MAGED2 p.Ala513=
c.1539C>T · VCV4755237
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0318%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.012 | GERP -3.6, phastCons 0.96 |
| Overall | ||
| CADD | 7.813 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0318%
South Asian · 18/56,540 alleles
Filtering AF
0.0205%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0169%
Overall
0.00223%
27/1,208,488 alleles · ultra-rare
exomes 26/1,095,574 · genomes 1/112,914 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0318% | 3,141 |
| Remaining individualsnot grpmax-eligible | 0.00421% | 23,743 |
| Admixed American | 0.00218% | 45,800 |
| European (non-Finnish) | 0.000671% | 148,985 |
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.Ala513=
- Coding
- c.1539C>T
- MANE Select
- NM_177433
- Type
- single nucleotide variant
- Location
- chrX:54815400 (GRCh38)
- Structure
- AlphaFold pLDDT 59.89
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-ala513 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown