Is FOXF1 p.Pro322fs (c.965del) pathogenic?

FOXF1 p.Pro322fs (c.965del) is classified Pathogenic in FOXF1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2018-11-27). No gnomAD frequency available for this variant; Associated with alveolar capillary dysplasia with misalignment of pulmonary veins.

What condition is associated with FOXF1 p.Pro322fs (c.965del)?

FOXF1 p.Pro322fs (c.965del) is associated with alveolar capillary dysplasia with misalignment of pulmonary veins (ClinVar).

How common is FOXF1 p.Pro322fs (c.965del) in the general population?

FOXF1 p.Pro322fs (c.965del) is no gnomAD frequency available for this variant (gnomAD).

How is Congenital alveolar capillary dysplasia inherited?

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

FOXF1 p.Pro322fs

c.965del · rs1969566429 · VCV975043

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

alveolar capillary dysplasia with misalignment of pulmonary veins

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon within the last 50 nt of the penultimate exon (1 of 2, 17 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.35	GERP -2.9, phastCons 0.05

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: FOXF1
Protein: p.Pro322fs
Coding: c.965del
MANE Select: NM_001451
dbSNP: rs1969566429
Type: Deletion
Location: chr16:86511531 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.43 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 59.41

Full FOXF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

alveolar capillary dysplasia with misalignment of pulmonary veins — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital alveolar capillary dysplasia (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Canada)

Similar variants

FOXF1 p.Leu300fs Pathogenic/Likely pathogenic ★★ same condition
FOXF1 c.*1176del Benign/Likely benign ★★ same condition
FOXF1 p.Ala268fs Pathogenic ★ same condition
FOXF1 p.Ala297fs Pathogenic ★ same condition
FOXF1 p.Asn317fs Likely pathogenic ★ same condition
FOXF1 p.Gly281fs Likely pathogenic ★ same condition
FOXF1 p.Lys7fs Pathogenic ★ same condition
FOXF1 p.Tyr284_Lys286delinsTer 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/foxf1-p-pro322fs (accessed [today's date]).

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