MAGED2 p.Lys125=
c.375G>A · VCV4951070
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00414%, nfe)
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 3.1 | GERP -0.75, phastCons 1 |
| Overall | ||
| CADD | 9.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00414%
European (non-Finnish) · 37/893,296 alleles
Filtering AF
0.00305%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00267%
Overall
0.00315%
38/1,206,033 alleles · very rare
exomes 31/1,095,568 · genomes 7/110,465 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00414% | 24,143 |
| African / African-American | 0.00177% | 56,622 |
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.Lys125=
- Coding
- c.375G>A
- MANE Select
- NM_177433
- Type
- single nucleotide variant
- Location
- chrX:54810051 (GRCh38)
- Structure
- AlphaFold pLDDT 59.89
- Residue 125
- 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-lys125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown