GMNN p.Pro94=
c.282A>G · rs768047063 · VCV1537542
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0186%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.1 | GERP -4.8 |
| Overall | ||
| CADD | 8.675 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0186%
Middle Eastern · 1/5,386 alleles
Filtering AF
0.000471%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000176%
Overall
0.000577%
8/1,385,782 alleles · ultra-rare
exomes 7/1,233,680 · genomes 1/152,102 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0186% | 5,386 |
| African / African-American | 0.00284% | 35,221 |
| Remaining individualsnot grpmax-eligible | 0.00184% | 54,354 |
| South Asian | 0.00124% | 80,558 |
| European (non-Finnish) | 0.000305% | 327,454 |
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
- GMNN
- Protein
- p.Pro94=
- Coding
- c.282A>G
- MANE Select
- NM_015895
- dbSNP
- rs768047063
- Type
- single nucleotide variant
- Location
- chr6:24784094 (GRCh38)
- Structure
- AlphaFold pLDDT 70.49 · 6 PDB
- Residue 94
- the 'necessary and sufficient for interaction with idas and cdt1' region
Similar variants
- GMNN p.Asp164Glu Uncertain significance ★★ ⚠ same type
- GMNN p.Glu118Gly Uncertain significance ★★ same type
- GMNN p.His53Arg Uncertain significance ★★ ⚠ same type
- GMNN p.Leu78Pro Uncertain significance ★★ ⚠ same type
- GMNN p.Met89Leu Uncertain significance ★★ ⚠ same type
- GMNN p.Pro31Ala Uncertain significance ★★ same type
- GEM p.Asp61Glu Benign ★★ same type
- GMNN c.274+12T>A Likely benign ★★ 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/gmnn-p-pro94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown