Is CFTR p.Pro1332= (c.3996T>C) pathogenic?

CFTR p.Pro1332= (c.3996T>C) is classified Likely benign in CFTR (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-04-20). Absent from gnomAD v4.1; Associated with cystic fibrosis.

What condition is associated with CFTR p.Pro1332= (c.3996T>C)?

CFTR p.Pro1332= (c.3996T>C) is associated with cystic fibrosis, CFTR-related disorder (ClinVar).

How common is CFTR p.Pro1332= (c.3996T>C) in the general population?

CFTR p.Pro1332= (c.3996T>C) is absent from gnomAD v4.1 (gnomAD).

How is Cystic fibrosis inherited?

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

CFTR p.Pro1332=

c.3996T>C · rs2116220796 · VCV1144742

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

cystic fibrosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.002	phastCons 0.94
Overall
CADD	7.609	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CFTR
Protein: p.Pro1332=
Coding: c.3996T>C
MANE Select: NM_000492
dbSNP: rs2116220796
Type: single nucleotide variant
Location: chr7:117664720 (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 1332: a UniProt-annotated variant site (in cf); a UniProt-annotated variant site (in cf and cbavd); the abc transporter 2 domain; a β-strand

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

Also linked: CFTR-related disorder

For Cystic fibrosis (Orphanet):

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

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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-pro1332 (accessed [today's date]).

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