Is FOXF1 p.Val262Phe (c.784G>T) pathogenic?

FOXF1 p.Val262Phe (c.784G>T) is classified Uncertain significance in FOXF1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-12-20). AlphaMissense: likely benign (0.1564); No allele count reported in gnomAD v4.1 (AN 1,557,136); Associated with FOXF1-related disorder.

What condition is associated with FOXF1 p.Val262Phe (c.784G>T)?

FOXF1 p.Val262Phe (c.784G>T) is associated with FOXF1-related disorder (ClinVar).

How common is FOXF1 p.Val262Phe (c.784G>T) in the general population?

FOXF1 p.Val262Phe (c.784G>T) is no allele count reported in gnomAD v4.1 (AN 1,557,136) (gnomAD).

What do computational predictors say about FOXF1 p.Val262Phe (c.784G>T)?

AlphaMissense predicts likely benign (score 0.1564) — an in-silico prediction, not a clinical call.

FOXF1 p.Val262Phe

c.784G>T · rs1373090237 · VCV3054465

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1564 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,557,136)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

FOXF1-related disorder

Computational evidence

Protein change
AlphaMissense	0.1564	likely benign
REVEL	0.495	indeterminate
SaProt	LLR -7.63	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 8.3	GERP -2.1, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 2,052 bp · p 0.019 · regional, not allelic
Overall
CADD	23.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,557,136). 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.Val262Phe
Coding: c.784G>T
MANE Select: NM_001451
dbSNP: rs1373090237
Type: single nucleotide variant
Location: chr16:86511353 (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

FOXF1-related disorder

Similar variants

FOXF1 p.Glu104Ter Pathogenic ★★ same condition
FOXF1 p.Ala60Thr Likely pathogenic ★ same condition
FOXF1 p.Ile61Thr Uncertain significance ★ ⚠ same condition
FOXF1 p.Pro49Leu Conflicting classifications of pathogenicity ★ ⚠ same condition
FOXF1 p.Arg86Gln Uncertain significance ⚠ same condition
FOXF1 p.Gly193Ala Uncertain significance ⚠ same condition
FOXF1 p.Pro289Arg Uncertain significance ⚠ same condition
FOXF1 c.*8G>A Likely benign 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-val262phe (accessed [today's date]).

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