MSN p.Ser527=
c.1581G>A · rs147556779 · VCV1170565
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.397%, afr)
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 0.69 | GERP -3.7, phastCons 0.96 |
| Overall | ||
| CADD | 7.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.397%
African / African-American · 226/56,919 alleles
Filtering AF
0.355%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.338%
Overall
0.0195%
235/1,207,016 alleles · rare
exomes 104/1,095,685 · genomes 131/111,331 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.397% | 252 |
| Remaining individualsnot grpmax-eligible | 0.00632% | 15,829 |
| Admixed American | 0.0044% | 22,743 |
| Finnishnot grpmax-eligible | 0.00215% | 46,448 |
| South Asian | 0.00178% | 56,330 |
| European (non-Finnish) | 0.000224% | 446,877 |
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.Ser527=
- Coding
- c.1581G>A
- MANE Select
- NM_002444
- dbSNP
- rs147556779
- Type
- single nucleotide variant
- Location
- chrX:65739740 (GRCh38)
- Structure
- AlphaFold pLDDT 86.77 · 10 PDB
- Residue 527
- a modified residue (phosphoserine); an α-helix
Similar variants
- MSN p.Ser527Ter Likely pathogenic ★ same residue
- MSN p.Ser527Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser527 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown