GPC3 p.Ala232=
c.696T>C · rs2071695506 · VCV1103639
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.007%, afr)
Conditions
2
Wilms tumor 1
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 -0.005 | GERP -4.4, phastCons 0.26 |
| Overall | ||
| CADD | 7.357 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.007%
African / African-American · 4/57,141 alleles
Filtering AF
0.00233%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0014%
Overall
0.000413%
5/1,209,433 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.007% | 14,285 |
| Admixed American | 0.00218% | 45,776 |
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.Ala232=
- Coding
- c.696T>C
- MANE Select
- NM_004484
- dbSNP
- rs2071695506
- Type
- single nucleotide variant
- Location
- chrX:133753818 (GRCh38)
- Structure
- AlphaFold pLDDT 75.60 · 4 PDB
- Residue 232
- a disulfide bond; an α-helix
Similar variants
- GPC3 p.Ala232Asp Likely pathogenic ★ same residue
- GPC3 p.Ala232Val Uncertain significance ★ ⚠ same residue
- 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
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-ala232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown