MME p.Pro98=
c.294C>T · rs200713056 · VCV752201
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -12 | GERP -4.6 |
| Overall | ||
| CADD | 0.381 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,060 alleles
Filtering AF
0.0092%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00735%
Overall
0.00359%
58/1,614,032 alleles · ultra-rare
exomes 53/1,461,844 · genomes 5/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,060 |
| South Asian | 0.0154% | 6,505 |
| Admixed American | 0.01% | 10,001 |
| African / African-American | 0.004% | 25,003 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| European (non-Finnish) | 0.00263% | 38,064 |
| East Asian | 0.00223% | 44,856 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
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
- MME
- Protein
- p.Pro98=
- Coding
- c.294C>T
- MANE Select
- NM_007289
- dbSNP
- rs200713056
- Type
- single nucleotide variant
- Location
- chr3:155115091 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.25 · 16 PDB
- Residue 98
- an α-helix; the peptidase m13 domain
Similar variants
- MME c.1497+1G>A Likely pathogenic ★★ same type
- MME c.1497+1G>C Likely pathogenic ★★ same type
- MME c.160+2T>C Likely pathogenic ★★ same type
- MME c.1601+2T>C Likely pathogenic ★★ same type
- MME c.1781-2A>G Pathogenic/Likely pathogenic ★★ same type
- MME c.439+1G>A Likely pathogenic ★★ same type
- MME c.440-2A>C Pathogenic/Likely pathogenic ★★ same type
- MME c.536-1G>A Pathogenic/Likely pathogenic ★★ 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/mme-p-pro98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown