GPC3 p.Pro544=
c.1632G>A · rs766482434 · VCV415273
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00712%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.72 | GERP 0.069, phastCons 0.63 |
| Overall | ||
| CADD | 2.293 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00712%
African / African-American · 4/56,213 alleles
Filtering AF
0.00236%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00142%
Overall
0.00142%
17/1,200,428 alleles · very rare
exomes 13/1,090,861 · genomes 4/109,567 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00712% | 14,053 |
| Admixed American | 0.00661% | 15,119 |
| East Asian | 0.00594% | 16,832 |
| Remaining individualsnot grpmax-eligible | 0.00423% | 23,652 |
| European (non-Finnish) | 0.000676% | 148,031 |
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.Pro544=
- Coding
- c.1632G>A
- MANE Select
- NM_004484
- dbSNP
- rs766482434
- Type
- single nucleotide variant
- Location
- chrX:133536235 (GRCh38)
- Structure
- AlphaFold pLDDT 75.60 · 4 PDB
Similar variants
- GPC3 p.Pro544Leu Benign/Likely benign ★★ same residue
- GPC3 p.Pro544Arg 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-pro544 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown