MAGED1
protein-codingMAGE family member D1, the group of MAGE family
Gene summary
This gene is a member of the melanoma antigen gene (MAGE) family. Most of the genes of this family encode tumor specific antigens that are not expressed in normal adult tissues except testis. Although the protein encoded by this gene shares strong homology with members of the MAGE family, it is expressed in almost all normal adult tissues. This gene has been demonstrated to be involved in the p75 neurotrophin receptor mediated programmed cell death pathway. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~99.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MAGED1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006986.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 12 | 2 | 3 | 17 | ||
| missense | 113 | 5 | 118 | |||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 19 | 19 | ||||
| Total | 0 | 0 | 148 | 7 | 3 | 158 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_008917.3 | 11 | MANE Select | |
| Ensembl | ENSP00000325333.8 | 11 | MANE Select | |
| RefSeq | NP_001005332.1 | 11 | Standard | |
| RefSeq | NP_001005333.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neurotrophin signaling pathway - Homo sapiens (human)
- Signal Transduction
- Caspase activation via extrinsic apoptotic signalling pathway
- Apoptosis
- Programmed Cell Death
Biological Process
- regulation of transcription, DNA-templated
- regulation of transcription by RNA polymerase II
- circadian regulation of gene expression
- regulation of circadian rhythm
- regulation of apoptotic process
Molecular Function
- transcription coactivator activity
- protein binding
- identical protein binding
Cellular Component
- chromatin
- nucleus
- cytoplasm
- plasma membrane
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375695
- Coding exons
- 12
- Length
- 99351
- Individuals with no LoFs
- 125698
- Homozygous LoFs
- 4
- Heterozygous LoFs
- 10
- Defined
- 125712
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.33 | 210 | 329 | 0.639 | 0.0000252 | 5420 |
| Missense (PolyPhen) | 15 | 63.709 | 0.23545 | 1142 | ||
| Synonymous | 1.34 | 103 | 122 | 0.846 | 0.00000924 | 1706 |
| Loss of Function | 4.50 | 2 | 27.4 | 0.0729 | 0.00000198 | 410 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00011 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00013 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000065 | 0.000046 | rare |
| European (Non-Finnish) | 0.00010 | 0.000070 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00023 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the apoptotic response after nerve growth factor (NGF) binding in neuronal cells. Inhibits cell cycle progression, and facilitates NGFR-mediated apoptosis. May act as a regulator of the function of DLX family members. May enhance ubiquitin ligase activity of RING-type zinc finger-containing E3 ubiquitin-protein ligases. Proposed to act through recruitment and/or stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex. Plays a role in the circadian rhythm regulation. May act as RORA co-regulator, modulating the expression of core clock genes such as ARNTL/BMAL1 and NFIL3, induced, or NR1D1, repressed. {ECO:0000269|PubMed:20864041}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- LoFtool
- 0.600
- RVIS EVS
- -0.54
- RVIS percentile EVS
- 20.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.881
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |