TRAP1 p.His311=
c.933T>C · rs142413437 · VCV559153
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.692%, afr)
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 -6.4 | GERP -3.8 |
| Overall | ||
| CADD | 0.466 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.692%
African / African-American · 519/75,036 alleles
Filtering AF
0.642%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.623%
Overall
0.0513%
828/1,614,004 alleles · rare
exomes 494/1,461,766 · genomes 334/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.692% | 145 |
| Admixed American | 0.132% | 760 |
| Ashkenazi Jewishnot grpmax-eligible | 0.108% | 925 |
| Middle Eastern | 0.099% | 1,010 |
| Remaining individualsnot grpmax-eligible | 0.0592% | 1,689 |
| European (non-Finnish) | 0.013% | 7,712 |
| Finnishnot grpmax-eligible | 0.00313% | 31,961 |
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.His311=
- Coding
- c.933T>C
- MANE Select
- NM_016292
- dbSNP
- rs142413437
- Type
- single nucleotide variant
- Location
- chr16:3674450 (GRCh38)
- Gene constraint
- LOEUF 1.343 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.28 · 24 PDB
- Residue 311
- 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-his311 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown