MAGED2 p.Val69=
c.207C>T · rs1287102249 · VCV731535
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0912%, amr)
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 0.47 | GERP 0.84, phastCons 0.86 |
| Overall | ||
| CADD | 8.946 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0912%
Admixed American · 39/42,766 alleles
Filtering AF
0.0686%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0607%
Overall
0.00336%
40/1,190,975 alleles · ultra-rare
exomes 30/1,080,349 · genomes 10/110,626 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0912% | 1,097 |
| European (non-Finnish) | 0.000113% | 885,434 |
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.Val69=
- Coding
- c.207C>T
- MANE Select
- NM_177433
- dbSNP
- rs1287102249
- Type
- single nucleotide variant
- Location
- chrX:54809883 (GRCh38)
- Structure
- AlphaFold pLDDT 59.89
- Residue 69
- the 'disordered' region
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-val69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown