TRAP1 p.Leu58=
c.174G>A · VCV3718239
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0684%, eas)
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 -9 | GERP -2.9 |
| Overall | ||
| CADD | 0.106 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0684%
East Asian · 29/42,414 alleles
Filtering AF
0.0488%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0423%
Overall
0.00452%
72/1,593,172 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0684% | 1,463 |
| South Asian | 0.0317% | 3,151 |
| Remaining individualsnot grpmax-eligible | 0.0244% | 4,105 |
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
- TRAP1
- Protein
- p.Leu58=
- Coding
- c.174G>A
- MANE Select
- NM_016292
- Type
- single nucleotide variant
- Location
- chr16:3690900 (GRCh38)
- Gene constraint
- LOEUF 1.343 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.28 · 24 PDB
Similar variants
- TRAP1 p.Ala319Val Uncertain significance ★★ ⚠ same type
- TRAP1 p.Ala409Thr Uncertain significance ★★ ⚠ same type
- TRAP1 p.Ala50Ser Uncertain significance ★★ ⚠ same type
- TRAP1 p.Ala64Thr Uncertain significance ★★ ⚠ same type
- TRAP1 p.Ala659Thr Uncertain significance ★★ ⚠ same type
- TRAP1 p.Ala7Val Uncertain significance ★★ ⚠ same type
- TRAP1 p.Arg271Pro Uncertain significance ★★ ⚠ same type
- TRAP1 p.Arg340His 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/trap1-p-leu58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown