H2AC4

H2A clustered histone 4, the group of H2A histones

Basic information

Region (hg38): 6:26033092-26033618

Previous symbols: [ "H2AFM", "HIST1H2AB" ]

Links

ENSG00000278463 ∙ NCBI:8335 ∙ OMIM:602795 ∙ HGNC:4734 ∙ Uniprot:P04908 ∙ 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 H2AC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2AC4 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in H2AC4

This is a list of pathogenic ClinVar variants found in the H2AC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-26033301-T-G		not specified	Uncertain significance (Jan 20, 2025)
6-26033334-T-C		not specified	Uncertain significance (Aug 17, 2022)
6-26033347-G-C		not specified	Uncertain significance (Nov 03, 2022)
6-26033363-T-C		not specified	Uncertain significance (Sep 26, 2022)
6-26033364-T-C		not specified	Uncertain significance (Oct 16, 2023)
6-26033380-G-A			Likely benign (Oct 01, 2022)
6-26033390-G-A		not specified	Uncertain significance (Apr 25, 2023)
6-26033411-G-A		not specified	Uncertain significance (Aug 04, 2021)
6-26033445-C-G		not specified	Uncertain significance (Feb 04, 2022)
6-26033453-T-C		not specified	Uncertain significance (Apr 21, 2022)
6-26033457-C-T		not specified	Uncertain significance (Feb 08, 2025)
6-26033462-C-T		not specified	Uncertain significance (Aug 29, 2023)
6-26033474-T-G		not specified	Uncertain significance (Apr 20, 2023)
6-26033481-G-C		not specified	Uncertain significance (Mar 07, 2025)
6-26033492-A-T		not specified	Uncertain significance (Feb 14, 2023)
6-26033504-G-A		not specified	Uncertain significance (Jul 17, 2023)
6-26033510-G-A		not specified	Uncertain significance (Sep 26, 2024)
6-26033516-C-T		not specified	Uncertain significance (Feb 16, 2023)
6-26033526-C-T		not specified	Uncertain significance (Nov 09, 2021)
6-26033532-C-T		not specified	Uncertain significance (Aug 14, 2023)
6-26033538-C-T		not specified	Uncertain significance (Sep 04, 2024)
6-26033564-G-A		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

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);Necroptosis - Homo sapiens (human);Alcoholism - Homo sapiens (human);Proteasome Degradation;B-WICH complex positively regulates rRNA expression;ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;SIRT1 negatively regulates rRNA expression;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Signaling by WNT;Signal Transduction;DNA methylation;Epigenetic regulation of gene expression;Gene expression (Transcription);Generic Transcription Pathway;Oxidative Stress Induced Senescence;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;Post-translational protein modification;HDACs deacetylate histones;Metabolism of proteins;Reproduction;RNA Polymerase I Promoter Clearance;RNA Polymerase I Promoter Opening;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;RMTs methylate histone arginines;Chromatin modifying enzymes;RNA Polymerase I Transcription;Amyloid fiber formation;RNA Polymerase I Chain Elongation;Meiotic recombination;Metalloprotease DUBs;Meiosis;Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3;RHO GTPases activate PKNs;HATs acetylate histones;Cellular responses to external stimuli;RHO GTPase Effectors;Signaling by Rho GTPases;UCH proteinases;Packaging Of Telomere Ends;Telomere Maintenance;Chromosome Maintenance;Ub-specific processing proteases;Condensation of Prophase Chromosomes;Deubiquitination;Signaling by Nuclear Receptors;Chromatin organization;Mitotic Prophase;M Phase;Estrogen-dependent gene expression;Transcriptional regulation by small RNAs;RUNX1 regulates transcription of genes involved in differentiation of HSCs;Cell Cycle;Cell Cycle, Mitotic;ESR-mediated signaling;Transcriptional regulation by RUNX1;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT;Gene Silencing by RNA;PRC2 methylates histones and DNA (Consensus)

Intolerance Scores

• loftool: 0.569
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.270
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hist1h2ag

Gene ontology

• Biological process: chromatin organization;negative regulation of cell population proliferation
• Cellular component: nucleosome;nuclear chromatin;nucleus;extracellular exosome
• Molecular function: DNA binding;protein binding;protein heterodimerization activity