FGF12 p.Asp36=
c.108C>T · rs555759767 · VCV2198182
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0374%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.7 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 13.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0374%
South Asian · 34/91,016 alleles
Filtering AF
0.0274%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.024%
Overall
0.00292%
47/1,611,022 alleles · ultra-rare
exomes 42/1,458,744 · genomes 5/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0374% | 2,677 |
| East Asian | 0.00892% | 11,212 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,481 |
| Admixed American | 0.00167% | 59,998 |
| African / African-American | 0.00133% | 74,986 |
| European (non-Finnish) | 0.00017% | 588,609 |
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.Asp36=
- Coding
- c.108C>T
- MANE Select
- NM_004113
- dbSNP
- rs555759767
- Type
- single nucleotide variant
- Location
- chr3:192360444 (GRCh38)
- Gene constraint
- LOEUF 0.932 · pLI 0.15 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.91 · 2 PDB
- Residue 36
- 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-asp36 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown