Is CFTR p.Cys76Phe (c.227G>T) pathogenic?

CFTR p.Cys76Phe (c.227G>T) is classified Uncertain significance in CFTR (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-28). AlphaMissense: likely pathogenic (0.618); Absent from gnomAD v4.1; Associated with cystic fibrosis.

What condition is associated with CFTR p.Cys76Phe (c.227G>T)?

CFTR p.Cys76Phe (c.227G>T) is associated with cystic fibrosis (ClinVar).

How common is CFTR p.Cys76Phe (c.227G>T) in the general population?

CFTR p.Cys76Phe (c.227G>T) 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.

What do computational predictors say about CFTR p.Cys76Phe (c.227G>T)?

AlphaMissense predicts likely pathogenic (score 0.618) — an in-silico prediction, not a clinical call.

CFTR p.Cys76Phe

c.227G>T · rs2484975440 · VCV2118701

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.618 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

cystic fibrosis

Computational evidence

Protein change
AlphaMissense	0.618	likely pathogenic
REVEL	0.918	moderately pathogenic-leaning
SaProt	LLR -9.36	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 187 kb · p 2.1e-08 · regional, not allelic
Overall
CADD	27.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Cys76Phe
Coding: c.227G>T
MANE Select: NM_000492
dbSNP: rs2484975440
Type: single nucleotide variant
Location: chr7:117509096 (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 76: 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.Cys76Ser Uncertain significance ★★ ⚠ same residue
CFTR p.Cys76Trp Uncertain significance ★★ ⚠ same residue
CFTR p.Cys76= Likely benign ★★ same residue
CFTR p.Cys76Arg Uncertain significance ★ ⚠ 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

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-cys76phe (accessed [today's date]).

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