GSS c.129+1663A>G
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
GSS-related disorders
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +1663 | deep intronic (+1663 nt into the intron) |
|---|---|---|
| SpliceAI | Δ0.77 | donor gain · deltas |
| Pangolin | Δ0.72 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.24 | GERP -1.3 |
| Overall | ||
| CADD | 5.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GSS
- Coding
- c.129+1663A>G
- MANE Select
- NM_000178
- Type
- single nucleotide variant
- Location
- chr20:34950061 (GRCh38)
- Gene constraint
- LOEUF 0.819 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.25 · 2 PDB
Disease context
GSS-related disorders
Similar variants
- GSS p.Arg236fs Likely pathogenic ★ same condition
- GSS p.Phe255fs Likely pathogenic ★ same condition
- GSS c.130-1G>C Pathogenic/Likely pathogenic ★★ same type
- GSS c.-9+5G>A Pathogenic ★★ same type
- GSS p.Arg125Cys Pathogenic/Likely pathogenic ★★ same type
- GSS p.Arg164Gln Pathogenic ★★ ⚠ same type
- GSS p.Arg164Ter Pathogenic/Likely pathogenic ★★ same type
- GSS p.Arg236Ter Pathogenic/Likely pathogenic ★★ 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/gss-c-129-plus-1663a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown