Is FOXF1 p.Ser88fs (c.260dup) pathogenic?

FOXF1 p.Ser88fs (c.260dup) is classified Pathogenic/Likely pathogenic in FOXF1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-12-10). Absent from gnomAD; Associated with FOXF1-related disorders.

What condition is associated with FOXF1 p.Ser88fs (c.260dup)?

FOXF1 p.Ser88fs (c.260dup) is associated with FOXF1-related disorders (ClinVar).

How common is FOXF1 p.Ser88fs (c.260dup) in the general population?

FOXF1 p.Ser88fs (c.260dup) is absent from gnomAD (gnomAD).

FOXF1 p.Ser88fs

c.260dup · rs2507450479 · VCV1708313

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

FOXF1-related disorders

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	predicted	premature termination codon in exon 1 of 2
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.7	GERP 1.8, phastCons 1

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.Ser88fs
Coding: c.260dup
MANE Select: NM_001451
dbSNP: rs2507450479
Type: Duplication
Location: chr16:86510825 (GRCh38)
Gene constraint: LOEUF 0.685 · pLI 0.43 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 59.41
Residue 88: a DNA-binding region

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

Disease context

FOXF1-related disorders

Similar variants

FOXF1 p.Gln76fs Likely pathogenic ★ same condition
FOXF1 c.*1176dup Likely benign same condition
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

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-ser88fs (accessed [today's date]).

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