Is FLCN p.Phe152fs (c.453del) pathogenic?

FLCN p.Phe152fs (c.453del) is classified Pathogenic in FLCN (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-08-29). No gnomAD frequency available for this variant; Associated with Birt-Hogg-Dube syndrome 1.

What condition is associated with FLCN p.Phe152fs (c.453del)?

FLCN p.Phe152fs (c.453del) is associated with Birt-Hogg-Dube syndrome 1, Birt-Hogg-Dube syndrome (ClinVar).

How common is FLCN p.Phe152fs (c.453del) in the general population?

FLCN p.Phe152fs (c.453del) is no gnomAD frequency available for this variant (gnomAD).

FLCN p.Phe152fs

c.453del · rs879255660 · VCV253230

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Birt-Hogg-Dube syndrome 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 6 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 8	GERP 1.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FLCN
Protein: p.Phe152fs
Coding: c.453del
MANE Select: NM_144997
dbSNP: rs879255660
Type: Deletion
Location: chr17:17224087 (GRCh38)
Gene constraint: LOEUF 0.487 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.14 · 4 PDB
Residue 152: the udenn flcn/smcr8-type domain; a β-strand

Full FLCN gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Birt-Hogg-Dube syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Birt-Hogg-Dube syndrome

Similar variants

FLCN p.Phe152Leu Uncertain significance ★★ ⚠ same residue
FLCN p.Phe152= Benign/Likely benign ★★ same residue
FLCN c.1301-7_1304del Likely pathogenic ★★ same condition
FLCN p.Ala365_Gly371del Likely pathogenic ★★ same condition
FLCN p.Ala64fs Pathogenic/Likely pathogenic ★★ same condition
FLCN p.Arg168fs Pathogenic ★★ same condition
FLCN p.Arg268_Leu269insTer Pathogenic ★★ same condition
FLCN p.Arg341fs 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-phe152fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown