GPC3 p.Ser571=
c.1713G>A · rs149209315 · VCV543100
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0759%, 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 -2.8 | GERP -2.7 |
| Overall | ||
| CADD | 0.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0759%
African / African-American · 43/56,671 alleles
Filtering AF
0.0578%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0515%
Overall
0.00398%
48/1,205,669 alleles · ultra-rare
exomes 25/1,095,205 · genomes 23/110,464 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0759% | 1,318 |
| Admixed American | 0.00659% | 15,170 |
| South Asian | 0.00177% | 56,551 |
| European (non-Finnish) | 0.000112% | 893,176 |
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.Ser571=
- Coding
- c.1713G>A
- MANE Select
- NM_004484
- dbSNP
- rs149209315
- Type
- single nucleotide variant
- Location
- chrX:133536154 (GRCh38)
- Structure
- AlphaFold pLDDT 75.60 · 4 PDB
Similar variants
- GPC3 p.Ser571Leu Uncertain significance ★ ⚠ same residue
- GPC3 p.Ser571Pro 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-ser571 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown