TRIP4 p.Lys89=
c.267A>G · VCV4695639
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000684%, nfe)
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 2.6 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 7.889 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000684%
European (non-Finnish) · 8/1,168,830 alleles
Filtering AF
0.000294%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000213%
Overall
0.000503%
8/1,591,784 alleles · very rare
exomes 8/1,439,434 · genomes 0/152,350 · 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
- TRIP4
- Protein
- p.Lys89=
- Coding
- c.267A>G
- MANE Select
- NM_016213
- Type
- single nucleotide variant
- Location
- chr15:64394111 (GRCh38)
- Gene constraint
- LOEUF 0.802 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 71.54 · 10 PDB
Similar variants
- TRIP4 p.Lys89Ter Pathogenic ★ same residue
- TRIP4 p.Lys89Gln Uncertain significance ★ ⚠ same residue
- TRIP4 c.272-1G>T Likely pathogenic ★★ same type
- TRIP4 p.Arg309Ter Pathogenic/Likely pathogenic ★★ same type
- TRIP4 p.Arg466Ter Pathogenic/Likely pathogenic ★★ same type
- TRIP4 p.Leu20Ter Pathogenic ★★ same type
- TRIP4 p.Trp297Ter Pathogenic ★★ same type
- TRIP4 p.Ala398Thr 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/trip4-p-lys89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown