GPC6 p.Ser100=
c.300C>T · VCV3701320
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, 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 -0.27 | GERP -1.6, phastCons 0.051 |
| Overall | ||
| CADD | 6.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,992 alleles
Overall
6.2e-05%
1/1,613,778 alleles · very rare
exomes 1/1,461,514 · genomes 0/152,264 · joint denominator
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.Ser100=
- Coding
- c.300C>T
- MANE Select
- NM_005708
- Type
- single nucleotide variant
- Location
- chr13:93545402 (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-ser100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown