FGFR3 p.Pro798=
c.2394A>C · rs904961491 · VCV2636717
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, nfe)
Conditions
1
FGFR3-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.162 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.7 | GERP -3.3 |
| Overall | ||
| CADD | 0.093 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
European (non-Finnish) · 13/1,178,146 alleles
Filtering AF
0.000616%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000474%
Overall
0.000809%
13/1,607,388 alleles · very rare
exomes 11/1,455,392 · genomes 2/151,996 · 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
- FGFR3
- Protein
- p.Pro798=
- Coding
- c.2394A>C
- MANE Select
- NM_000142
- dbSNP
- rs904961491
- Type
- single nucleotide variant
- Location
- chr4:1807235 (GRCh38)
- Gene constraint
- LOEUF 0.458 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.25 · 16 PDB
- Residue 798
- the 'disordered' region
Disease context
FGFR3-related disorder
Similar variants
- FGFR3 p.Pro798Leu Uncertain significance ★ ⚠ same residue
- FGFR3 p.Ala391Glu Pathogenic ★★ same condition
- FGFR3 p.Arg248Cys Pathogenic ★★ same condition
- FGFR3 p.Asn540Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
- FGFR3 p.Asn540Thr Pathogenic/Likely pathogenic ★★ same condition
- FGFR3 p.Gly370Cys Pathogenic ★★ ⚠ same condition
- FGFR3 p.Lys650Glu Pathogenic ★★ same condition
- FGFR3 p.Pro250Arg Pathogenic/Likely 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/fgfr3-p-pro798 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown