MAGEL2 p.Pro366=
c.1098G>A · rs1251729902 · VCV1911697
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00151%, nfe)
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 -7.8 | GERP -2.6 |
| Overall | ||
| CADD | 5.246 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00151%
European (non-Finnish) · 17/1,122,304 alleles
Filtering AF
0.000923%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000754%
Overall
0.00114%
17/1,486,634 alleles · very rare
exomes 17/1,334,456 · genomes 0/152,178 · 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
- MAGEL2
- Protein
- p.Pro366=
- Coding
- c.1098G>A
- MANE Select
- NM_019066
- dbSNP
- rs1251729902
- Type
- single nucleotide variant
- Location
- chr15:23646645 (GRCh38)
- Structure
- AlphaFold pLDDT 44.28 · 1 PDB
- Residue 366
- the 'disordered' region
Similar variants
- MAGEL2 p.Arg1187Ter Likely pathogenic ★★ same type
- MAGEL2 p.Gln1042Ter Pathogenic ★★ same type
- MAGEL2 p.Gln636Ter Pathogenic ★★ same type
- MAGEL2 p.Gln638Ter Pathogenic/Likely pathogenic ★★ same type
- MAGEL2 p.Gln644Ter Pathogenic/Likely pathogenic ★★ same type
- MAGEL2 p.Gln666Ter Pathogenic/Likely pathogenic ★★ same type
- MAGEL2 p.Trp686Ter Pathogenic/Likely pathogenic ★★ same type
- MAGEL2 p.Ala1026Val 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/magel2-p-pro366 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown