GPC3 p.Phe324=
c.972T>C · rs183678432 · VCV239947
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.11%, eas)
Conditions
2
Wilms tumor 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.233 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -0.53, phastCons 0.99 |
| Overall | ||
| CADD | 5.944 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.11%
East Asian · 37/33,748 alleles
Filtering AF
0.0818%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.072%
Overall
0.00571%
69/1,209,119 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.11% | 912 |
| South Asian | 0.0335% | 2,988 |
| Middle Eastern | 0.023% | 4,354 |
| Remaining individualsnot grpmax-eligible | 0.021% | 4,759 |
| Admixed American | 0.00219% | 45,729 |
| European (non-Finnish) | 0.000112% | 894,286 |
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.Phe324=
- Coding
- c.972T>C
- MANE Select
- NM_004484
- dbSNP
- rs183678432
- Type
- single nucleotide variant
- Location
- chrX:133753542 (GRCh38)
- Structure
- AlphaFold pLDDT 75.60 · 4 PDB
- Residue 324
- a disulfide bond; 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 p.Gly556Arg Pathogenic/Likely pathogenic ★★ ⚠ same condition
- GPC3 c.1292+6C>T 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-phe324 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown