Is FGFR2 p.Val86= (c.258G>A) pathogenic?

FGFR2 p.Val86= (c.258G>A) is classified Likely benign in FGFR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-25). Absent from gnomAD v4.1; Associated with FGFR2-related craniosynostosis.

What condition is associated with FGFR2 p.Val86= (c.258G>A)?

FGFR2 p.Val86= (c.258G>A) is associated with FGFR2-related craniosynostosis (ClinVar).

How common is FGFR2 p.Val86= (c.258G>A) in the general population?

FGFR2 p.Val86= (c.258G>A) is absent from gnomAD v4.1 (gnomAD).

FGFR2 p.Val86=

c.258G>A · VCV3688096

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

FGFR2-related craniosynostosis

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 1.8	GERP 0.96, phastCons 1
Overall
CADD	9.775	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: FGFR2
Protein: p.Val86=
Coding: c.258G>A
MANE Select: NM_000141
Type: single nucleotide variant
Location: chr10:121565556 (GRCh38)
Gene constraint: LOEUF 0.278 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 74.33 · 65 PDB
Residue 86: the ig-like c2-type 1 domain

Full FGFR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

FGFR2-related craniosynostosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FGFR2 p.Val86Gly Uncertain significance ★★ ⚠ same residue
FGFR2 p.Val86Met Uncertain significance ★ ⚠ same residue
FGFR2 c.1084+1G>A Pathogenic ★★ same condition
FGFR2 c.1084+2T>C Pathogenic ★★ same condition
FGFR2 c.1084+3A>G Pathogenic ★★ same condition
FGFR2 c.940-1G>T Pathogenic ★★ same condition
FGFR2 p.Ala648Thr Pathogenic ★★ same condition
FGFR2 p.Asp321Ala 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/fgfr2-p-val86 (accessed [today's date]).

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