Is OAT p.Pro417= (c.1251G>A) pathogenic?

OAT p.Pro417= (c.1251G>A) is classified Likely benign in OAT (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-02-17). Very rare (popmax 0.00729%, nfe); Associated with ornithine aminotransferase deficiency.

What condition is associated with OAT p.Pro417= (c.1251G>A)?

OAT p.Pro417= (c.1251G>A) is associated with ornithine aminotransferase deficiency (ClinVar).

How common is OAT p.Pro417= (c.1251G>A) in the general population?

OAT p.Pro417= (c.1251G>A) is very rare (popmax 0.00729%, 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 p.Pro417=

c.1251G>A · rs570318690 · VCV1088800

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00729%, 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 · no allele here is in the release
Constraint at this position
Conservation	phyloP -6.4	GERP -4.1
Overall
CADD	5.838	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00729% European (non-Finnish) · 86/1,179,938 alleles

Filtering AF 0.00604% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00557%

Overall 0.00558% 90/1,613,874 alleles · very rare exomes 86/1,461,726 · genomes 4/152,148 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00729%	13,720
Remaining individualsnot grpmax-eligible	0.0032%	31,239
East Asian	0.00223%	44,894
South Asian	0.0011%	91,084

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.Pro417=
Coding: c.1251G>A
MANE Select: NM_000274
dbSNP: rs570318690
Type: single nucleotide variant
Location: chr10:124398011 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 417: a UniProt-annotated variant site (in gacr; loss of protein stability; loss of ornithine aminotransferase activity)

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.Pro417Leu Pathogenic/Likely pathogenic ★★ same residue
OAT p.Pro417Ser Conflicting classifications of pathogenicity ★ ⚠ 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

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-pro417 (accessed [today's date]).

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