H2AC1

H2A clustered histone 1, the group of H2A histones

Basic information

Region (hg38): 6:25723397-25726562

Previous symbols: [ "HIST1H2AA" ]

Links

ENSG00000164508 ∙ NCBI:221613 ∙ OMIM:613499 ∙ HGNC:18729 ∙ Uniprot:Q96QV6 ∙ 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 H2AC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2AC1 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in H2AC1

This is a list of pathogenic ClinVar variants found in the H2AC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-25726139-C-T		not specified	Uncertain significance (Feb 06, 2025)
6-25726146-C-A		not specified	Uncertain significance (Mar 01, 2023)
6-25726159-A-T		not specified	Uncertain significance (Dec 04, 2024)
6-25726167-T-C		not specified	Uncertain significance (Jun 07, 2023)
6-25726217-G-A		not specified	Uncertain significance (May 08, 2023)
6-25726229-C-G		not specified	Uncertain significance (Apr 24, 2023)
6-25726286-G-C		not specified	Uncertain significance (Aug 15, 2024)
6-25726298-G-C		not specified	Uncertain significance (Jun 17, 2024)
6-25726298-G-T		not specified	Uncertain significance (Dec 01, 2024)
6-25726373-A-G		not specified	Uncertain significance (Oct 25, 2023)
6-25726396-T-C		not specified	Uncertain significance (Jan 28, 2025)
6-25726421-C-G		not specified	Uncertain significance (Jun 07, 2024)
6-25726425-G-A		not specified	Uncertain significance (May 23, 2023)
6-25726446-C-T		not specified	Uncertain significance (Dec 07, 2024)
6-25726466-C-A		not specified	Uncertain significance (Jun 22, 2023)
6-25726487-T-C		not specified	Uncertain significance (Nov 03, 2022)
6-25726490-G-T		not specified	Uncertain significance (Apr 26, 2023)
6-25726499-T-A		not specified	Uncertain significance (Sep 01, 2021)
6-25726506-C-T		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H2AC1	protein_coding	protein_coding	ENST00000297012	1	500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00142	0.261	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.704	111	92.0	1.21	0.00000652	823
Missense in Polyphen		25	34.342	0.72796		317
Synonymous	-5.57	78	35.7	2.19	0.00000231	294
Loss of Function	-2.19	3	0.838	3.58	3.38e-8	15

LoF frequencies by population

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

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);Post-translational protein modification;HDACs deacetylate histones;Metabolism of proteins;RMTs methylate histone arginines;Chromatin modifying enzymes;Metalloprotease DUBs;HATs acetylate histones;UCH proteinases;Ub-specific processing proteases;Deubiquitination;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.729
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.919
• hipred: Y
• hipred_score: 0.537
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hist1h2aa

Gene ontology

• Biological process: chromatin organization
• Cellular component: nuclear chromosome, telomeric region;nucleosome;nuclear chromatin;nucleus;extracellular exosome
• Molecular function: DNA binding;protein heterodimerization activity