FGF12 p.Ser39=
c.117C>T · rs199881884 · VCV2054294
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0352%, 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 -1.1 | GERP -4.4 |
| Overall | ||
| CADD | 7.652 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0352%
South Asian · 32/90,836 alleles
Filtering AF
0.0256%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0223%
Overall
0.00474%
76/1,601,984 alleles · ultra-rare
exomes 71/1,449,736 · genomes 5/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0352% | 2,839 |
| Admixed American | 0.0133% | 7,495 |
| Remaining individualsnot grpmax-eligible | 0.00966% | 10,351 |
| European (non-Finnish) | 0.00248% | 40,310 |
| Finnishnot grpmax-eligible | 0.00156% | 64,008 |
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
- FGF12
- Protein
- p.Ser39=
- Coding
- c.117C>T
- MANE Select
- NM_004113
- dbSNP
- rs199881884
- Type
- single nucleotide variant
- Location
- chr3:192360435 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI 0.15 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.91 · 2 PDB
- Residue 39
- the 'disordered' region
Similar variants
- FGF12 p.Arg52His Pathogenic/Likely pathogenic ★★ same type
- FGF12 p.Gly50Ser Pathogenic/Likely pathogenic ★★ same type
- FGF12 c.125-3C>G Uncertain significance ★★ same type
- FGF12 c.14-47513G>T Uncertain significance ★★ ⚠ same type
- FGF12 c.14-47520A>G Uncertain significance ★★ ⚠ same type
- FGF12 c.14-47558G>C Uncertain significance ★★ ⚠ same type
- FGF12 c.14-47562G>A Uncertain significance ★★ same type
- FGF12 c.14-47655C>T 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/fgf12-p-ser39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown