H2BC18

H2B clustered histone 18, the group of H2B histones

Basic information

Region (hg38): 1:149782689-149812373

Previous symbols: [ "HIST2H2BF" ]

Links

ENSG00000203814 ∙ NCBI:440689 ∙ ∙ HGNC:24700 ∙ Uniprot:Q5QNW6 ∙ 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 H2BC18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2BC18 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						0
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in H2BC18

This is a list of pathogenic ClinVar variants found in the H2BC18 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-149782764-G-A			Likely benign (May 18, 2018)
1-149784064-C-T			Likely benign (May 17, 2018)
1-149784140-C-G		not specified	Uncertain significance (Mar 02, 2023)
1-149784224-C-T		IGG receptor I, phagocytic, familial deficiency of	Pathogenic (Mar 15, 1995)
1-149788581-C-T		not specified	Uncertain significance (Feb 02, 2024)
1-149790164-C-A		not specified	Uncertain significance (Jan 19, 2022)
1-149790230-C-T		Peritoneal Gliomatosis	Uncertain significance (Aug 01, 2019)
1-149790308-C-T		not specified	Uncertain significance (Oct 20, 2023)
1-149790323-G-C		not specified	Uncertain significance (May 24, 2023)
1-149790325-G-C		not specified	Uncertain significance (Nov 03, 2023)
1-149791297-T-C		not specified	Uncertain significance (Jul 12, 2022)
1-149791298-G-A		not specified	Likely benign (Mar 23, 2022)
1-149791327-C-A		not specified	Uncertain significance (Mar 21, 2023)
1-149791332-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-149791405-T-C		not specified	Likely benign (Mar 01, 2024)
1-149791413-C-T		not specified	Uncertain significance (Oct 12, 2022)
1-149791461-AAAG-A			Benign (Feb 01, 2018)
1-149791483-G-T		not specified	Uncertain significance (Apr 17, 2023)
1-149791485-G-T		not specified	Uncertain significance (Mar 31, 2023)
1-149791497-G-C		not specified	Uncertain significance (Aug 11, 2022)
1-149811986-G-T		not specified	Uncertain significance (Dec 06, 2023)
1-149812179-C-T		not specified	Uncertain significance (Jun 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H2BC18	protein_coding	protein_coding	ENST00000545683	2	29684

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00463	0.460	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.693	62	79.4	0.781	0.00000459	856
Missense in Polyphen		16	26.704	0.59917		335
Synonymous	-5.21	75	35.5	2.11	0.00000227	275
Loss of Function	-0.303	3	2.49	1.21	1.06e-7	47

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000537	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000163	0.000163

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);Post-translational protein modification;HDACs deacetylate histones;Metabolism of proteins;Chromatin modifying enzymes;HATs acetylate histones;Ub-specific processing proteases;Deubiquitination;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.783
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.415
• ghis: 0.424

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.485

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hist2h2bb

Gene ontology

• Biological process: nucleosome assembly
• Cellular component: nucleosome;nucleus;nucleoplasm;cytosol;extracellular exosome
• Molecular function: molecular_function;DNA binding;protein heterodimerization activity