MSN p.Asp409=
c.1227C>T · VCV4698509
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0248%, sas)
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 1.1 | GERP -0.1, phastCons 1 |
| Overall | ||
| CADD | 10.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0248%
South Asian · 14/56,484 alleles
Filtering AF
0.0149%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.012%
Overall
0.00132%
16/1,208,379 alleles · ultra-rare
exomes 16/1,096,772 · genomes 0/111,607 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0248% | 4,035 |
| Admixed American | 0.0022% | 45,492 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,541 |
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.Asp409=
- Coding
- c.1227C>T
- MANE Select
- NM_002444
- Type
- single nucleotide variant
- Location
- chrX:65737314 (GRCh38)
- Structure
- AlphaFold pLDDT 86.77 · 10 PDB
- Residue 409
- the 'disordered' region
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-asp409 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown