MAGEB3

Chr X

MAGE family member B3

Also known as: CT3.5

NCBI Gene: 4114 ENSG00000198798 UniProt: O15480 OMIM: 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.

OMIM ResearchSummary from RefSeq

This gene is a MAGE-B subfamily member of the MAGE gene family. MAGE family member proteins direct the expression of tumor antigens recognized on a human melanoma by autologous cytolytic T lymphocytes. There are two known clusters of MAGE genes on chromosome X. The members of the MAGE-A subfamily are located in the Xq28 region, while the members of the MAGE-B subfamily are clustered in the Xp21 region. [provided by RefSeq, Jul 2008]

OMIM ResearchGenerating clinical summary…

LOEUF 1.61

Clinical Summary— MAGEB3

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.00) despite low pLI — interpret in context.

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ClinVar Variants

32 VUS of 38 total submissions

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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 OE?0.00 (0.00–1.61)

0≤0.351.4

Missense OE?0.84 (0.72–0.98)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 0 / 1.3Missense obs/exp: 108 / 128.6Syn Z: -0.07

ClinVar Variant Classifications

38 submitted variants in ClinVar

ClinVar

Classification Summary

VUS32

Likely Benign3

Benign1

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	32	32
Likely Benign	3	3
Benign	1	1
Total	36	36

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

View in ClinVar →

70 pathogenic / likely-pathogenic (of 73) ClinVar copy-number / structural variants overlap MAGEB3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →