H2BW2

H2B.W histone 2, the group of H2B histones

Basic information

Region (hg38): X:104039956-104042454

Previous symbols: [ "H2BFM", "H2BM" ]

Links

ENSG00000101812 ∙ NCBI:286436 ∙ ∙ HGNC:27867 ∙ Uniprot:P0C1H6 ∙ 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 H2BW2 gene.

• not_specified (40 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2BW2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001388464.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			38	2		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	3	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H2BW2	protein_coding	protein_coding	ENST00000355016	2	28753

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0140	0.691	49823	25087	21301	96211	0.280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.04	84	61.1	1.37	0.00000580	968
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.249	0.241
Ashkenazi Jewish	0.501	0.389
East Asian	0.400	0.319
Finnish	0.403	0.317
European (Non-Finnish)	0.425	0.331
Middle Eastern	0.400	0.319
South Asian	0.481	0.327
Other	0.403	0.310

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) (Consensus)

Intolerance Scores

• rvis_EVS: 0.61
• rvis_percentile_EVS: 83

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: H2bfm

Gene ontology

• Biological process: nucleosome assembly
• Cellular component: nucleosome;nucleus
• Molecular function: DNA binding;protein heterodimerization activity