MAGEA1
Basic information
Region (hg38): X:153179284-153183880
Previous symbols: [ "MAGE1" ]
Links
Phenotypes
GenCC
Source:
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 MAGEA1 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 1 | 0 |
Variants in MAGEA1
This is a list of pathogenic ClinVar variants found in the MAGEA1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-153182511-G-A | not specified | Uncertain significance (Dec 12, 2023) | ||
| X-153182538-G-A | not specified | Uncertain significance (Apr 13, 2022) | ||
| X-153182597-T-A | not specified | Uncertain significance (Jan 22, 2024) | ||
| X-153182618-A-G | not specified | Uncertain significance (Apr 19, 2024) | ||
| X-153182878-C-G | not specified | Uncertain significance (Oct 05, 2021) | ||
| X-153183010-C-T | Likely benign (Aug 05, 2018) | |||
| X-153183044-A-G | not specified | Uncertain significance (Feb 28, 2024) | ||
| X-153183054-A-G | not specified | Uncertain significance (Mar 21, 2023) | ||
| X-153183162-A-C | not specified | Uncertain significance (Aug 12, 2021) | ||
| X-153183170-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
| X-153183261-G-A | not specified | Uncertain significance (Jun 30, 2022) | ||
| X-153183282-G-A | not specified | Uncertain significance (Jan 23, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MAGEA1 | protein_coding | protein_coding | ENST00000356661 | 1 | 4594 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.982 | 87 | 117 | 0.744 | 0.00000886 | 1995 |
| Missense in Polyphen | 12 | 30.753 | 0.39021 | 641 | ||
| Synonymous | 0.328 | 46 | 48.9 | 0.940 | 0.00000367 | 655 |
| Loss of Function |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | ||
| East Asian | ||
| Finnish | ||
| European (Non-Finnish) | ||
| Middle Eastern | ||
| South Asian | ||
| Other |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in transcriptional regulation through interaction with SNW1 and recruiting histone deactelyase HDAC1. May inhibit notch intracellular domain (NICD) transactivation. May play a role in embryonal development and tumor transformation or aspects of tumor progression. Antigen recognized on a melanoma by autologous cytolytic T-lymphocytes. {ECO:0000269|PubMed:15316101}.;
- Pathway
- Notch Signaling Pathway;Notch
(Consensus)
Recessive Scores
- pRec
- 0.145
Intolerance Scores
- loftool
- 0.446
- rvis_EVS
- 1.1
- rvis_percentile_EVS
- 91.96
Haploinsufficiency Scores
- pHI
- 0.173
- hipred
- N
- hipred_score
- 0.166
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.660
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;negative regulation of Notch signaling pathway
- Cellular component
- nucleus;cytoplasm;plasma membrane
- Molecular function
- protein binding;histone deacetylase binding