FLRT3 p.Gln255=
c.765A>G · rs143179643 · VCV770298
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.97%, amr)
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 2.9 | GERP 0.94, phastCons 1 |
| Overall | ||
| CADD | 6.727 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.97%
Admixed American · 2,382/59,964 alleles
Filtering AF
3.84%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.79%
Overall
0.2%
3,232/1,613,820 alleles · low-frequency
exomes 2,817/1,461,534 · genomes 415/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 3.97% | 25 |
| East Asian | 0.644% | 155 |
| Finnishnot grpmax-eligible | 0.425% | 235 |
| Remaining individualsnot grpmax-eligible | 0.2% | 500 |
| Ashkenazi Jewishnot grpmax-eligible | 0.128% | 779 |
| Middle Eastern | 0.033% | 3,028 |
| African / African-American | 0.0227% | 4,413 |
| South Asian | 0.0143% | 7,007 |
| European (non-Finnish) | 0.00797% | 12,551 |
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
- FLRT3
- Protein
- p.Gln255=
- Coding
- c.765A>G
- MANE Select
- NM_198391
- dbSNP
- rs143179643
- Type
- single nucleotide variant
- Location
- chr20:14326742 (GRCh38)
- Gene constraint
- LOEUF 0.585 · pLI 0.55 (gnomAD)
- Structure
- AlphaFold pLDDT 74.57 · 3 PDB
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-gln255 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown