H2BC26

H2B clustered histone 26, the group of H2B histones

Basic information

Region (hg38): 1:228458103-228463104

Previous symbols: [ "HIST3H2BB", "H2BU1" ]

Links

ENSG00000196890NCBI:128312OMIM:615046HGNC:20514Uniprot:Q8N257AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the H2BC26 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2BC26 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
clinvar
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 H2BC26

This is a list of pathogenic ClinVar variants found in the H2BC26 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
1-228458140-C-T not specified Uncertain significance (Apr 27, 2024)3283331
1-228458155-C-T not specified Uncertain significance (Jun 28, 2023)2606780
1-228458157-G-A not specified Uncertain significance (Nov 24, 2024)3523691
1-228458158-C-T not specified Uncertain significance (Feb 14, 2024)3103808
1-228458167-A-T not specified Uncertain significance (Jun 13, 2023)2559921
1-228458194-C-T not specified Uncertain significance (Dec 13, 2021)3103809
1-228458209-G-A not specified Uncertain significance (Nov 14, 2024)3523692
1-228458217-C-T not specified Uncertain significance (Dec 12, 2023)3103810
1-228458238-A-C not specified Uncertain significance (Jan 04, 2024)3103805
1-228458277-C-T not specified Uncertain significance (Aug 12, 2022)3103806
1-228458316-A-C not specified Uncertain significance (Dec 06, 2022)3103807
1-228458337-A-G not specified Uncertain significance (Jun 29, 2023)2608340
1-228458406-C-T not specified Uncertain significance (Mar 17, 2023)2526320

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
H2BC26protein_codingprotein_codingENST00000369160 1452
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00005160.14600000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.6109377.91.190.00000348813
Missense in Polyphen1714.021.2125177
Synonymous-5.377534.82.160.00000163270
Loss of Function-1.6152.352.139.75e-834

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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;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;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
0.614
rvis_EVS
-0.32
rvis_percentile_EVS
31.46

Haploinsufficiency Scores

pHI
0.827
hipred
N
hipred_score
0.375
ghis
0.503

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.965

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Hist3h2bb-ps
Phenotype

Gene ontology

Biological process
nucleosome assembly
Cellular component
nucleosome;nucleus;nucleoplasm;cytosol
Molecular function
molecular_function;DNA binding;protein heterodimerization activity