GPC3 p.Lys68=
c.204G>A · rs61754632 · VCV415272
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 11 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.6%, afr)
Conditions
3
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP -0.5, phastCons 1 |
| Overall | ||
| CADD | 9.753 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.6%
African / African-American · 2,041/56,725 alleles
Filtering AF
3.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.42%
Overall
0.201%
2,426/1,207,011 alleles · low-frequency
exomes 1,235/1,096,481 · genomes 1,191/110,530 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.6% | 28 |
| Remaining individualsnot grpmax-eligible | 0.316% | 317 |
| Admixed American | 0.308% | 325 |
| Middle Eastern | 0.184% | 543 |
| European (non-Finnish) | 0.0094% | 10,637 |
| South Asian | 0.00529% | 18,888 |
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.Lys68=
- Coding
- c.204G>A
- MANE Select
- NM_004484
- dbSNP
- rs61754632
- Type
- single nucleotide variant
- Location
- chrX:133953183 (GRCh38)
- Structure
- AlphaFold pLDDT 75.60 · 4 PDB
Similar variants
- GPC3 p.Lys68Asn 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 p.Gly556Arg Pathogenic/Likely 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-lys68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown