TRIP13 p.Phe309=
c.927C>T · VCV3703407
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.256%, 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 -4.7 | GERP -5 |
| Overall | ||
| CADD | 7.305 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.256%
East Asian · 115/44,850 alleles
Filtering AF
0.218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.204%
Overall
0.0088%
142/1,613,596 alleles · rare
exomes 127/1,461,720 · genomes 15/151,876 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.256% | 390 |
| African / African-American | 0.0187% | 5,350 |
| Admixed American | 0.00334% | 29,975 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,246 |
| European (non-Finnish) | 0.000763% | 131,099 |
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
- TRIP13
- Protein
- p.Phe309=
- Coding
- c.927C>T
- MANE Select
- NM_004237
- Type
- single nucleotide variant
- Location
- chr5:911903 (GRCh38)
- Gene constraint
- LOEUF 0.592 · pLI 0.19 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 6 PDB
- Residue 309
- an α-helix
Similar variants
- TRIP13 p.Ala92Glu Uncertain significance ★★ ⚠ same type
- TRIP13 p.Arg28Ser Uncertain significance ★★ ⚠ same type
- TRIP13 p.Arg347Cys Uncertain significance ★★ ⚠ same type
- TRIP13 p.Asp238Asn Uncertain significance ★★ ⚠ same type
- TRIP13 p.Ile330Val Uncertain significance ★★ ⚠ same type
- TRIP13 p.Lys379Arg Uncertain significance ★★ ⚠ same type
- TRIP13 p.Val307Met Uncertain significance ★★ ⚠ same type
- TRIP13 c.1021-18G>A Likely benign ★★ 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/trip13-p-phe309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown