MID1 p.Ser492Pro
c.1474T>C · VCV3765947
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9816 | likely pathogenic |
|---|---|---|
| REVEL | 0.484 | indeterminate |
| SaProt | LLR -12.06 | damaging |
| ⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.9 | GERP 0.72, phastCons 1 |
| Regional constraint | o/e 0.72 | unconstrained · MANE · 118 kb · p 3.3e-08 · regional, not allelic |
| Overall | ||
| CADD | 24.0 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- MID1
- Protein
- p.Ser492Pro
- Coding
- c.1474T>C
- MANE Select
- NM_000381
- Type
- single nucleotide variant
- Location
- chrX:10455051 (GRCh38)
- Structure
- AlphaFold pLDDT 86.51 · 5 PDB
- Residue 492
- the b30.2/spry domain; an α-helix; the 'disordered' region
Similar variants
- MID1 p.Ser492= Likely benign ★ same residue
- MID1 p.Ala130Thr Pathogenic/Likely pathogenic ★★ same type
- MID1 p.Arg277Ter Pathogenic ★★ same type
- MID1 p.Arg368Ter Pathogenic ★★ same type
- MID1 p.Arg495Ter Pathogenic ★★ same type
- MID1 c.864+4T>G Uncertain significance ★★ same type
- MID1 p.Ala114Thr Uncertain significance ★★ ⚠ same type
- MID1 p.Ala211Pro 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/mid1-p-ser492pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown