TRIP13 p.Phe248=
c.744C>T · VCV3714358
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.236 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -4.9 |
| Overall | ||
| CADD | 5.526 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
Admixed American · 4/60,002 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.00124%
20/1,614,056 alleles · very rare
exomes 18/1,461,880 · genomes 2/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00667% | 15,001 |
| European (non-Finnish) | 0.00127% | 78,669 |
| South Asian | 0.0011% | 91,086 |
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.Phe248=
- Coding
- c.744C>T
- MANE Select
- NM_004237
- Type
- single nucleotide variant
- Location
- chr5:908059 (GRCh38)
- Gene constraint
- LOEUF 0.592 · pLI 0.19 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 6 PDB
- Residue 248
- a β-strand
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-phe248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown