MTFMT p.Gln57=
c.171G>A · rs1255086137 · VCV2073930
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00538%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -2.3 |
| Overall | ||
| CADD | 1.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00538%
East Asian · 2/37,176 alleles
Filtering AF
0.000891%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000333%
Overall
0.000198%
3/1,518,858 alleles · very rare
exomes 3/1,366,562 · genomes 0/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00538% | 18,588 |
| European (non-Finnish) | 8.8e-05% | 1,136,094 |
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
- MTFMT
- Protein
- p.Gln57=
- Coding
- c.171G>A
- MANE Select
- NM_139242
- dbSNP
- rs1255086137
- Type
- single nucleotide variant
- Location
- chr15:65029443 (GRCh38)
- Gene constraint
- LOEUF 1.304 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.08
Similar variants
- MTFMT p.Gln57His Uncertain significance ★ ⚠ same residue
- MTFMT c.722-2A>G Likely pathogenic ★★ same type
- MTFMT p.Arg128Ter Pathogenic/Likely pathogenic ★★ same type
- MTFMT p.Arg332Ter Pathogenic ★★ same type
- MTFMT p.Ser125Leu Pathogenic/Likely pathogenic ★★ same type
- MTFMT p.Ser209Leu Pathogenic ★★ ⚠ same type
- MTFMT p.Trp9Ter Pathogenic ★★ same type
- MTFMT p.Ala213Thr 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/mtfmt-p-gln57 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown