Is OAT p.Gly375= (c.1125A>G) pathogenic?

OAT p.Gly375= (c.1125A>G) is classified Likely benign in OAT (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-01-27). Very rare (popmax 6.23e-05%); Associated with ornithine aminotransferase deficiency.

What condition is associated with OAT p.Gly375= (c.1125A>G)?

OAT p.Gly375= (c.1125A>G) is associated with ornithine aminotransferase deficiency (ClinVar).

How common is OAT p.Gly375= (c.1125A>G) in the general population?

OAT p.Gly375= (c.1125A>G) is very rare (popmax 6.23e-05%) (gnomAD).

How is Gyrate atrophy of choroid and retina inherited?

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

OAT p.Gly375=

c.1125A>G · rs1589697304 · VCV726976

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 6.23e-05%)

Conditions

ornithine aminotransferase 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 -1.9	GERP -4
Overall
CADD	3.152	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.23e-05%

Overall 6.23e-05% 1/1,605,032 alleles · very rare exomes 1/1,452,646 · genomes 0/152,386 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: OAT
Protein: p.Gly375=
Coding: c.1125A>G
MANE Select: NM_000274
dbSNP: rs1589697304
Type: single nucleotide variant
Location: chr10:124400874 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 375: a UniProt-annotated variant site (in gacr; decreased protein abundance)

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

Disease context

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

For Gyrate atrophy of choroid and retina (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: 1-9 / 100 000 (Finland)

Similar variants

OAT p.Gly375Ala Likely pathogenic ★★ same residue
OAT p.Gly375fs Likely pathogenic ★ same residue
OAT p.Gly375Arg Uncertain significance ★ ⚠ same residue
OAT c.1014+1G>A Likely pathogenic ★★ same condition
OAT c.199+2T>A Likely pathogenic ★★ same condition
OAT c.425-2A>G Pathogenic ★★ same condition
OAT c.520+1G>A Likely pathogenic ★★ same condition
OAT c.648+1G>A 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/oat-p-gly375 (accessed [today's date]).

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