GATM p.Phe253=
c.759T>C · rs2541989059 · VCV2834918
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
AGAT 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 4.1 | GERP 0.58, phastCons 1 |
| Overall | ||
| CADD | 10.8 | 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
- GATM
- Protein
- p.Phe253=
- Coding
- c.759T>C
- MANE Select
- NM_001482
- dbSNP
- rs2541989059
- Type
- single nucleotide variant
- Location
- chr15:45366425 (GRCh38)
- Gene constraint
- LOEUF 0.597 · pLI 0.33 (gnomAD)
- Structure
- AlphaFold pLDDT 90.24 · 11 PDB
Disease context
AGAT deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor L-Arginine:glycine amidinotransferase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy
Similar variants
- GATM c.484+1G>T Pathogenic ★★★ same condition
- GATM p.Ala185Pro Likely pathogenic ★★★ same condition
- GATM p.Arg169Ter Pathogenic ★★★ same condition
- GATM p.Arg260Ter Likely pathogenic ★★★ same condition
- GATM p.Arg413Gln Likely pathogenic ★★★ ⚠ same condition
- GATM p.Arg413Trp Likely pathogenic ★★★ same condition
- GATM p.Trp149Ter Pathogenic ★★★ same condition
- GATM p.Trp210Ter 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/gatm-p-phe253 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown