Is OAT p.Gln35Arg (c.104A>G) pathogenic?

OAT p.Gln35Arg (c.104A>G) is classified Uncertain significance in OAT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-03). AlphaMissense: likely benign (0.0674); Very rare (popmax 0.0022%, sas); Associated with Inborn genetic diseases.

What condition is associated with OAT p.Gln35Arg (c.104A>G)?

OAT p.Gln35Arg (c.104A>G) is associated with Inborn genetic diseases (ClinVar).

How common is OAT p.Gln35Arg (c.104A>G) in the general population?

OAT p.Gln35Arg (c.104A>G) is very rare (popmax 0.0022%, sas) (gnomAD).

What do computational predictors say about OAT p.Gln35Arg (c.104A>G)?

AlphaMissense predicts likely benign (score 0.0674) — an in-silico prediction, not a clinical call.

OAT p.Gln35Arg

c.104A>G · VCV4626614

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0674 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0674	likely benign
REVEL	0.212	benign-leaning
SaProt	LLR -4.98	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 3.4	GERP 1.7, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 14 kb · p 1.6e-05 · regional, not allelic
Overall
CADD	17.96	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 0.0022% South Asian · 2/91,084 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000137%

Overall 0.000496% 8/1,614,024 alleles · very rare exomes 6/1,461,884 · genomes 2/152,140 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,542
Admixed American	0.00167%	59,996
Remaining individualsnot grpmax-eligible	0.0016%	62,486
European (non-Finnish)	0.000339%	295,006

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.Gln35Arg
Coding: c.104A>G
MANE Select: NM_000274
Type: single nucleotide variant
Location: chr10:124412068 (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

Similar variants

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OAT p.Asp205Gly Uncertain significance ★★ ⚠ same condition
OAT p.Asp263Val Uncertain significance ★★ ⚠ same condition
OAT p.Asp410Asn Uncertain significance ★★ ⚠ same condition
OAT p.Ile431Val Uncertain significance ★★ ⚠ 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-gln35arg (accessed [today's date]).

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