Is CFTR p.Pro960fs (c.2879del) pathogenic?

CFTR p.Pro960fs (c.2879del) is classified Pathogenic in CFTR (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-15). Associated with cystic fibrosis.

What condition is associated with CFTR p.Pro960fs (c.2879del)?

CFTR p.Pro960fs (c.2879del) is associated with cystic fibrosis (ClinVar).

How is Cystic fibrosis inherited?

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

CFTR p.Pro960fs

c.2879del · VCV4733345

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

cystic fibrosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 17 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.041	GERP -3.2, phastCons 0.028

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

Variant & gene context

Gene: CFTR
Protein: p.Pro960fs
Coding: c.2879del
MANE Select: NM_000492
Type: Deletion
Location: chr7:117603752 (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 960: a UniProt-annotated variant site (in cf); the abc transmembrane type-1 2 domain

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.Pro960Ser Uncertain significance ★★ ⚠ same residue
CFTR p.Pro960= Likely benign ★ same residue
CFTR p.Lys1177fs Pathogenic ★★★★ same condition
CFTR c.(?_1 Pathogenic ★★★ same condition
CFTR c.1211del Pathogenic ★★★ same condition
CFTR c.(1584+1_1585-1 Pathogenic ★★★ same condition
CFTR c.(164+1_165-1 Pathogenic ★★★ same condition
CFTR c.(273+1_274-1 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-pro960fs (accessed [today's date]).

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