MAGEL2 p.Pro153=
c.459C>T · rs559833820 · VCV2645002
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00138%, afr)
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 -1.8 | GERP -2 |
| Overall | ||
| CADD | 1.207 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00138%
African / African-American · 1/72,596 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000196%
3/1,533,780 alleles · very rare
exomes 2/1,382,872 · genomes 1/150,908 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00138% | 72,596 |
| European (non-Finnish) | 0.000175% | 572,836 |
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.Pro153=
- Coding
- c.459C>T
- MANE Select
- NM_019066
- dbSNP
- rs559833820
- Type
- single nucleotide variant
- Location
- chr15:23647284 (GRCh38)
- Structure
- AlphaFold pLDDT 44.28 · 1 PDB
- Residue 153
- the 'disordered' region
Similar variants
- MAGEL2 p.Pro153Leu Uncertain significance ⚠ same residue
- 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
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-pro153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown