MCIDAS p.Pro94=
c.282G>A · VCV4970382
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00148%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.22 | GERP -0.25, phastCons 0.22 |
| Overall | ||
| CADD | 13.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00148%
European (non-Finnish) · 17/1,145,126 alleles
Filtering AF
0.000904%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000739%
Overall
0.00111%
17/1,531,920 alleles · very rare
exomes 17/1,379,606 · genomes 0/152,314 · joint denominator
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
- MCIDAS
- Protein
- p.Pro94=
- Coding
- c.282G>A
- MANE Select
- NM_001190787
- Type
- single nucleotide variant
- Location
- chr5:55226603 (GRCh38)
- Gene constraint
- LOEUF 0.989 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.68 · 1 PDB
- Residue 94
- the 'necessary and sufficient for its degradation during the cell cycle' region; the 'disordered' region
Similar variants
- MCIDAS p.Leu335Ter Pathogenic/Likely pathogenic ★★ same type
- MCIDAS p.Ala228Ser Uncertain significance ★★ ⚠ same type
- MCIDAS p.Ala362Val Uncertain significance ★★ ⚠ same type
- MCIDAS p.Ala93Pro Uncertain significance ★★ ⚠ same type
- MCIDAS p.Arg285Thr Uncertain significance ★★ ⚠ same type
- MCIDAS p.Asp141Gly Uncertain significance ★★ ⚠ same type
- MCIDAS p.Ile77Val Uncertain significance ★★ ⚠ same type
- MCIDAS p.Pro364Arg 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/mcidas-p-pro94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown