TRAP1 p.Leu414=
c.1242C>G · rs373510798 · VCV3054502
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0541%, sas)
Conditions
1
TRAP1-related disorder
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 1.7 | GERP -0.24, phastCons 1 |
| Overall | ||
| CADD | 7.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0541%
South Asian · 49/90,530 alleles
Filtering AF
0.042%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0378%
Overall
0.00838%
135/1,610,856 alleles · ultra-rare
exomes 125/1,458,576 · genomes 10/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0541% | 1,848 |
| European (non-Finnish) | 0.00687% | 14,557 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,161 |
| Admixed American | 0.0017% | 58,982 |
| Finnishnot grpmax-eligible | 0.00156% | 63,982 |
| African / African-American | 0.00134% | 74,662 |
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.Leu414=
- Coding
- c.1242C>G
- MANE Select
- NM_016292
- dbSNP
- rs373510798
- Type
- single nucleotide variant
- Location
- chr16:3666112 (GRCh38)
- Gene constraint
- LOEUF 1.343 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.28 · 24 PDB
- Residue 414
- an α-helix
Disease context
TRAP1-related disorder
Similar variants
- TRAP1 p.Lys95Glu Uncertain significance ★★ ⚠ same condition
- TRAP1 p.Ser118Cys Uncertain significance ★★ ⚠ same condition
- TRAP1 c.1166-4C>T Likely benign same condition
- TRAP1 p.Gly30= Likely benign same condition
- TRAP1 p.His322= Likely benign same condition
- TRAP1 p.Ile411= Likely benign same condition
- TRAP1 p.Ser362= Likely benign same condition
- TRAP1 p.Ser84= Likely benign same condition
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-leu414 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown