MSN p.Thr558=
c.1674C>T · rs1198738550 · VCV1629647
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0158%, 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 -0.72 | GERP -2.5, phastCons 0.007 |
| Overall | ||
| CADD | 9.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0158%
African / African-American · 9/56,955 alleles
Filtering AF
0.00821%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00616%
Overall
0.000992%
12/1,209,083 alleles · ultra-rare
exomes 5/1,097,764 · genomes 7/111,319 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0158% | 6,328 |
| Admixed American | 0.00438% | 22,832 |
| European (non-Finnish) | 0.000112% | 894,895 |
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.Thr558=
- Coding
- c.1674C>T
- MANE Select
- NM_002444
- dbSNP
- rs1198738550
- Type
- single nucleotide variant
- Location
- chrX:65739833 (GRCh38)
- Structure
- AlphaFold pLDDT 86.77 · 10 PDB
- Residue 558
- a modified residue (phosphothreonine; by rock2 and stk10); an α-helix
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-thr558 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown