TRMT1 p.Glu503=
c.1509G>A · rs35206121 · VCV782623
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.55%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.36 | GERP -1.1, phastCons 0.092 |
| Overall | ||
| CADD | 2.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.55%
East Asian · 692/44,670 alleles
Filtering AF
1.45%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.42%
Overall
0.196%
3,154/1,605,098 alleles · low-frequency
exomes 2,820/1,452,740 · genomes 334/152,358 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.55% | 65 |
| Finnishnot grpmax-eligible | 1.24% | 80 |
| Remaining individualsnot grpmax-eligible | 0.182% | 550 |
| Ashkenazi Jewishnot grpmax-eligible | 0.126% | 791 |
| European (non-Finnish) | 0.122% | 823 |
| South Asian | 0.0938% | 1,066 |
| Middle Eastern | 0.0165% | 6,050 |
| African / African-American | 0.0107% | 9,360 |
| Admixed American | 0.00506% | 19,765 |
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.Glu503=
- Coding
- c.1509G>A
- MANE Select
- NM_001136035
- dbSNP
- rs35206121
- Type
- single nucleotide variant
- Location
- chr19:13107648 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.68 · 1 PDB
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-glu503 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown