FLRT1 p.Ser259Leu
c.776C>T · rs776773158 · VCV566239
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0119%, amr)
Conditions
1
peripheral neuropathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.189 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 2, phastCons 1 |
| Regional constraint | o/e 0.78 | unconstrained · MANE · 2,021 bp · p 5.7e-12 · regional, not allelic |
| Overall | ||
| CADD | 24.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0119%
Admixed American · 7/58,772 alleles
Filtering AF
0.00553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00387%
Overall
0.00118%
19/1,606,674 alleles · ultra-rare
exomes 19/1,454,354 · genomes 0/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0119% | 8,396 |
| South Asian | 0.00111% | 90,124 |
| European (non-Finnish) | 0.000935% | 106,997 |
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
- FLRT1
- Protein
- p.Ser259Leu
- Coding
- c.776C>T
- MANE Select
- NM_013280
- dbSNP
- rs776773158
- Type
- single nucleotide variant
- Location
- chr11:64117043 (GRCh38)
- Gene constraint
- LOEUF 0.682 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 73.46
Similar variants
- FLRT1 p.Ser259= Likely benign ★ same residue
- FLRT1 p.Ala148Gly Uncertain significance ★★ same condition
- FLRT1 p.Ala461Thr Uncertain significance ★★ same condition
- FLRT1 p.Arg149Cys Uncertain significance ★★ same condition
- FLRT1 p.Arg326Lys Uncertain significance ★★ same condition
- FLRT1 p.Arg452His Uncertain significance ★★ same condition
- FLRT1 p.Arg586Gln Uncertain significance ★★ same condition
- FLRT1 p.Arg592Gln Uncertain significance ★★ same condition
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/flrt1-p-ser259leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown