FLRT3 p.Gln321=
c.963A>G · VCV3606497
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00768%, sas)
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 -12 | GERP -4.3 |
| Overall | ||
| CADD | 0.096 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00768%
South Asian · 7/91,088 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.000806%
13/1,613,804 alleles · very rare
exomes 12/1,461,634 · genomes 1/152,170 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00768% | 13,013 |
| African / African-American | 0.00267% | 37,455 |
| East Asian | 0.00223% | 44,874 |
| European (non-Finnish) | 0.000254% | 393,289 |
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.Gln321=
- Coding
- c.963A>G
- MANE Select
- NM_198391
- Type
- single nucleotide variant
- Location
- chr20:14326544 (GRCh38)
- Gene constraint
- LOEUF 0.585 · pLI 0.55 (gnomAD)
- Structure
- AlphaFold pLDDT 74.57 · 3 PDB
- Residue 321
- the lrrct domain; an α-helix
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-gln321 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown