Is OAT p.Ser84Cys (c.251C>G) pathogenic?

OAT p.Ser84Cys (c.251C>G) is classified Uncertain significance in OAT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-16). AlphaMissense: likely benign (0.1964); Very rare (popmax 0.000169%, nfe); Associated with Inborn genetic diseases.

What condition is associated with OAT p.Ser84Cys (c.251C>G)?

OAT p.Ser84Cys (c.251C>G) is associated with Inborn genetic diseases (ClinVar).

How common is OAT p.Ser84Cys (c.251C>G) in the general population?

OAT p.Ser84Cys (c.251C>G) is very rare (popmax 0.000169%, nfe) (gnomAD).

What do computational predictors say about OAT p.Ser84Cys (c.251C>G)?

AlphaMissense predicts likely benign (score 0.1964) — an in-silico prediction, not a clinical call.

OAT p.Ser84Cys

c.251C>G · VCV3882180

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1964 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000169%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1964	likely benign
REVEL	0.722	pathogenic-leaning
SaProt	LLR -9.41	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 14 kb · p 1.6e-05 · regional, not allelic
Overall
CADD	24.7	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 0.000169% European (non-Finnish) · 2/1,179,994 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000124% 2/1,614,006 alleles · very rare exomes 2/1,461,764 · genomes 0/152,242 · joint denominator

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.Ser84Cys
Coding: c.251C>G
MANE Select: NM_000274
Type: single nucleotide variant
Location: chr10:124408914 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 84: an α-helix

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

OAT p.Ala379Thr Uncertain significance ★★ ⚠ same condition
OAT p.Arg16His Uncertain significance ★★ ⚠ same condition
OAT p.Asn118Tyr Uncertain significance ★★ ⚠ same condition
OAT p.Asp205Asn Uncertain significance ★★ ⚠ same condition
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-ser84cys (accessed [today's date]).

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