Is EOGT p.Leu159Phe (c.475C>T) pathogenic?

EOGT p.Leu159Phe (c.475C>T) is classified Uncertain significance in EOGT (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-06-24). AlphaMissense: likely benign (0.1611); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with EOGT p.Leu159Phe (c.475C>T)?

EOGT p.Leu159Phe (c.475C>T) is associated with Inborn genetic diseases (ClinVar).

How common is EOGT p.Leu159Phe (c.475C>T) in the general population?

EOGT p.Leu159Phe (c.475C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EOGT p.Leu159Phe (c.475C>T)?

AlphaMissense predicts likely benign (score 0.1611) — an in-silico prediction, not a clinical call.

EOGT p.Leu159Phe

c.475C>T · rs2471613467 · VCV2313226

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1611 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1611	likely benign
REVEL	0.17	moderately benign-leaning
SaProt	LLR -4.86	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.7	GERP -0.13, phastCons 1
Regional constraint	o/e 1.10	unconstrained · MANE · 32 kb · p 0.016 · regional, not allelic
Overall
CADD	19.83	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: EOGT
Protein: p.Leu159Phe
Coding: c.475C>T
MANE Select: NM_001278689
dbSNP: rs2471613467
Type: single nucleotide variant
Location: chr3:69005180 (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

EOGT p.Arg149His Uncertain significance ★★ ⚠ same condition
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-leu159phe (accessed [today's date]).

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