Is MAGED2 p.Ala211= (c.633C>T) pathogenic?

MAGED2 p.Ala211= (c.633C>T) is classified Likely benign in MAGED2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-15). Very rare (popmax 0.00708%, sas); Associated with MAGED2-related disorder.

What condition is associated with MAGED2 p.Ala211= (c.633C>T)?

MAGED2 p.Ala211= (c.633C>T) is associated with MAGED2-related disorder (ClinVar).

How common is MAGED2 p.Ala211= (c.633C>T) in the general population?

MAGED2 p.Ala211= (c.633C>T) is very rare (popmax 0.00708%, sas) (gnomAD).

MAGED2 p.Ala211=

c.633C>T · rs775770634 · VCV3053493

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00708%, sas)

Conditions

MAGED2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.042	GERP -0.27, phastCons 0.93
Overall
CADD	9.769	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00708% South Asian · 4/56,466 alleles

Filtering AF 0.00235% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00141%

Overall 0.000331% 4/1,209,393 alleles · very rare exomes 4/1,095,497 · genomes 0/113,896 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MAGED2
Protein: p.Ala211=
Coding: c.633C>T
MANE Select: NM_177433
dbSNP: rs775770634
Type: single nucleotide variant
Location: chrX:54810916 (GRCh38)
Structure: AlphaFold pLDDT 59.89

Full MAGED2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MAGED2-related disorder

Similar variants

MAGED2 p.Arg178Ter Pathogenic ★ same condition
MAGED2 p.Arg203Ter Likely pathogenic ★ same condition
MAGED2 p.Glu312Ter Conflicting classifications of pathogenicity ★ same condition
MAGED2 p.Thr132Ile Uncertain significance ⚠ same condition
MAGED2 p.Ala389Gly Uncertain significance ★★ ⚠ same type
MAGED2 p.Ala97Gly Uncertain significance ★★ ⚠ same type
MAGED2 p.Arg257His Uncertain significance ★★ ⚠ same type
MAGED2 p.Pro153Ser Uncertain significance ★★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/maged2-p-ala211 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown