FPGS p.Ala503=
c.1509G>A · VCV4084639
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0567%, amr)
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 -6 | GERP -2.5 |
| Overall | ||
| CADD | 3.596 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0567%
Admixed American · 34/59,936 alleles
Filtering AF
0.0417%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0365%
Overall
0.0036%
58/1,612,536 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0567% | 1,763 |
| European (non-Finnish) | 0.00187% | 53,619 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,448 |
| African / African-American | 0.00134% | 74,878 |
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
- FPGS
- Protein
- p.Ala503=
- Coding
- c.1509G>A
- MANE Select
- NM_004957
- Type
- single nucleotide variant
- Location
- chr9:127813349 (GRCh38)
- Gene constraint
- LOEUF 1.174 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.05
Similar variants
- FPGS p.Ala503Thr Uncertain significance ★ ⚠ same residue
- FPGS p.Ile22Val Benign ★★ same type
- FPGS p.Ala10Ser Uncertain significance ★ ⚠ same type
- FPGS p.Ala15Gly Uncertain significance ★ ⚠ same type
- FPGS p.Ala19Gly Uncertain significance ★ ⚠ same type
- FPGS p.Ala307Ser Uncertain significance ★ ⚠ same type
- FPGS p.Ala395Thr Uncertain significance ★ ⚠ same type
- FPGS p.Ala423Gly 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/fpgs-p-ala503 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown