FLRT1 p.Val343=
c.1029G>A · rs751115779 · VCV2641907
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.399%, 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 4.4 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 11.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.399%
South Asian · 363/91,090 alleles
Filtering AF
0.365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.351%
Overall
0.0235%
380/1,614,170 alleles · rare
exomes 370/1,461,786 · genomes 10/152,384 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.399% | 251 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,167 |
| European (non-Finnish) | 0.000169% | 590,005 |
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.Val343=
- Coding
- c.1029G>A
- MANE Select
- NM_013280
- dbSNP
- rs751115779
- Type
- single nucleotide variant
- Location
- chr11:64117296 (GRCh38)
- Gene constraint
- LOEUF 0.682 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 73.46
- Residue 343
- the lrrct domain
Similar variants
- FLRT1 p.Val343Leu Uncertain significance ★ same residue
- FLRT1 p.Ala148Gly Uncertain significance ★★ same type
- FLRT1 p.Ala461Thr Uncertain significance ★★ same type
- FLRT1 p.Arg149Cys Uncertain significance ★★ same type
- FLRT1 p.Arg326Lys Uncertain significance ★★ same type
- FLRT1 p.Arg452His Uncertain significance ★★ same type
- FLRT1 p.Arg465Gln Uncertain significance ★★ same type
- FLRT1 p.Arg586Gln 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/flrt1-p-val343 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown