FLRT3 p.Ile290=
c.870C>T · VCV4798188
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 9.806 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- FLRT3
- Protein
- p.Ile290=
- Coding
- c.870C>T
- MANE Select
- NM_198391
- Type
- single nucleotide variant
- Location
- chr20:14326637 (GRCh38)
- Gene constraint
- LOEUF 0.585 · pLI 0.55 (gnomAD)
- Structure
- AlphaFold pLDDT 74.57 · 3 PDB
- Residue 290
- a turn
Similar variants
- FLRT3 p.Arg163Cys Uncertain significance ★★ ⚠ same type
- FLRT3 p.Leu109Val Uncertain significance ★★ ⚠ same type
- FLRT3 p.Ser25Pro Uncertain significance ★★ ⚠ same type
- FLRT3 p.Ser284Arg Uncertain significance ★★ ⚠ same type
- FLRT3 p.Ser33Pro Uncertain significance ★★ ⚠ same type
- FLRT3 p.Thr199Ser Uncertain significance ★★ ⚠ same type
- FLRT3 p.Thr419Ser Uncertain significance ★★ ⚠ same type
- FLRT3 p.Trp381Arg 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/flrt3-p-ile290 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown