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.

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.

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			25	1		26
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	27	2	1

Variants in H2BW2

This is a list of pathogenic ClinVar variants found in the H2BW2 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-104039981-C-T		not specified	Uncertain significance (Oct 12, 2021)
X-104039992-G-A		not specified	Uncertain significance (Jun 29, 2023)
X-104040018-A-G			Likely benign (Feb 01, 2024)
X-104040055-G-A		not specified	Uncertain significance (Aug 12, 2021)
X-104040058-G-T		not specified	Uncertain significance (Aug 12, 2021)
X-104040061-A-C		not specified	Uncertain significance (Apr 20, 2023)
X-104040068-C-T		not specified	Uncertain significance (Dec 09, 2023)
X-104040103-G-C		not specified	Uncertain significance (Jun 03, 2022)
X-104040126-C-A		not specified	Uncertain significance (Jan 03, 2022)
X-104040152-G-C		not specified	Uncertain significance (Oct 06, 2021)
X-104040163-T-G		not specified	Uncertain significance (Feb 25, 2025)
X-104040164-A-C		not specified	Uncertain significance (Sep 25, 2024)
X-104040193-C-T			Benign (Aug 24, 2018)
X-104040232-G-C		not specified	Uncertain significance (Feb 01, 2025)
X-104040248-A-T		not specified	Uncertain significance (May 04, 2023)
X-104040251-T-C		not specified	Conflicting classifications of pathogenicity (May 15, 2024)
X-104040259-C-T		not specified	Uncertain significance (Feb 27, 2024)
X-104040260-G-A		not specified	Uncertain significance (Nov 25, 2024)
X-104040265-G-A		not specified	Uncertain significance (Dec 26, 2023)
X-104040269-C-A		not specified	Uncertain significance (Jun 11, 2024)
X-104040271-G-A		not specified	Uncertain significance (May 31, 2023)
X-104040273-G-T		not specified	Uncertain significance (Sep 08, 2024)
X-104040302-G-A		not specified	Uncertain significance (Nov 25, 2024)
X-104040313-A-C		not specified	Uncertain significance (May 21, 2024)
X-104040320-G-T		not specified	Uncertain significance (Jan 23, 2023)

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