GSS p.Arg360=
c.1080G>A · rs2519019567 · VCV2766506
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
glutathione synthetase deficiency with 5-oxoprolinuria
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.13 | GERP -2, phastCons 0.002 |
| Overall | ||
| CADD | 8.83 | 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
- Protein
- p.Arg360=
- Coding
- c.1080G>A
- MANE Select
- NM_000178
- dbSNP
- rs2519019567
- Type
- single nucleotide variant
- Location
- chr20:34931367 (GRCh38)
- Gene constraint
- LOEUF 0.819 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.25 · 2 PDB
- Residue 360
- an α-helix
Disease context
glutathione synthetase deficiency with 5-oxoprolinuria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glutathione synthetase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Neonatal
Similar variants
- GSS p.Arg360Trp Uncertain significance ★★ ⚠ same residue
- GSS c.130-1G>C Pathogenic/Likely pathogenic ★★ same condition
- GSS c.-9+5G>A Pathogenic ★★ same condition
- GSS p.Arg125Cys Pathogenic/Likely pathogenic ★★ same condition
- GSS p.Arg164Gln Pathogenic ★★ ⚠ same condition
- GSS p.Arg164Ter Pathogenic/Likely pathogenic ★★ same condition
- GSS p.Arg236Ter Pathogenic/Likely pathogenic ★★ same condition
- GSS p.Arg237Ter 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/gss-p-arg360 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown