FGFR2 p.Thr331=
c.993C>T · rs752595302 · VCV3042515
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.135%, amr)
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 1.9 | GERP -4.3, phastCons 1 |
| Overall | ||
| CADD | 15.26 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.135%
Admixed American · 81/59,982 alleles
Filtering AF
0.111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.103%
Overall
0.00607%
98/1,613,970 alleles · rare
exomes 89/1,461,858 · genomes 9/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.135% | 741 |
| African / African-American | 0.0107% | 9,362 |
| East Asian | 0.00891% | 11,224 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| European (non-Finnish) | 0.000254% | 393,340 |
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.Thr331=
- Coding
- c.993C>T
- MANE Select
- NM_000141 · reported on NM_022970
- dbSNP
- rs752595302
- Type
- single nucleotide variant
- Location
- chr10:121518776 (GRCh38)
- Gene constraint
- LOEUF 0.278 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.33 · 65 PDB
- Residue 331
- the ig-like c2-type 3 domain; a UniProt-annotated variant site (in cs)
Similar variants
- FGFR2 p.Asn331Ile Pathogenic ★ same residue
- FGFR2 p.Asn331Ser Uncertain significance ★ ⚠ same residue
- 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
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-thr331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown