GPC6 p.Asp202=
c.606C>T · rs376665919 · VCV1986883
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
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 -4.3 | GERP -3.4 |
| Overall | ||
| CADD | 4.458 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/59,968 alleles
Filtering AF
0.009%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00682%
Overall
0.00105%
17/1,613,616 alleles · ultra-rare
exomes 16/1,461,692 · genomes 1/151,924 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0167% | 5,997 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,826 |
| African / African-American | 0.00134% | 74,824 |
| European (non-Finnish) | 0.000254% | 393,290 |
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
- GPC6
- Protein
- p.Asp202=
- Coding
- c.606C>T
- MANE Select
- NM_005708
- dbSNP
- rs376665919
- Type
- single nucleotide variant
- Location
- chr13:93830440 (GRCh38)
- Gene constraint
- LOEUF 0.384 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 82.67
Similar variants
- GPC6 p.Arg171Trp Pathogenic/Likely pathogenic ★★ same type
- GPC6 p.Ala232Thr Uncertain significance ★★ same type
- GPC6 p.Ala377Thr Uncertain significance ★★ ⚠ same type
- GPC6 p.Ala519Thr Uncertain significance ★★ ⚠ same type
- GPC6 p.Arg110Gln Uncertain significance ★★ ⚠ same type
- GPC6 p.Arg126Trp Uncertain significance ★★ ⚠ same type
- GPC6 p.Arg363His Uncertain significance ★★ same type
- GPC6 p.Arg383Gln Uncertain significance ★★ ⚠ same type
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/gpc6-p-asp202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown