H2AB1

H2A.B variant histone 1, the group of H2A histones

Basic information

Region (hg38): X:154884972-154885558

Previous symbols: [ "H2AFB1" ]

Links

ENSG00000274183 ∙ NCBI:474382 ∙ OMIM:301037 ∙ HGNC:22516 ∙ Uniprot:P0C5Y9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the H2AB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2AB1 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				1		1
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in H2AB1

This is a list of pathogenic ClinVar variants found in the H2AB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-154885089-G-T		not specified	Uncertain significance (Aug 28, 2024)
X-154885101-C-T		not specified	Uncertain significance (May 23, 2023)
X-154885105-C-T		not specified	Uncertain significance (Jun 29, 2023)
X-154885114-G-A		not specified	Uncertain significance (Jun 24, 2022)
X-154885126-C-T		not specified	Uncertain significance (Dec 11, 2024)
X-154885140-T-C		not specified	Uncertain significance (Mar 25, 2024)
X-154885160-C-T			Likely benign (Apr 01, 2022)
X-154885168-G-A		not specified	Uncertain significance (Dec 08, 2023)
X-154885290-C-T		not specified	Uncertain significance (Feb 27, 2025)
X-154885356-A-G		not specified	Likely benign (Mar 31, 2023)
X-154885372-C-G		not specified	Uncertain significance (Dec 30, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Atypical histone H2A which can replace conventional H2A in some nucleosomes and is associated with active transcription and mRNA processing (PubMed:22795134). 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 (PubMed:15257289, PubMed:16287874, PubMed:16957777, PubMed:17591702, PubMed:17726088, PubMed:18329190, PubMed:22795134). Nucleosomes containing this histone are less rigid and organize less DNA than canonical nucleosomes in vivo (PubMed:15257289, PubMed:16957777, PubMed:17591702, PubMed:24336483). They are enriched in actively transcribed genes and associate with the elongating form of RNA polymerase (PubMed:17591702, PubMed:24753410). They associate with spliceosome components and are required for mRNA splicing (PubMed:22795134). {ECO:0000269|PubMed:15257289, ECO:0000269|PubMed:16287874, ECO:0000269|PubMed:16957777, ECO:0000269|PubMed:17591702, ECO:0000269|PubMed:17726088, ECO:0000269|PubMed:18329190, ECO:0000269|PubMed:22795134, ECO:0000269|PubMed:24336483, ECO:0000269|PubMed:24753410}.
• Pathway: Systemic lupus erythematosus - Homo sapiens (human);Necroptosis - Homo sapiens (human);Alcoholism - Homo sapiens (human);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;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);Generic Transcription Pathway;Oxidative Stress Induced Senescence;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;Metabolism of proteins;Reproduction;RNA Polymerase I Promoter Clearance;RNA Polymerase I Promoter Opening;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;RNA Polymerase I Transcription;Amyloid fiber formation;RNA Polymerase I Chain Elongation;Meiotic recombination;Meiosis;Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3;RHO GTPases activate PKNs;Cellular responses to external stimuli;RHO GTPase Effectors;Signaling by Rho GTPases;Packaging Of Telomere Ends;Telomere Maintenance;Chromosome Maintenance;Condensation of Prophase Chromosomes;Signaling by Nuclear Receptors;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;Cell Cycle, Mitotic;ESR-mediated signaling;Transcriptional regulation by RUNX1;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)

Haploinsufficiency Scores

• pHI: 0.108

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0193

Mouse Genome Informatics

• Gene name: H2afb3

Gene ontology

• Biological process: chromatin organization;nucleosome assembly;mRNA processing
• Cellular component: nuclear nucleosome;nuclear chromatin;nucleus;transcriptionally active chromatin
• Molecular function: DNA binding;protein heterodimerization activity