TRIP13 p.Ser74=
c.222T>A · VCV4821777
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00136%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.018 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.94 | GERP -4.3, phastCons 0.001 |
| Overall | ||
| CADD | 5.865 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
European (non-Finnish) · 16/1,179,738 alleles
Filtering AF
0.000803%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00065%
Overall
0.000992%
16/1,612,646 alleles · very rare
exomes 15/1,460,426 · genomes 1/152,220 · joint denominator
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.Ser74=
- Coding
- c.222T>A
- MANE Select
- NM_004237
- Type
- single nucleotide variant
- Location
- chr5:894916 (GRCh38)
- Gene constraint
- LOEUF 0.592 · pLI 0.19 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 6 PDB
- Residue 74
- 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-ser74 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown