MAGED2 p.Asp519=
c.1557C>T · rs775755120 · VCV2867335
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.167%, sas)
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 -3 | GERP -3.6 |
| Overall | ||
| CADD | 2.596 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.167%
South Asian · 94/56,337 alleles
Filtering AF
0.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.129%
Overall
0.00969%
117/1,207,318 alleles · rare
exomes 113/1,094,341 · genomes 4/112,977 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.167% | 599 |
| Admixed American | 0.0175% | 5,708 |
| Remaining individualsnot grpmax-eligible | 0.00843% | 11,863 |
| European (non-Finnish) | 0.00123% | 81,213 |
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.Asp519=
- Coding
- c.1557C>T
- MANE Select
- NM_177433
- dbSNP
- rs775755120
- Type
- single nucleotide variant
- Location
- chrX:54815418 (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-asp519 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown