TRIP13 p.Ser41=
c.123T>C · rs1252521225 · VCV747571
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00672%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.402 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.2 | GERP -4.3 |
| Overall | ||
| CADD | 0.753 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00672%
Admixed American · 4/59,564 alleles
Filtering AF
0.00227%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00136%
Overall
0.000248%
4/1,611,178 alleles · very rare
exomes 3/1,459,030 · genomes 1/152,148 · 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.Ser41=
- Coding
- c.123T>C
- MANE Select
- NM_004237
- dbSNP
- rs1252521225
- Type
- single nucleotide variant
- Location
- chr5:894817 (GRCh38)
- Gene constraint
- LOEUF 0.592 · pLI 0.19 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 6 PDB
- Residue 41
- 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-ser41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown