H2BW1

H2B.W histone 1, the group of H2B histones

Basic information

Region (hg38): X:104011147-104013708

Previous symbols: [ "H2BFWT" ]

Links

ENSG00000123569 ∙ NCBI:158983 ∙ OMIM:300507 ∙ HGNC:27252 ∙ Uniprot:Q7Z2G1 ∙ 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 H2BW1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2BW1 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			22	1		23
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			6			6
Total	0	0	28	3	0

Variants in H2BW1

This is a list of pathogenic ClinVar variants found in the H2BW1 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-104012717-T-G		not specified	Uncertain significance (Apr 07, 2023)
X-104012729-GT-G		H2BW1-related disorder	Likely benign (Nov 01, 2022)
X-104012747-T-C		not specified	Uncertain significance (Jun 16, 2024)
X-104012755-A-G			Benign (Dec 31, 2019)
X-104013178-A-G			Likely benign (Sep 01, 2022)
X-104013180-C-G		not specified	Uncertain significance (Jul 05, 2024)
X-104013192-C-T		not specified	Uncertain significance (Jun 17, 2024)
X-104013198-C-T		H2BW1-related disorder	Likely benign (Nov 19, 2022)
X-104013215-T-G		not specified	Uncertain significance (Oct 07, 2024)
X-104013221-G-A		not specified	Uncertain significance (Mar 14, 2023)
X-104013246-G-A		not specified	Uncertain significance (Jun 17, 2024)
X-104013248-G-A		H2BW1-related disorder	Likely benign (Apr 28, 2022)
X-104013276-T-C		not specified	Uncertain significance (Feb 14, 2025)
X-104013284-C-A		not specified	Uncertain significance (Aug 02, 2022)
X-104013285-G-A		not specified	Uncertain significance (Oct 22, 2021)
X-104013363-G-A		not specified	Uncertain significance (Feb 10, 2022)
X-104013376-G-C		H2BW1-related disorder	Likely benign (Aug 14, 2019)
X-104013396-G-C		not specified	Uncertain significance (Apr 28, 2023)
X-104013399-C-G		not specified	Uncertain significance (Dec 14, 2023)
X-104013401-C-T		not specified	Uncertain significance (Dec 26, 2023)
X-104013402-G-A		H2BW1-related disorder	Benign (Sep 30, 2019)
X-104013404-C-G		not specified	Uncertain significance (Oct 14, 2023)
X-104013408-A-C		not specified	Uncertain significance (Dec 21, 2023)
X-104013418-G-A		H2BW1-related disorder	Likely benign (Sep 23, 2019)
X-104013429-C-T		not specified	Likely benign (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H2BW1	protein_coding	protein_coding	ENST00000217926	2	2541

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00246	0.561	124403	36	54	124493	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.602	110	93.6	1.18	0.00000912	1110
Missense in Polyphen		21	18.685	1.1239		293
Synonymous	0.965	29	36.4	0.796	0.00000330	387
Loss of Function	0.288	4	4.67	0.856	3.69e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000945	0.000786
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000699	0.000503
Middle Eastern	0.00	0.00
South Asian	0.000997	0.000621
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Atypical histone H2B. Nucleosomes containing it are structurally and dynamically indistinguishable from those containing conventional H2B. However, unlike conventional H2B, does not recruit chromosome condensation factors and does not participate in the assembly of mitotic chromosomes. May be important for telomere function. {ECO:0000269|PubMed:16449661}.
• Pathway: Systemic lupus erythematosus - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Alcoholism - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0929

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

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