FLCN p.Pro93=
c.279G>C · rs138688941 · VCV2744189
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
Birt-Hogg-Dube syndrome
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 -14 | GERP -2.9 |
| Overall | ||
| CADD | 0.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,026 alleles
Overall
6.2e-05%
1/1,614,134 alleles · very rare
exomes 1/1,461,890 · genomes 0/152,244 · joint denominator
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
- FLCN
- Protein
- p.Pro93=
- Coding
- c.279G>C
- MANE Select
- NM_144997
- dbSNP
- rs138688941
- Type
- single nucleotide variant
- Location
- chr17:17226293 (GRCh38)
- Gene constraint
- LOEUF 0.487 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.14 · 4 PDB
- Residue 93
- the udenn flcn/smcr8-type domain; an α-helix
Similar variants
- FLCN p.Pro93Ala Uncertain significance ★★ ⚠ same residue
- FLCN p.Pro93Arg Uncertain significance ★★ ⚠ same residue
- FLCN p.Pro93Ser Uncertain significance ★★ ⚠ same residue
- FLCN p.Pro93Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- FLCN c.1062+1G>A Pathogenic ★★ same condition
- FLCN c.1062+2T>G Pathogenic ★★ same condition
- FLCN c.1063-1G>T Likely pathogenic ★★ same condition
- FLCN c.1063-2A>G Pathogenic/Likely pathogenic ★★ 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/flcn-p-pro93 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown