H2AC21

H2A clustered histone 21, the group of H2A histones

Basic information

Region (hg38): 1:149887469-149887965

Previous symbols: [ "HIST2H2AB" ]

Links

ENSG00000184270 ∙ NCBI:317772 ∙ OMIM:615014 ∙ HGNC:20508 ∙ Uniprot:Q8IUE6 ∙ 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 H2AC21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the H2AC21 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				6		6
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	6	0

Variants in H2AC21

This is a list of pathogenic ClinVar variants found in the H2AC21 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-149887541-G-A		not specified	Uncertain significance (Jun 27, 2022)
1-149887618-C-A		not specified	Uncertain significance (Feb 06, 2025)
1-149887728-A-G			Likely benign (Nov 01, 2023)
1-149887731-T-C			Likely benign (Nov 01, 2023)
1-149887734-C-G			Likely benign (Nov 01, 2023)
1-149887771-G-C		not specified	Uncertain significance (Jul 14, 2021)
1-149887779-T-G			Likely benign (Nov 01, 2023)
1-149887785-G-C			Likely benign (Nov 01, 2023)
1-149887787-C-G		not specified	Uncertain significance (Sep 01, 2024)
1-149887823-G-C		not specified	Uncertain significance (Oct 06, 2024)
1-149887838-G-A		not specified	Uncertain significance (Dec 24, 2024)
1-149887839-G-C		not specified	Uncertain significance (Dec 15, 2023)
1-149887848-A-G			Likely benign (Nov 01, 2023)
1-149887852-G-A		not specified	Uncertain significance (Apr 05, 2023)
1-149887864-C-T		not specified	Uncertain significance (Dec 01, 2024)
1-149887876-T-C		not specified	Uncertain significance (Nov 08, 2024)
1-149887879-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-149887885-G-A		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
H2AC21	protein_coding	protein_coding	ENST00000331128	1	448

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.615	0.355	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.866	59	80.9	0.729	0.00000358	810
Missense in Polyphen		16	31.307	0.51107		330
Synonymous	-2.74	59	37.6	1.57	0.00000174	288
Loss of Function	1.61	0	3.02	0.00	1.27e-7	34

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: 0.171

Intolerance Scores

• loftool: 0.467
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.943
• hipred: Y
• hipred_score: 0.621
• ghis: 0.408

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hist2h2ab

Gene ontology

• Biological process: chromatin organization;biological_process
• Cellular component: nucleosome;nuclear chromatin;nucleus;extracellular exosome
• Molecular function: molecular_function;DNA binding;protein heterodimerization activity