FGF3 p.Ala113=
c.339C>T · rs1219364101 · VCV1608947
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00227%, sas)
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 -5.2 | GERP -2 |
| Overall | ||
| CADD | 6.432 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00227%
South Asian · 2/88,152 alleles
Filtering AF
0.000377%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000161%
Overall
0.000567%
9/1,586,144 alleles · very rare
exomes 8/1,433,924 · genomes 1/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00227% | 44,076 |
| European (non-Finnish) | 0.000602% | 166,034 |
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
- FGF3
- Protein
- p.Ala113=
- Coding
- c.339C>T
- MANE Select
- NM_005247
- dbSNP
- rs1219364101
- Type
- single nucleotide variant
- Location
- chr11:69810686 (GRCh38)
- Gene constraint
- LOEUF 1.815 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.32
Similar variants
- FGF3 p.Ala113Thr Uncertain significance ★ ⚠ same residue
- FGF3 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same type
- FGF3 p.Arg209Ter Pathogenic/Likely pathogenic ★★ same type
- FGF3 p.Arg95Trp Pathogenic/Likely pathogenic ★★ same type
- FGF3 p.Tyr106Ter Pathogenic/Likely pathogenic ★★ same type
- FGF3 p.Arg132Trp Uncertain significance ★★ ⚠ same type
- FGF3 p.Arg145Gln Uncertain significance ★★ ⚠ same type
- FGF3 p.Arg171His Uncertain significance ★★ ⚠ 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/fgf3-p-ala113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown