Is CFTR p.Phe650= (c.1950C>T) pathogenic?

CFTR p.Phe650= (c.1950C>T) is classified Likely benign in CFTR (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-11). Ultra-rare (popmax 0.0165%, mid); Associated with cystic fibrosis.

What condition is associated with CFTR p.Phe650= (c.1950C>T)?

CFTR p.Phe650= (c.1950C>T) is associated with cystic fibrosis, CFTR-related disorder (ClinVar).

How common is CFTR p.Phe650= (c.1950C>T) in the general population?

CFTR p.Phe650= (c.1950C>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

How is Cystic fibrosis inherited?

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

CFTR p.Phe650=

c.1950C>T · rs200204024 · VCV495906

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

cystic fibrosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.22	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -8.9	GERP -3.6
Overall
CADD	10.06	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,062 alleles

Filtering AF 0.00359% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00255%

Overall 0.00211% 34/1,613,968 alleles · ultra-rare exomes 26/1,461,758 · genomes 8/152,210 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,062
South Asian	0.00769%	13,009
Remaining individualsnot grpmax-eligible	0.0064%	15,627
East Asian	0.00223%	44,860
European (non-Finnish)	0.00169%	59,000
African / African-American	0.00133%	75,016

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.Phe650=
Coding: c.1950C>T
MANE Select: NM_000492
dbSNP: rs200204024
Type: single nucleotide variant
Location: chr7:117592117 (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 650: a UniProt-annotated variant site (in cf); 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

Also linked: CFTR-related disorder

For Cystic fibrosis (Orphanet):

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

Similar variants

CFTR p.Phe650Leu Uncertain significance ★★ ⚠ same residue
CFTR p.Phe650Ser Uncertain significance ★ ⚠ same residue
CFTR p.Phe650fs Pathogenic ★ 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

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-phe650 (accessed [today's date]).

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