Is CFTR p.Phe1099= (c.3297C>T) pathogenic?

CFTR p.Phe1099= (c.3297C>T) is classified Likely benign in CFTR (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-06-17). Ultra-rare (popmax 0.0164%, mid); Associated with cystic fibrosis.

What condition is associated with CFTR p.Phe1099= (c.3297C>T)?

CFTR p.Phe1099= (c.3297C>T) is associated with cystic fibrosis (ClinVar).

How common is CFTR p.Phe1099= (c.3297C>T) in the general population?

CFTR p.Phe1099= (c.3297C>T) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

How is Cystic fibrosis inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CFTR p.Phe1099=

c.3297C>T · rs747754623 · VCV2453660

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

cystic fibrosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.151	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.08	GERP -0.2, phastCons 0.53
Overall
CADD	7.999	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,082 alleles

Overall 6.84e-05% 1/1,461,450 alleles · ultra-rare

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: CFTR
Protein: p.Phe1099=
Coding: c.3297C>T
MANE Select: NM_000492
dbSNP: rs747754623
Type: single nucleotide variant
Location: chr7:117611738 (GRCh38)
Gene constraint: LOEUF 1.152 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.96 · 60 PDB
Residue 1099: a UniProt-annotated variant site (in cf); the abc transmembrane type-1 2 domain; an α-helix

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

Disease context

cystic fibrosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Cystic fibrosis (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

CFTR p.Phe1099Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
CFTR c.1585-1G>A Pathogenic ★★★★ same condition
CFTR c.1766+1G>A Pathogenic ★★★★ same condition
CFTR c.2657+5G>A Pathogenic ★★★★ same condition
CFTR c.2988+1G>A Pathogenic ★★★★ same condition
CFTR c.3718-2477C>T Pathogenic ★★★★ same condition
CFTR c.489+1G>T Pathogenic ★★★★ same condition
CFTR c.579+1G>T 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/cftr-p-phe1099 (accessed [today's date]).

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