MME p.Asp54=
c.162T>C · rs35926730 · VCV1613245
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, 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 · T>A here scores Δ0.93 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.47 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 14.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,974 alleles
Overall
0.000126%
2/1,587,146 alleles · ultra-rare
exomes 2/1,434,826 · genomes 0/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,974 |
| European (non-Finnish) | 8.62e-05% | 1,160,042 |
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.Asp54=
- Coding
- c.162T>C
- MANE Select
- NM_007289
- dbSNP
- rs35926730
- Type
- single nucleotide variant
- Location
- chr3:155085060 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.25 · 16 PDB
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-asp54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown