MOGS p.Ala688Thr
c.2062G>A · rs186098891 · VCV565682
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0834 | likely benign |
|---|---|---|
| REVEL | 0.16 | moderately benign-leaning |
| SaProt | LLR -5.88 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 1.7, phastCons 1 |
| Regional constraint | o/e 1.03 | unconstrained · MANE · 601 bp · p 0.59 · regional, not allelic |
| Overall | ||
| CADD | 24.3 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.107% | 935 |
| Remaining individualsnot grpmax-eligible | 0.0592% | 1,689 |
| Admixed American | 0.0383% | 2,610 |
| African / African-American | 0.0226% | 4,415 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0022% | 45,542 |
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
- MOGS
- Protein
- p.Ala688Thr
- Coding
- c.2062G>A
- MANE Select
- NM_006302
- dbSNP
- rs186098891
- Type
- single nucleotide variant
- Location
- chr2:74461727 (GRCh38)
- Gene constraint
- LOEUF 0.85 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.42
Similar variants
- MOGS p.Arg495Ter Pathogenic/Likely pathogenic ★★ same condition
- MOGS p.Gln124Ter Pathogenic ★★ same condition
- MOGS p.Gln505Ter Pathogenic/Likely pathogenic ★★ same condition
- MOGS p.Ala22Glu Uncertain significance ★★ ⚠ same condition
- MOGS p.Ala292Asp Uncertain significance ★★ ⚠ same condition
- MOGS p.Ala292Pro Uncertain significance ★★ ⚠ same condition
- MOGS p.Ala41Val Uncertain significance ★★ ⚠ same condition
- MOGS p.Ala510Thr Uncertain significance ★★ ⚠ same condition
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/mogs-p-ala688thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown