MTFMT p.Gln355=
c.1065G>A · rs35477493 · VCV138266
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 12.6%, sas) — too common for a highly-penetrant pathogenic allele
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 0.39 | GERP -3.4, phastCons 0.99 |
| Overall | ||
| CADD | 4.762 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
12.6%
South Asian · 11,483/91,034 alleles
Filtering AF
12.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 12.3%
Overall
2.88%
46,420/1,613,556 alleles · common
exomes 42,221/1,461,422 · genomes 4,199/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 12.6% | 8 |
| Ashkenazi Jewishnot grpmax-eligible | 6.28% | 16 |
| Middle Eastern | 3.63% | 28 |
| Amishnot grpmax-eligible | 3.63% | 28 |
| Remaining individualsnot grpmax-eligible | 3.26% | 31 |
| Finnishnot grpmax-eligible | 2.9% | 34 |
| African / African-American | 2.22% | 45 |
| European (non-Finnish) | 2.2% | 46 |
| Admixed American | 2.03% | 49 |
| East Asian | 0.328% | 305 |
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.Gln355=
- Coding
- c.1065G>A
- MANE Select
- NM_139242
- dbSNP
- rs35477493
- Type
- single nucleotide variant
- Location
- chr15:65003167 (GRCh38)
- Gene constraint
- LOEUF 1.304 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.08
- Residue 355
- a UniProt-annotated variant site (in mc1dn27)
Similar variants
- MTFMT p.Gln355Glu 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-gln355 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown