TRAP1 p.Thr249=
c.747C>T · VCV3666106
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0717%, amr)
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 -4.5 | GERP -3.8 |
| Overall | ||
| CADD | 0.324 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0717%
Admixed American · 43/59,936 alleles
Filtering AF
0.0547%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0487%
Overall
0.00384%
62/1,613,654 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0717% | 1,394 |
| East Asian | 0.00669% | 14,953 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,474 |
| Finnishnot grpmax-eligible | 0.00156% | 64,036 |
| European (non-Finnish) | 0.00119% | 84,277 |
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.Thr249=
- Coding
- c.747C>T
- MANE Select
- NM_016292
- Type
- single nucleotide variant
- Location
- chr16:3676103 (GRCh38)
- Gene constraint
- LOEUF 1.343 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.28 · 24 PDB
- Residue 249
- a β-strand
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-thr249 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown