Is OAT p.Asp41Glu (c.123T>A) pathogenic?

OAT p.Asp41Glu (c.123T>A) is classified Likely benign in OAT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-03). AlphaMissense: likely benign (0.0646); Ultra-rare (popmax 0.02%, afr); Associated with Inborn genetic diseases.

What condition is associated with OAT p.Asp41Glu (c.123T>A)?

OAT p.Asp41Glu (c.123T>A) is associated with Inborn genetic diseases (ClinVar).

How common is OAT p.Asp41Glu (c.123T>A) in the general population?

OAT p.Asp41Glu (c.123T>A) is ultra-rare (popmax 0.02%, afr) (gnomAD).

What do computational predictors say about OAT p.Asp41Glu (c.123T>A)?

AlphaMissense predicts likely benign (score 0.0646) — an in-silico prediction, not a clinical call.

OAT p.Asp41Glu

c.123T>A · VCV3923387

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0646 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.02%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0646	likely benign
REVEL	0.255	benign-leaning
SaProt	LLR -5.37	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 -3.9	GERP -3.4
Regional constraint	o/e 0.81	unconstrained · MANE · 14 kb · p 1.6e-05 · regional, not allelic
Overall
CADD	0.064	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 0.02% African / African-American · 15/75,054 alleles

Filtering AF 0.0123% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00987%

Overall 0.00105% 17/1,614,204 alleles · ultra-rare exomes 9/1,461,880 · genomes 8/152,324 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.02%	5,004
Remaining individualsnot grpmax-eligible	0.0032%	31,253

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.Asp41Glu
Coding: c.123T>A
MANE Select: NM_000274
Type: single nucleotide variant
Location: chr10:124412049 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.29 · 35 PDB
Residue 41: 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.Asp41= Conflicting classifications of pathogenicity ★ same residue
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

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-asp41glu (accessed [today's date]).

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