NAGS p.Arg342=
c.1026C>A · rs2143987399 · VCV1667565
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
hyperammonemia due to N-acetylglutamate synthase deficiency
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 0.85 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 13.68 | 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
- NAGS
- Protein
- p.Arg342=
- Coding
- c.1026C>A
- MANE Select
- NM_153006
- dbSNP
- rs2143987399
- Type
- single nucleotide variant
- Location
- chr17:44006639 (GRCh38)
- Gene constraint
- LOEUF 1.178 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.38 · 1 PDB
- Residue 342
- the 'amino-acid kinase domain (aak)' region
Disease context
hyperammonemia due to N-acetylglutamate synthase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hyperammonemia due to N-acetylglutamate synthase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- All ages
- Prevalence
- <1 / 1 000 000 (Europe)
Similar variants
- NAGS p.Arg342Leu Uncertain significance ⚠ same residue
- NAGS p.Arg342fs Pathogenic ★★ same residue
- NAGS c.1097-1G>C Pathogenic ★★ same condition
- NAGS c.1097-2A>G Pathogenic/Likely pathogenic ★★ same condition
- NAGS c.701+1G>A Likely pathogenic ★★ same condition
- NAGS c.915+1G>T Likely pathogenic ★★ same condition
- NAGS c.916-2A>T Pathogenic/Likely pathogenic ★★ same condition
- NAGS p.Arg208Ter 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/nags-p-arg342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown