MAGED2 p.Ser303=
c.909G>A · VCV4761505
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0326%, eas)
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 4.2 | GERP 0.91, phastCons 1 |
| Overall | ||
| CADD | 11.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0326%
East Asian · 11/33,766 alleles
Filtering AF
0.0182%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0141%
Overall
0.00174%
21/1,207,281 alleles · ultra-rare
exomes 18/1,094,820 · genomes 3/112,461 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0326% | 3,070 |
| Remaining individualsnot grpmax-eligible | 0.00421% | 23,761 |
| South Asian | 0.00176% | 56,797 |
| European (non-Finnish) | 0.000785% | 127,470 |
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.Ser303=
- Coding
- c.909G>A
- MANE Select
- NM_177433
- Type
- single nucleotide variant
- Location
- chrX:54811312 (GRCh38)
- Structure
- AlphaFold pLDDT 59.89
- Residue 303
- the mage domain
Similar variants
- 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
- MAGED2 p.Pro436Ser Uncertain significance ★★ ⚠ same type
- MAGED2 c.1085+101A>G Benign ★★ same type
- MAGED2 c.1166-46C>A Benign ★★ same type
- MAGED2 c.1208+122G>C Benign ★★ 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-ser303 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown