Is OAT p.Lys155fs (c.463_479del) pathogenic?

OAT p.Lys155fs (c.463479del) is classified Likely pathogenic in OAT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-31). Associated with ornithine aminotransferase deficiency.

What condition is associated with OAT p.Lys155fs (c.463_479del)?

OAT p.Lys155fs (c.463_479del) 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.Lys155fs

c.463_479del · VCV4818081

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 4 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.18	GERP -4.1, phastCons 0.91

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

Variant & gene context

Gene: OAT
Protein: p.Lys155fs
Coding: c.463_479del
MANE Select: NM_000274
Type: Deletion
Location: chr10:124408583 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 155: 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.Lys155= 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-lys155fs (accessed [today's date]).

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