FGFR3 p.Ser84=
c.252G>A · rs367973461 · VCV196219
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
rare (popmax 0.199%, mid)
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 -12 | GERP -2 |
| Overall | ||
| CADD | 2.922 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.199%
Middle Eastern · 12/6,028 alleles
Filtering AF
0.173%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.164%
Overall
0.072%
1,161/1,612,322 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.199% | 502 |
| South Asian | 0.197% | 509 |
| Remaining individualsnot grpmax-eligible | 0.0833% | 1,201 |
| Admixed American | 0.0817% | 1,224 |
| European (non-Finnish) | 0.0727% | 1,375 |
| African / African-American | 0.0133% | 7,505 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,580 |
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.Ser84=
- Coding
- c.252G>A
- MANE Select
- NM_000142
- dbSNP
- rs367973461
- Type
- single nucleotide variant
- Location
- chr4:1799396 (GRCh38)
- Gene constraint
- LOEUF 0.458 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.25 · 16 PDB
- Residue 84
- the ig-like c2-type 1 domain
Similar variants
- FGFR3 p.Ser84Leu Pathogenic/Likely pathogenic ★★ ⚠ same residue
- FGFR3 p.Ala391Glu Pathogenic ★★ same type
- FGFR3 p.Arg248Cys Pathogenic ★★ same type
- FGFR3 p.Arg621His Pathogenic/Likely pathogenic ★★ same type
- FGFR3 p.Asn540Asp Pathogenic/Likely pathogenic ★★ same type
- FGFR3 p.Asn540Lys Pathogenic ★★ same type
- FGFR3 p.Asn540Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
- FGFR3 p.Asn540Thr Pathogenic/Likely pathogenic ★★ same type
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-ser84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown