Is FLCN p.Pro28= (c.84A>G) pathogenic?

FLCN p.Pro28= (c.84A>G) is classified Benign/Likely benign in FLCN (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-09-28). Ultra-rare (popmax 0.0121%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with FLCN p.Pro28= (c.84A>G)?

FLCN p.Pro28= (c.84A>G) is associated with hereditary neoplastic syndrome, Birt-Hogg-Dube syndrome, Birt-Hogg-Dube syndrome 1 (ClinVar).

How common is FLCN p.Pro28= (c.84A>G) in the general population?

FLCN p.Pro28= (c.84A>G) is ultra-rare (popmax 0.0121%, sas) (gnomAD).

FLCN p.Pro28=

c.84A>G · rs754450145 · VCV2566334

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0121%, sas)

Conditions

hereditary neoplastic 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 -11	GERP -3.1
Overall
CADD	0.88	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0121% South Asian · 11/91,082 alleles

Filtering AF 0.00676% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00522%

Overall 0.000682% 11/1,613,772 alleles · ultra-rare exomes 11/1,461,448 · genomes 0/152,324 · 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.Pro28=
Coding: c.84A>G
MANE Select: NM_144997
dbSNP: rs754450145
Type: single nucleotide variant
Location: chr17:17228054 (GRCh38)
Gene constraint: LOEUF 0.487 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.14 · 4 PDB

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Birt-Hogg-Dube syndrome Birt-Hogg-Dube syndrome 1

Similar variants

FLCN p.Pro28Ala Uncertain significance ★★ ⚠ same residue
FLCN p.Pro28Arg Benign/Likely benign ★★ same residue
FLCN p.Pro28Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
FLCN p.Pro28Thr 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

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-pro28 (accessed [today's date]).

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