TRAP1 p.Ala680=
c.2040T>C · rs748790554 · VCV2055138
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0583%, 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 -7.1 | GERP -3.5 |
| Overall | ||
| CADD | 0.061 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0583%
Admixed American · 35/59,994 alleles
Filtering AF
0.0431%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0378%
Overall
0.00235%
38/1,613,896 alleles · ultra-rare
exomes 27/1,461,810 · genomes 11/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0583% | 1,714 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| African / African-American | 0.00134% | 74,900 |
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.Ala680=
- Coding
- c.2040T>C
- MANE Select
- NM_016292
- dbSNP
- rs748790554
- Type
- single nucleotide variant
- Location
- chr16:3658204 (GRCh38)
- Gene constraint
- LOEUF 1.343 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.28 · 24 PDB
- Residue 680
- an α-helix
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-ala680 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown