Is EOGT p.Arg366Gln (c.1097G>A) pathogenic?

EOGT p.Arg366Gln (c.1097G>A) is classified Uncertain significance in EOGT (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-12). AlphaMissense: likely benign (0.191); Very rare (popmax 0.00334%, amr); Associated with Inborn genetic diseases.

What condition is associated with EOGT p.Arg366Gln (c.1097G>A)?

EOGT p.Arg366Gln (c.1097G>A) is associated with Inborn genetic diseases (ClinVar).

How common is EOGT p.Arg366Gln (c.1097G>A) in the general population?

EOGT p.Arg366Gln (c.1097G>A) is very rare (popmax 0.00334%, amr) (gnomAD).

What do computational predictors say about EOGT p.Arg366Gln (c.1097G>A)?

AlphaMissense predicts likely benign (score 0.191) — an in-silico prediction, not a clinical call.

EOGT p.Arg366Gln

c.1097G>A · rs775566374 · VCV2261114

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.191 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00334%, amr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.191	likely benign
REVEL	0.394	indeterminate
SaProt	LLR -10.02	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.2, phastCons 1
Regional constraint	o/e 1.10	unconstrained · MANE · 32 kb · p 0.016 · regional, not allelic
Overall
CADD	33.0	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 0.00334% Admixed American · 2/59,958 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.000496% 8/1,613,320 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00334%	29,979
South Asian	0.0033%	30,347
Remaining individualsnot grpmax-eligible	0.0016%	62,450
African / African-American	0.00134%	74,900
European (non-Finnish)	8.48e-05%	1,179,512

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: EOGT
Protein: p.Arg366Gln
Coding: c.1097G>A
MANE Select: NM_001278689
dbSNP: rs775566374
Type: single nucleotide variant
Location: chr3:68987500 (GRCh38)
Gene constraint: LOEUF 1.121 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.71

Full EOGT 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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EOGT p.Arg470Trp Uncertain significance ★★ ⚠ same condition
EOGT p.Asp525Glu Uncertain significance ★★ ⚠ same condition
EOGT p.Glu487Gly Uncertain significance ★★ ⚠ same condition
EOGT p.His481Arg Uncertain significance ★★ ⚠ same condition
EOGT p.Ile466Val 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/eogt-p-arg366gln (accessed [today's date]).

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