Is OAT p.Ile380Val (c.1138A>G) pathogenic?

OAT p.Ile380Val (c.1138A>G) is classified Likely benign in OAT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-20). AlphaMissense: likely benign (0.0565); Rare (popmax 0.472%, sas); Associated with ornithine aminotransferase deficiency.

What condition is associated with OAT p.Ile380Val (c.1138A>G)?

OAT p.Ile380Val (c.1138A>G) is associated with ornithine aminotransferase deficiency (ClinVar).

How common is OAT p.Ile380Val (c.1138A>G) in the general population?

OAT p.Ile380Val (c.1138A>G) is rare (popmax 0.472%, sas) (gnomAD).

How is Gyrate atrophy of choroid and retina inherited?

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

What do computational predictors say about OAT p.Ile380Val (c.1138A>G)?

AlphaMissense predicts likely benign (score 0.0565) — an in-silico prediction, not a clinical call.

OAT p.Ile380Val

c.1138A>G · rs545710763 · VCV705667

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0565 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.472%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

ornithine aminotransferase deficiency

Computational evidence

Protein change
AlphaMissense	0.0565	likely benign
REVEL	0.242	benign-leaning
SaProt	LLR -9.73	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.66	GERP 1, phastCons 0.48
Regional constraint	o/e 0.81	unconstrained · MANE · 14 kb · p 1.6e-05 · regional, not allelic
Overall
CADD	13.76	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.472% South Asian · 428/90,670 alleles

Filtering AF 0.435% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.421%

Overall 0.0293% 470/1,604,158 alleles · rare exomes 443/1,451,822 · genomes 27/152,336 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.472%	212
Middle Eastern	0.0903%	1,107
Remaining individualsnot grpmax-eligible	0.0435%	2,297
Ashkenazi Jewishnot grpmax-eligible	0.0136%	7,379
East Asian	0.00224%	44,736
Admixed American	0.00167%	59,972
European (non-Finnish)	0.000426%	234,596

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.Ile380Val
Coding: c.1138A>G
MANE Select: NM_000274
dbSNP: rs545710763
Type: single nucleotide variant
Location: chr10:124400861 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 380: a β-strand

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.Ile380fs Pathogenic ★ 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
OAT c.772-1G>A Pathogenic/Likely pathogenic ★★ same condition
OAT c.900+1G>A 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-ile380val (accessed [today's date]).

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