Is OAT p.Val98Ala (c.293T>C) pathogenic?

OAT p.Val98Ala (c.293T>C) is classified Uncertain significance in OAT (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely benign (0.2195); Absent from gnomAD v4.1.

How common is OAT p.Val98Ala (c.293T>C) in the general population?

OAT p.Val98Ala (c.293T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about OAT p.Val98Ala (c.293T>C)?

AlphaMissense predicts likely benign (score 0.2195) — an in-silico prediction, not a clinical call.

OAT p.Val98Ala

c.293T>C · rs483352687 · VCV100806

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2195 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2195	likely benign
REVEL	0.818	moderately pathogenic-leaning
SaProt	LLR -10.08	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8	GERP 2, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 14 kb · p 1.6e-05 · regional, not allelic
Overall
CADD	25.2	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: OAT
Protein: p.Val98Ala
Coding: c.293T>C
MANE Select: NM_000274
dbSNP: rs483352687
Type: single nucleotide variant
Location: chr10:124408872 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 98: an α-helix

Full OAT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

OAT c.1014+1G>A Likely pathogenic ★★ same type
OAT c.199+2T>A Likely pathogenic ★★ same type
OAT c.425-2A>G Pathogenic ★★ same type
OAT c.520+1G>A Likely pathogenic ★★ same type
OAT c.648+1G>A Likely pathogenic ★★ same type
OAT c.772-1G>A Pathogenic/Likely pathogenic ★★ same type
OAT c.900+1G>A Pathogenic/Likely pathogenic ★★ same type
OAT p.Arg180Thr Pathogenic/Likely pathogenic ★★ same type

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-val98ala (accessed [today's date]).

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