MAGEL2 p.Ser671=
c.2013G>A · rs373471090 · VCV2168416
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00272%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.015 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.36 | GERP -1.1, phastCons 0.21 |
| Overall | ||
| CADD | 9.616 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00272%
African / African-American · 2/73,664 alleles
Filtering AF
0.00148%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00125%
Overall
0.00179%
28/1,565,362 alleles · very rare
exomes 25/1,413,218 · genomes 3/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00272% | 36,832 |
| European (non-Finnish) | 0.00216% | 46,316 |
| Admixed American | 0.00187% | 53,408 |
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.Ser671=
- Coding
- c.2013G>A
- MANE Select
- NM_019066
- dbSNP
- rs373471090
- Type
- single nucleotide variant
- Location
- chr15:23645730 (GRCh38)
- Structure
- AlphaFold pLDDT 44.28 · 1 PDB
- Residue 671
- the 'disordered' region
Similar variants
- MAGEL2 p.Ser671Leu 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-ser671 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown