MACROH2A2
macroH2A.2 histone, the group of H2A histones|Macro domain containing
Basic information
Region (hg38): 10:70052544-70112282
Previous symbols: [ "H2AFY2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MACROH2A2 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 | |||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 0 | 1 |
Variants in MACROH2A2
This is a list of pathogenic ClinVar variants found in the MACROH2A2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-70075668-C-T | not specified | Uncertain significance (May 10, 2022) | ||
| 10-70075689-T-A | not specified | Uncertain significance (Mar 31, 2024) | ||
| 10-70075776-C-T | not specified | Uncertain significance (Dec 06, 2023) | ||
| 10-70091801-A-C | not specified | Uncertain significance (May 30, 2023) | ||
| 10-70091866-C-A | not specified | Uncertain significance (Aug 15, 2023) | ||
| 10-70091892-G-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 10-70091896-C-T | not specified | Uncertain significance (Aug 11, 2022) | ||
| 10-70091909-G-C | not specified | Uncertain significance (Jan 30, 2024) | ||
| 10-70091910-G-A | not specified | Uncertain significance (Feb 21, 2024) | ||
| 10-70091910-G-C | not specified | Uncertain significance (Sep 29, 2022) | ||
| 10-70091911-G-C | not specified | Uncertain significance (Apr 12, 2023) | ||
| 10-70091911-G-T | not specified | Uncertain significance (Aug 21, 2023) | ||
| 10-70091923-C-A | not specified | Uncertain significance (Mar 13, 2023) | ||
| 10-70091944-C-T | not specified | Uncertain significance (May 05, 2023) | ||
| 10-70095660-T-G | not specified | Uncertain significance (Apr 18, 2023) | ||
| 10-70095679-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 10-70100291-G-A | not specified | Uncertain significance (Oct 26, 2021) | ||
| 10-70109034-C-T | Benign (Jul 13, 2018) | |||
| 10-70109038-G-A | not specified | Uncertain significance (Jun 11, 2021) | ||
| 10-70109173-A-C | not specified | Uncertain significance (Mar 26, 2024) | ||
| 10-70111541-C-T | not specified | Uncertain significance (May 11, 2022) | ||
| 10-70111587-G-A | Benign (Jul 13, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MACROH2A2 | protein_coding | protein_coding | ENST00000373255 | 8 | 59485 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.976 | 0.0236 | 125743 | 0 | 4 | 125747 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.92 | 110 | 236 | 0.466 | 0.0000151 | 2408 |
| Missense in Polyphen | 25 | 101.36 | 0.24664 | 1044 | ||
| Synonymous | 0.557 | 100 | 107 | 0.932 | 0.00000809 | 747 |
| Loss of Function | 3.46 | 1 | 15.9 | 0.0629 | 7.53e-7 | 212 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Variant histone H2A which replaces conventional H2A in a subset of nucleosomes where it represses transcription. 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. May be involved in stable X chromosome inactivation. {ECO:0000269|PubMed:15621527}.;
- Pathway
- Systemic lupus erythematosus - Homo sapiens (human);Necroptosis - Homo sapiens (human);Alcoholism - Homo sapiens (human);Preimplantation Embryo
(Consensus)
Recessive Scores
- pRec
- 0.183
Intolerance Scores
- loftool
- rvis_EVS
- -0.54
- rvis_percentile_EVS
- 20.54
Haploinsufficiency Scores
- pHI
- 0.171
- hipred
- Y
- hipred_score
- 0.617
- ghis
- 0.558
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.921
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- H2afy2
- Phenotype
- vision/eye phenotype; immune system phenotype; pigmentation phenotype; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- h2afy2
- Affected structure
- midbrain hindbrain boundary neural tube
- Phenotype tag
- abnormal
- Phenotype quality
- cleft
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;chromatin organization;nucleosome assembly;brain development;dosage compensation;positive regulation of keratinocyte differentiation;negative regulation of gene expression, epigenetic;establishment of protein localization to chromatin;negative regulation of transcription of nucleolar large rRNA by RNA polymerase I
- Cellular component
- nuclear chromosome, telomeric region;nucleosome;nuclear chromatin;Barr body;nucleoplasm;extracellular exosome
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA binding;chromatin DNA binding;transcription regulatory region DNA binding;protein heterodimerization activity