Is CFTR p.Val562= (c.1686A>G) pathogenic?

CFTR p.Val562= (c.1686A>G) is classified Likely benign in CFTR (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-04). No allele count reported in gnomAD v4.1 (AN 1,603,094); Associated with cystic fibrosis.

What condition is associated with CFTR p.Val562= (c.1686A>G)?

CFTR p.Val562= (c.1686A>G) is associated with cystic fibrosis (ClinVar).

How common is CFTR p.Val562= (c.1686A>G) in the general population?

CFTR p.Val562= (c.1686A>G) is no allele count reported in gnomAD v4.1 (AN 1,603,094) (gnomAD).

How is Cystic fibrosis inherited?

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

CFTR p.Val562=

c.1686A>G · rs2116025296 · VCV1778004

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,603,094)

Conditions

cystic fibrosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.79	GERP 0.36, phastCons 0.96
Overall
CADD	5.681	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,603,094). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CFTR
Protein: p.Val562=
Coding: c.1686A>G
MANE Select: NM_000492
dbSNP: rs2116025296
Type: single nucleotide variant
Location: chr7:117590359 (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 562: a UniProt-annotated variant site (in cf); a UniProt-annotated variant site (in cbavd and cf; uncertain significance; found in cis of the ivs8 tg11-t5 allele which affects exon 9 splicing; no effect on protein maturation; trafficking to the cell membrane; nor on channel activity); the abc transporter 1 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.Val562Ala Uncertain significance ★★ ⚠ same residue
CFTR p.Val562Leu Uncertain significance ★★ ⚠ same residue
CFTR p.Val562Ile 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

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-val562 (accessed [today's date]).

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