Is OAT p.Val160Met (c.478G>A) pathogenic?

OAT p.Val160Met (c.478G>A) is classified Conflicting classifications of pathogenicity in OAT (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-01-21). AlphaMissense: likely benign (0.1224); Ultra-rare (popmax 0.012%, afr); Associated with ornithine aminotransferase deficiency.

What condition is associated with OAT p.Val160Met (c.478G>A)?

OAT p.Val160Met (c.478G>A) is associated with ornithine aminotransferase deficiency (ClinVar).

How common is OAT p.Val160Met (c.478G>A) in the general population?

OAT p.Val160Met (c.478G>A) is ultra-rare (popmax 0.012%, afr) (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.Val160Met (c.478G>A)?

AlphaMissense predicts likely benign (score 0.1224) — an in-silico prediction, not a clinical call.

OAT p.Val160Met

c.478G>A · rs148433929 · VCV878556

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.1224 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.012%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

ornithine aminotransferase deficiency

Computational evidence

Protein change
AlphaMissense	0.1224	likely benign
REVEL	0.438	indeterminate
SaProt	LLR -10.62	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.3	GERP 2, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 14 kb · p 1.6e-05 · regional, not allelic
Overall
CADD	26.2	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 0.012% African / African-American · 9/74,896 alleles

Filtering AF 0.00994% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00931%

Overall 0.0166% 268/1,612,528 alleles · ultra-rare exomes 249/1,460,506 · genomes 19/152,022 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.335%	299
Remaining individualsnot grpmax-eligible	0.0224%	4,457
African / African-Americangrpmax	0.012%	8,322
European (non-Finnish)	0.0115%	8,675
Admixed American	0.00667%	14,986
South Asian	0.00549%	18,205
East Asian	0.00223%	44,868

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Val160Met
Coding: c.478G>A
MANE Select: NM_000274
dbSNP: rs148433929
Type: single nucleotide variant
Location: chr10:124408584 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 160: 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.Val160Leu Uncertain significance ★ ⚠ same residue
OAT p.Val160= Likely benign ★ 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-val160met (accessed [today's date]).

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