TRMT5 p.Gln504=
c.1512A>G · rs757111083 · VCV1636831
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0122%, sas)
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 -0.004 | GERP -1.6, phastCons 0.013 |
| Overall | ||
| CADD | 3.169 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0122%
South Asian · 11/90,306 alleles
Filtering AF
0.00682%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00526%
Overall
0.000807%
13/1,609,948 alleles · ultra-rare
exomes 12/1,457,746 · genomes 1/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0122% | 8,210 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,336 |
| European (non-Finnish) | 8.48e-05% | 1,178,575 |
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
- TRMT5
- Protein
- p.Gln504=
- Coding
- c.1512A>G
- MANE Select
- NM_020810
- dbSNP
- rs757111083
- Type
- single nucleotide variant
- Location
- chr14:60975127 (GRCh38)
- Gene constraint
- LOEUF 0.969 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.50
- Residue 504
- the 'disordered' region
Similar variants
- TRMT5 p.Ala188Asp Uncertain significance ★★ ⚠ same type
- TRMT5 p.Ala45Thr Uncertain significance ★★ ⚠ same type
- TRMT5 p.Ala45Val Uncertain significance ★★ ⚠ same type
- TRMT5 p.Arg120Cys Uncertain significance ★★ ⚠ same type
- TRMT5 p.Arg125His Uncertain significance ★★ ⚠ same type
- TRMT5 p.Arg15Thr Uncertain significance ★★ ⚠ same type
- TRMT5 p.Arg266Gln Uncertain significance ★★ ⚠ same type
- TRMT5 p.Arg291His 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/trmt5-p-gln504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown