MSN p.Ala418=
c.1254C>T · rs778773269 · VCV2716025
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00598%, eas)
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 0.35 | GERP -3.4, phastCons 0.99 |
| Overall | ||
| CADD | 6.796 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00598%
East Asian · 2/33,438 alleles
Filtering AF
0.000991%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000371%
Overall
0.000249%
3/1,203,331 alleles · very rare
exomes 2/1,091,369 · genomes 1/111,962 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00598% | 16,719 |
| South Asian | 0.0018% | 55,524 |
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
- MSN
- Protein
- p.Ala418=
- Coding
- c.1254C>T
- MANE Select
- NM_002444
- dbSNP
- rs778773269
- Type
- single nucleotide variant
- Location
- chrX:65738527 (GRCh38)
- Structure
- AlphaFold pLDDT 86.77 · 10 PDB
Similar variants
- MSN p.Arg171Trp Pathogenic ★★ same type
- MSN p.Ala122Thr Uncertain significance ★★ ⚠ same type
- MSN p.Arg273Trp Uncertain significance ★★ ⚠ same type
- MSN p.Arg293Cys Uncertain significance ★★ ⚠ same type
- MSN p.Arg294Cys Uncertain significance ★★ ⚠ same type
- MSN p.Arg295His Uncertain significance ★★ ⚠ same type
- MSN p.Arg393His Uncertain significance ★★ ⚠ same type
- MSN p.Glu346Asp 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/msn-p-ala418 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown