Is OAT c.1015del pathogenic?

OAT c.1015del is classified Likely pathogenic in OAT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-06). Very rare (popmax 8.5e-05%, nfe); Associated with ornithine aminotransferase deficiency.

What condition is associated with OAT c.1015del?

OAT c.1015del is associated with ornithine aminotransferase deficiency (ClinVar).

How common is OAT c.1015del in the general population?

OAT c.1015del is very rare (popmax 8.5e-05%, nfe) (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 c.1015del

VCV3591308

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.5e-05%, nfe)

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 · substitutions only
Constraint at this position
Conservation	phyloP 8	GERP 1.8, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.5e-05% European (non-Finnish) · 1/1,176,776 alleles

Overall 6.21e-05% 1/1,609,204 alleles · very rare exomes 1/1,457,002 · genomes 0/152,202 · 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
Coding: c.1015del
MANE Select: NM_000274
Type: Deletion
Location: chr10:124400984 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB

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 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
OAT p.Phe177_Trp178insTer 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-c-1015del (accessed [today's date]).

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