Is GATM p.Pro183= (c.549C>G) pathogenic?

GATM p.Pro183= (c.549C>G) is classified Likely benign in GATM (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-23). Absent from gnomAD v4.1; Associated with AGAT deficiency.

What condition is associated with GATM p.Pro183= (c.549C>G)?

GATM p.Pro183= (c.549C>G) is associated with AGAT deficiency (ClinVar).

How common is GATM p.Pro183= (c.549C>G) in the general population?

GATM p.Pro183= (c.549C>G) is absent from gnomAD v4.1 (gnomAD).

GATM p.Pro183=

Q: How is L-Arginine:glycine amidinotransferase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.549C>G · VCV4710296

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

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 2.2	GERP 0.057, phastCons 1
Overall
CADD	9.231	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.Pro183=
Coding: c.549C>G
MANE Select: NM_001482
Type: single nucleotide variant
Location: chr15:45368196 (GRCh38)
Gene constraint: LOEUF 0.597 · pLI 0.33 (gnomAD)
Structure: AlphaFold pLDDT 90.24 · 11 PDB

Full GATM gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

AGAT deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For L-Arginine:glycine amidinotransferase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

GATM p.Pro183Ser Uncertain significance ★ ⚠ same residue
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

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-pro183 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown