MAGEB3

Chr X

MAGE family member B3

Also known as: CT3.5

NCBI Gene: 4114ENSG00000198798UniProt: O15480OMIM: 300152

MAGEB3 encodes a MAGE-B subfamily protein that directs expression of tumor antigens recognized by cytolytic T lymphocytes in melanoma. Mutations cause X-linked intellectual disability with distinctive facial features and behavioral abnormalities. This gene shows X-linked inheritance and is located in the MAGE-B gene cluster on chromosome Xp21.

OMIMResearchSummary from RefSeq
LOEUF 1.61
Clinical Summary— MAGEB3
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.00) despite low pLI — interpret in context.
📋
ClinVar Variants
68 unique Pathogenic / Likely Pathogenic· 34 VUS of 109 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.61LOEUF
pLI 0.432
Z-score 1.07
OE 0.00 (0.00–1.61)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.65Z-score
OE missense 0.84 (0.72–0.98)
108 obs / 128.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.00 (0.00–1.61)
0≤0.351.4
Missense OE0.84 (0.72–0.98)
0≤0.61.4
Synonymous OE1.01
0≤1.21.6
LoF obs/exp: 0 / 1.3Missense obs/exp: 108 / 128.6Syn Z: -0.07

ClinVar Variant Classifications

109 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic67
Likely Pathogenic1
VUS34
Likely Benign3
Benign1
67
Pathogenic
1
Likely Pathogenic
34
VUS
3
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
67
0
67
Likely Pathogenic
0
0
1
0
1
VUS
0
32
2
0
34
Likely Benign
0
3
0
0
3
Benign
0
1
0
0
1
Total036700106

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

View in ClinVar →

Protein Context — Lollipop Plot

MAGEB3 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Trophinin Is an Important Biomarker and Prognostic Factor in Osteosarcoma: Data Mining from Oncomine and the Cancer Genome Atlas Databases
Cai P et al.·Biomed Res Int
2021
X-linked palindromic gene families 4930567H17Rik and Mageb5 are dispensable for male mouse fertility
Stark-Dykema ER et al.·Sci Rep
2022Functional
Genetic and Clinical Characterization of Complex Glycerol Kinase Deficiency in Two Male Siblings: A Case Report
Bregvadze K et al.·Clin Med Insights Endocrinol Diabetes
2025Case report
Identification of two distinct head and neck squamous cell carcinoma subtypes based on fatty acid metabolism-related signatures: Implications for immunotherapy and chemotherapy
Zou J et al.·Medicine (Baltimore)
2024
Pluripotent Stem Cells: Cancer Study, Therapy, and Vaccination
Barati M et al.·Stem Cell Rev Rep
2021
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 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