GSC p.Val25=
c.75G>C · rs766083410 · VCV724486
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0285%, 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 1.3 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 12.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0285%
Admixed American · 15/52,610 alleles
Filtering AF
0.0176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0142%
Overall
0.00504%
78/1,546,302 alleles · ultra-rare
exomes 71/1,394,172 · genomes 7/152,130 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0285% | 3,507 |
| Remaining individualsnot grpmax-eligible | 0.00994% | 10,061 |
| European (non-Finnish) | 0.00485% | 20,613 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00352% | 28,432 |
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
- GSC
- Protein
- p.Val25=
- Coding
- c.75G>C
- MANE Select
- NM_173849
- dbSNP
- rs766083410
- Type
- single nucleotide variant
- Location
- chr14:94769941 (GRCh38)
- Gene constraint
- LOEUF 1.398 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.68 · 1 PDB
Similar variants
- GSC p.Val25Met Uncertain significance ★ ⚠ same residue
- GSC p.Ala26Val Uncertain significance ★★ ⚠ same type
- GSC p.Ala30Val Uncertain significance ★★ ⚠ same type
- GSC p.Lys183Gln Uncertain significance ★★ ⚠ same type
- GSC p.Tyr54Ser Uncertain significance ★★ ⚠ same type
- GSC c.356-186C>T Benign ★★ same type
- GSC p.Ala72Thr Benign ★★ same type
- GSC p.Asn140= Benign/Likely benign ★★ 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/gsc-p-val25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown