TRAP1 p.Gln146=
c.438G>A · VCV4754396
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0312%, 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 2.6 | GERP 0.63, phastCons 1 |
| Overall | ||
| CADD | 9.567 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0312%
East Asian · 14/44,886 alleles
Filtering AF
0.0188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0151%
Overall
0.000991%
16/1,614,008 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0312% | 3,206 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,241 |
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.Gln146=
- Coding
- c.438G>A
- MANE Select
- NM_016292
- Type
- single nucleotide variant
- Location
- chr16:3686029 (GRCh38)
- Gene constraint
- LOEUF 1.343 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.28 · 24 PDB
- Residue 146
- a β-strand
Similar variants
- TRAP1 p.Gln146Glu Uncertain significance ★ ⚠ same residue
- 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
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-gln146 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown