MTFMT p.Thr85=
c.255A>C · rs571157439 · VCV1572427
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00666%, amr)
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 -3 | GERP -2.9 |
| Overall | ||
| CADD | 2.173 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00666%
Admixed American · 4/60,026 alleles
Filtering AF
0.00225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000805%
13/1,614,038 alleles · very rare
exomes 6/1,461,708 · genomes 7/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00666% | 15,006 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
| African / African-American | 0.00133% | 75,054 |
| European (non-Finnish) | 0.000593% | 168,557 |
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.Thr85=
- Coding
- c.255A>C
- MANE Select
- NM_139242
- dbSNP
- rs571157439
- Type
- single nucleotide variant
- Location
- chr15:65026995 (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.Thr85Ser 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-thr85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown