Is OAT p.Arg16His (c.47G>A) pathogenic?

OAT p.Arg16His (c.47G>A) is classified Uncertain significance in OAT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-12-03). AlphaMissense: likely benign (0.1028); Very rare (popmax 0.00668%, eas); Associated with Inborn genetic diseases.

What condition is associated with OAT p.Arg16His (c.47G>A)?

OAT p.Arg16His (c.47G>A) is associated with Inborn genetic diseases, ornithine aminotransferase deficiency, inherited retinal dystrophy (ClinVar).

How common is OAT p.Arg16His (c.47G>A) in the general population?

OAT p.Arg16His (c.47G>A) is very rare (popmax 0.00668%, eas) (gnomAD).

What do computational predictors say about OAT p.Arg16His (c.47G>A)?

AlphaMissense predicts likely benign (score 0.1028) — an in-silico prediction, not a clinical call.

OAT p.Arg16His

c.47G>A · rs146755810 · VCV2142487

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1028 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00668%, eas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1028	likely benign
REVEL	0.452	indeterminate
SaProt	LLR -9.72	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.9	GERP -0.61, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 14 kb · p 1.6e-05 · regional, not allelic
Overall
CADD	20.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% East Asian · 3/44,892 alleles

Filtering AF 0.00226% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00135%

Overall 0.00167% 27/1,613,970 alleles · very rare exomes 23/1,461,866 · genomes 4/152,104 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00668%	14,964
Admixed American	0.00667%	14,997
African / African-American	0.00534%	18,722
Remaining individualsnot grpmax-eligible	0.0032%	31,242
European (non-Finnish)	0.0011%	90,771
South Asian	0.0011%	91,090

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.Arg16His
Coding: c.47G>A
MANE Select: NM_000274
dbSNP: rs146755810
Type: single nucleotide variant
Location: chr10:124412125 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: ornithine aminotransferase deficiency inherited retinal dystrophy

Similar variants

OAT p.Arg16Cys Uncertain significance ★★ ⚠ same residue
OAT p.Arg16= 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-arg16his (accessed [today's date]).

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