Is EOGT p.Val474Phe (c.1420G>T) pathogenic?

EOGT p.Val474Phe (c.1420G>T) is classified Uncertain significance in EOGT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-12). AlphaMissense: ambiguous (0.3712); Very rare (popmax 0.00263%, nfe); Associated with Inborn genetic diseases.

What condition is associated with EOGT p.Val474Phe (c.1420G>T)?

EOGT p.Val474Phe (c.1420G>T) is associated with Inborn genetic diseases (ClinVar).

How common is EOGT p.Val474Phe (c.1420G>T) in the general population?

EOGT p.Val474Phe (c.1420G>T) is very rare (popmax 0.00263%, nfe) (gnomAD).

What do computational predictors say about EOGT p.Val474Phe (c.1420G>T)?

AlphaMissense predicts ambiguous (score 0.3712) — an in-silico prediction, not a clinical call.

EOGT p.Val474Phe

c.1420G>T · VCV4249429

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3712 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00263%, nfe)

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3712	ambiguous
REVEL	0.66	pathogenic-leaning
SaProt	LLR -11.25	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 1.2, phastCons 1
Regional constraint	o/e 1.10	unconstrained · MANE · 32 kb · p 0.016 · regional, not allelic
Overall
CADD	24.4	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 0.00263% European (non-Finnish) · 31/1,179,378 alleles

Filtering AF 0.00188% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00164%

Overall 0.00212% 31/1,459,924 alleles · very rare

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.Val474Phe
Coding: c.1420G>T
MANE Select: NM_001278689
Type: single nucleotide variant
Location: chr3:68978350 (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.Arg377Trp Uncertain significance ★★ ⚠ same condition
EOGT p.Arg452His Uncertain significance ★★ ⚠ same condition
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-val474phe (accessed [today's date]).

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