H2AC1
Basic information
Region (hg38): 6:25723397-25726562
Previous symbols: [ "HIST1H2AA" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (26 variants)
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. These statistics are base on transcript: NM_000170745.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 25 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 25 | 1 | 0 |
GnomAD
Source:
| 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:
- 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
- Phenotype
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