H2AB1

protein-coding

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

Gene summary

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent histone that is a member of the histone H2A family. This gene is part of a region that is repeated three times on chromosome X, once in intron 22 of the F8 gene and twice closer to the Xq telomere. This record represents the most centromeric copy which is in intron 22 of the F8 gene. [provided by RefSeq, Oct 2015]

Previous symbols:

H2AFB1

MANE transcript

NM_001017990.2

Inheritance

—

ClinVar variants

U:15B:2

Top phenotype

Hereditary factor VIII deficiency disease

Max pathogenic AF

—

Genomic locus

chrX:154,884,972-154,885,558

External References & Databases

Ensembl (ENSG00000274183)

Transcript & Mutation Effects

hg38 • Region Span ~0.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to H2AB1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 15

not providedTotal: 1

Hereditary factor VIII deficiency diseaseTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001017990.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			15 clinvar	1 clinvar		16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	2	0	17

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001017990.2	RefSeq	NP_001017990.1	1	MANE Select
ENST00000620016.2	Ensembl	ENSP00000484261.2	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

chromatin organization
nucleosome assembly
mRNA processing

Molecular Function

DNA binding
protein heterodimerization activity

Cellular Component

nuclear nucleosome
nuclear chromatin
nucleus
transcriptionally active chromatin

dbNSFP Gene Annotations

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}.;

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0193