H2BW2

protein-coding

H2B.W histone 2, the group of H2B histones

Gene summary

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene encodes a replication-independent histone that is a member of the H2B histone family. [provided by RefSeq, Nov 2015]

Previous symbols:

H2BFM
H2BM

MANE transcript

NM_001388464.1

Inheritance

—

ClinVar variants

U:41B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chrX:104,039,956-104,042,454

External References & Databases

Ensembl (ENSG00000101812)

Transcript & Mutation Effects

hg38 • Region Span ~2.5 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 H2BW2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 43

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001388464.1. 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			41 clinvar	2 clinvar		43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	3	0	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001388464.1	RefSeq	NP_001375393.1	2	MANE Select
ENST00000675318.3	Ensembl	ENSP00000502072.2	2	MANE Select
NM_001164416.4	RefSeq	NP_001157888.2	2	Standard
ENST00000355016.8	Ensembl	ENSP00000347119.4	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Systemic lupus erythematosus - Homo sapiens (human)
Viral carcinogenesis - Homo sapiens (human)
Alcoholism - Homo sapiens (human)

Biological Process

nucleosome assembly

Molecular Function

DNA binding
protein heterodimerization activity

Cellular Component

nucleosome
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355016
Coding exons: 2
Length: 28753
Individuals with no LoFs: 49823
Homozygous LoFs: 25087
Heterozygous LoFs: 21301
Defined: 96211
p: 0.280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.04	84	61.1	1.37	0.00000580	968
Missense (PolyPhen)		27	17.019	1.5865		349
Synonymous	-2.05	38	24.9	1.52	0.00000230	309
Loss of Function	0.602	3	4.36	0.689	4.44e-7	59

Population LoF Frequency

Population	CAF	p-value	Status
African	0.059	0.050	notable
Latino/Admixed American	0.19	0.15	notable
Ashkenazi Jewish	0.50	0.39	notable
East Asian	0.40	0.32	notable
Finnish	0.40	0.32	notable
European (Non-Finnish)	0.43	0.33	notable
South Asian	0.48	0.33	notable
Other	0.40	0.31	notable

dbNSFP Gene Annotations

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.;

Intolerance Scores

RVIS EVS: 0.61
RVIS percentile EVS: 83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium