FLCN p.Phe213=
c.639T>C · rs867115278 · VCV2002311
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -1.5 | GERP -3.3 |
| Overall | ||
| CADD | 6.737 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- FLCN
- Protein
- p.Phe213=
- Coding
- c.639T>C
- MANE Select
- NM_144997
- dbSNP
- rs867115278
- Type
- single nucleotide variant
- Location
- chr17:17222641 (GRCh38)
- Gene constraint
- LOEUF 0.487 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.14 · 4 PDB
- Residue 213
- the udenn flcn/smcr8-type domain; a UniProt-annotated variant site (in psp); the 'essential for interaction with ldha' region; an α-helix
Similar variants
- FLCN p.Phe213Ile Uncertain significance ★ ⚠ same residue
- FLCN p.Phe213Leu Uncertain significance ★★ ⚠ 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
- FLCN c.1176+1G>A Likely pathogenic ★★ same condition
- FLCN c.1176+1G>C 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-phe213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown