Is OAT p.Glu47fs (c.141del) pathogenic?

OAT p.Glu47fs (c.141del) is classified Likely pathogenic in OAT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-26). Associated with ornithine aminotransferase deficiency.

What condition is associated with OAT p.Glu47fs (c.141del)?

OAT p.Glu47fs (c.141del) is associated with ornithine aminotransferase deficiency (ClinVar).

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.Glu47fs

c.141del · VCV4818077

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

ornithine aminotransferase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.31	GERP -0.7

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: OAT
Protein: p.Glu47fs
Coding: c.141del
MANE Select: NM_000274
Type: Deletion
Location: chr10:124412031 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 47: an α-helix

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.Glu47= Likely benign ★ same residue
OAT c.881_900+51del Likely pathogenic ★★ same condition
OAT p.Ala61fs Pathogenic/Likely pathogenic ★★ same condition
OAT p.Glu318fs Pathogenic ★★ same condition
OAT p.Gly67fs Pathogenic/Likely pathogenic ★★ same condition
OAT p.His53fs Pathogenic ★★ same condition
OAT p.Leu259fs Pathogenic/Likely pathogenic ★★ same condition
OAT p.Phe172fs 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/oat-p-glu47fs (accessed [today's date]).

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