FGFR2 p.Pro477=
c.1431A>G · rs1436326576 · VCV3048729
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, eas)
Conditions
1
FGFR2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.5 | GERP -4.3 |
| Overall | ||
| CADD | 5.654 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,884 alleles
Filtering AF
0.00434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00031%
5/1,614,026 alleles · ultra-rare
exomes 4/1,461,864 · genomes 1/152,162 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- FGFR2
- Protein
- p.Pro477=
- Coding
- c.1431A>G
- MANE Select
- NM_000141
- dbSNP
- rs1436326576
- Type
- single nucleotide variant
- Location
- chr10:121503798 (GRCh38)
- Gene constraint
- LOEUF 0.278 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.33 · 65 PDB
Similar variants
- FGFR2 c.940-1G>A Pathogenic/Likely pathogenic ★★ same condition
- FGFR2 p.Ala337Pro Pathogenic/Likely pathogenic ★★ same condition
- FGFR2 p.Ala344= Pathogenic ★★ same condition
- FGFR2 p.Ala344Gly Pathogenic ★★ same condition
- FGFR2 p.Arg678Gly Pathogenic/Likely pathogenic ★★ same condition
- FGFR2 p.Asn549His Pathogenic/Likely pathogenic ★★ same condition
- FGFR2 p.Cys278Phe Pathogenic ★★ same condition
- FGFR2 p.Cys342Arg 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-pro477 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown