Is FGF3 p.Phe92fs (c.269_272dup) pathogenic?

FGF3 p.Phe92fs (c.269272dup) is classified Likely pathogenic in FGF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-19). Associated with FGF3-related disorders.

What condition is associated with FGF3 p.Phe92fs (c.269_272dup)?

FGF3 p.Phe92fs (c.269_272dup) is associated with FGF3-related disorders (ClinVar).

FGF3 p.Phe92fs

c.269_272dup · VCV4912863

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

FGF3-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
NMD	predicted	premature termination codon in exon 2 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.8	GERP -3.5, phastCons 1

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

Variant & gene context

Gene: FGF3
Protein: p.Phe92fs
Coding: c.269_272dup
MANE Select: NM_005247
Type: Duplication
Location: chr11:69816371 (GRCh38)
Gene constraint: LOEUF 1.815 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.32

Full FGF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

FGF3-related disorders

Similar variants

FGF3 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same condition
FGF3 p.Tyr106Ter Pathogenic/Likely pathogenic ★★ same condition
FGF3 c.220+2T>C Likely pathogenic ★ same condition
FGF3 p.Arg46fs Likely pathogenic ★ same condition
FGF3 p.Arg95fs Likely pathogenic ★ same condition
FGF3 p.Ser108Leu Conflicting classifications of pathogenicity ★ ⚠ same condition
FGF3 p.Arg89fs Likely pathogenic same condition
FGF3 p.Tyr111= 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/fgf3-p-phe92fs (accessed [today's date]).

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