Is GPC3 p.Ser413= (c.1239C>T) pathogenic?

GPC3 p.Ser413= (c.1239C>T) is classified Likely benign in GPC3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-27). Very rare (popmax 0.000112%, nfe); Associated with Wilms tumor 1.

What condition is associated with GPC3 p.Ser413= (c.1239C>T)?

GPC3 p.Ser413= (c.1239C>T) is associated with Wilms tumor 1 (ClinVar).

How common is GPC3 p.Ser413= (c.1239C>T) in the general population?

GPC3 p.Ser413= (c.1239C>T) is very rare (popmax 0.000112%, nfe) (gnomAD).

GPC3 p.Ser413=

c.1239C>T · rs2124430790 · VCV1123898

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000112%, nfe)

Conditions

Wilms tumor 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.12	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.1	GERP 0.17, phastCons 1
Overall
CADD	10.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000112% European (non-Finnish) · 1/889,732 alleles

Overall 9.16e-05% 1/1,091,718 alleles · very rare

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.Ser413=
Coding: c.1239C>T
MANE Select: NM_004484
dbSNP: rs2124430790
Type: single nucleotide variant
Location: chrX:133692422 (GRCh38)
Structure: AlphaFold pLDDT 75.60 · 4 PDB
Residue 413: a disulfide bond

Full GPC3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Wilms tumor 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GPC3 p.Ser413Arg 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
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-ser413 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown