Is FLCN p.His367= (c.1101C>T) pathogenic?

FLCN p.His367= (c.1101C>T) is classified Benign/Likely benign in FLCN (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-01). Very rare (popmax 0.00667%, amr); Associated with hereditary neoplastic syndrome.

What condition is associated with FLCN p.His367= (c.1101C>T)?

FLCN p.His367= (c.1101C>T) is associated with hereditary neoplastic syndrome, Birt-Hogg-Dube syndrome, Birt-Hogg-Dube syndrome 1 (ClinVar).

How common is FLCN p.His367= (c.1101C>T) in the general population?

FLCN p.His367= (c.1101C>T) is very rare (popmax 0.00667%, amr) (gnomAD).

FLCN p.His367=

c.1101C>T · rs1451481907 · VCV775049

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00667%, amr)

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 -4.7	GERP -4
Overall
CADD	2.348	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00667% Admixed American · 4/60,002 alleles

Filtering AF 0.00226% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00135%

Overall 0.000434% 7/1,613,956 alleles · very rare exomes 4/1,461,714 · genomes 3/152,242 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00667%	15,001
African / African-American	0.00133%	74,948
European (non-Finnish)	0.000169%	590,009

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.His367=
Coding: c.1101C>T
MANE Select: NM_144997
dbSNP: rs1451481907
Type: single nucleotide variant
Location: chr17:17217144 (GRCh38)
Gene constraint: LOEUF 0.487 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.14 · 4 PDB
Residue 367: the cdenn flcn/smcr8-type domain; a UniProt-annotated variant site (in psp); a UniProt-annotated variant site (in bhd1); an α-helix

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.His367Arg Uncertain significance ★★ ⚠ same residue
FLCN p.His367Gln Uncertain significance ★★ ⚠ same residue
FLCN p.His367Tyr Uncertain significance ★★ ⚠ same residue
FLCN p.His367Asn 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-his367 (accessed [today's date]).

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