MAGEC1

Chr X

MAGE family member C1

Also known as: CT7, CT7.1

NCBI Gene: 9947ENSG00000155495UniProt: O60732

This gene is a member of the melanoma antigen gene (MAGE) family. The proteins of this family are tumor-specific antigens that can be recognized by autologous cytolytic T lymphocytes. This protein contains a large number of unique short repetitive sequences in front of the MAGE-homologous sequence, and therefore is about 800 aa longer than the other MAGE proteins. [provided by RefSeq, Jul 2008]

0
Active trials
88
Pathogenic / LP
335
ClinVar variants
3
Pubs (1 yr)
-5.2
Missense Z
1.91
LOEUF
Clinical Summary— MAGEC1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.08) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
88 Pathogenic / Likely Pathogenic· 194 VUS of 335 total submissions
Some data sources returned errors (1)

pubtator: TimeoutError: The operation was aborted due to timeout

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.91LOEUF
pLI 0.080
Z-score -0.28
OE 1.35 (0.30–1.91)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-5.17Z-score
OE missense 1.75 (1.64–1.86)
665 obs / 381.0 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.35 (0.30–1.91)
0≤0.351.4
Missense OE1.75 (1.64–1.86)
0≤0.61.4
Synonymous OE1.46
0≤1.21.6
LoF obs/exp: 1 / 0.7Missense obs/exp: 665 / 381.0Syn Z: -4.50
GOFDN
DN
0.77top 25%
GOF
0.79top 10%
LOF
0.3551th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

335 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic86
Likely Pathogenic2
VUS194
Likely Benign41
Benign2
Conflicting10
86
Pathogenic
2
Likely Pathogenic
194
VUS
41
Likely Benign
2
Benign
10
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
86
0
86
Likely Pathogenic
0
0
2
0
2
VUS
0
187
7
0
194
Likely Benign
3
25
3
10
41
Benign
0
2
0
0
2
Conflicting
—10
Total32149810335

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

MAGEC1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients