MSN p.Val472=
c.1416G>A · VCV3609144
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00536%, 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 1.1 | GERP -0.84, phastCons 1 |
| Overall | ||
| CADD | 6.652 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00536%
European (non-Finnish) · 48/895,497 alleles
Filtering AF
0.00415%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00367%
Overall
0.00474%
52/1,098,059 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00536% | 18,656 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,824 |
| African / African-American | 0.00346% | 28,918 |
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.Val472=
- Coding
- c.1416G>A
- MANE Select
- NM_002444
- Type
- single nucleotide variant
- Location
- chrX:65739041 (GRCh38)
- Structure
- AlphaFold pLDDT 86.77 · 10 PDB
- Residue 472
- 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-val472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown