores
- loftool
- 0.658
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.621
- ghis
- 0.410
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- 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 |
Gene ontology
- Biological process
- nucleosome assembly;protein ubiquitination
- Cellular component
- nucleosome;nucleus;nucleoplasm;cytosol;extracellular exosome
- Molecular function
- molecular_function;DNA binding;protein heterodimerization activity