GPC3 p.Glu99=
c.297G>A · rs753227537 · VCV1127646
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00525%, afr)
Conditions
1
Wilms tumor 1
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 1.4 | GERP -0.5, phastCons 1 |
| Overall | ||
| CADD | 8.747 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00525%
African / African-American · 3/57,138 alleles
Filtering AF
0.00139%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000686%
Overall
0.000248%
3/1,207,693 alleles · very rare
exomes 1/1,095,811 · genomes 2/111,882 · joint denominator
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
- GPC3
- Protein
- p.Glu99=
- Coding
- c.297G>A
- MANE Select
- NM_004484
- dbSNP
- rs753227537
- Type
- single nucleotide variant
- Location
- chrX:133953090 (GRCh38)
- Structure
- AlphaFold pLDDT 75.60 · 4 PDB
- Residue 99
- an α-helix
Similar variants
- GPC3 c.337+2T>A Likely pathogenic ★★ same condition
- GPC3 p.Arg199Ter Pathogenic ★★ same condition
- GPC3 p.Arg254Ter Pathogenic ★★ same condition
- GPC3 p.Arg387Ter Pathogenic ★★ same condition
- GPC3 p.Arg86Ter Pathogenic ★★ same condition
- GPC3 p.Glu298Ter Pathogenic ★★ same condition
- GPC3 c.1292+6C>T Uncertain significance ★★ same condition
- GPC3 p.Ala141Thr Uncertain significance ★★ ⚠ 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/gpc3-p-glu99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown