TRMT1 p.Ala362=
c.1086G>A · rs117741379 · VCV779285
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.17%, nfe)
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 -14 | GERP -2.7 |
| Overall | ||
| CADD | 0.035 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.17%
European (non-Finnish) · 13,818/1,179,992 alleles
Filtering AF
1.15%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.15%
Overall
0.942%
15,208/1,614,002 alleles · low-frequency
exomes 14,244/1,461,720 · genomes 964/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.17% | 85 |
| Remaining individualsnot grpmax-eligible | 0.832% | 120 |
| Amishnot grpmax-eligible | 0.658% | 152 |
| South Asian | 0.359% | 279 |
| Finnishnot grpmax-eligible | 0.338% | 296 |
| Ashkenazi Jewishnot grpmax-eligible | 0.226% | 442 |
| Admixed American | 0.198% | 504 |
| Middle Eastern | 0.181% | 551 |
| African / African-American | 0.161% | 620 |
| East Asian | 0.00669% | 14,958 |
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
- TRMT1
- Protein
- p.Ala362=
- Coding
- c.1086G>A
- MANE Select
- NM_001136035
- dbSNP
- rs117741379
- Type
- single nucleotide variant
- Location
- chr19:13109935 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.68 · 1 PDB
- Residue 362
- the trm1 methyltransferase domain
Similar variants
- TRMT1 p.Arg390Ter Pathogenic/Likely pathogenic ★★ same type
- TRMT1 p.Arg512Ter Likely pathogenic ★★ same type
- TRMT1 p.Ala337Thr Uncertain significance ★★ ⚠ same type
- TRMT1 p.Ala343Val Uncertain significance ★★ ⚠ same type
- TRMT1 p.Arg195Trp Uncertain significance ★★ ⚠ same type
- TRMT1 p.Arg358His Uncertain significance ★★ ⚠ same type
- TRMT1 p.Arg410Cys Uncertain significance ★★ ⚠ same type
- TRMT1 p.Asp449Asn 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/trmt1-p-ala362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown