Is EOGT p.Lys188Ile (c.563A>T) pathogenic?

EOGT p.Lys188Ile (c.563A>T) is classified Likely benign in EOGT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-06-18). AlphaMissense: likely benign (0.1096); Low-frequency (popmax 2.91%, afr).

How common is EOGT p.Lys188Ile (c.563A>T) in the general population?

EOGT p.Lys188Ile (c.563A>T) is low-frequency (popmax 2.91%, afr) (gnomAD).

What do computational predictors say about EOGT p.Lys188Ile (c.563A>T)?

AlphaMissense predicts likely benign (score 0.1096) — an in-silico prediction, not a clinical call.

EOGT p.Lys188Ile

c.563A>T · rs116138787 · VCV445295

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1096 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.91%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1096	likely benign
REVEL	0.08	moderately benign-leaning
SaProt	LLR -5.74	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 0.71	GERP -1.5
Regional constraint	o/e 1.10	unconstrained · MANE · 32 kb · p 0.016 · regional, not allelic
Overall
CADD	18.31	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 2.91% African / African-American · 2,181/75,022 alleles

Filtering AF 2.81% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.76%

Overall 0.169% 2,720/1,614,114 alleles · low-frequency exomes 1,448/1,461,818 · genomes 1,272/152,296 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.91%	34
Admixed American	0.235%	426
Middle Eastern	0.182%	551
South Asian	0.167%	599
Remaining individualsnot grpmax-eligible	0.165%	607
European (non-Finnish)	0.0112%	8,939

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.Lys188Ile
Coding: c.563A>T
MANE Select: NM_001278689
dbSNP: rs116138787
Type: single nucleotide variant
Location: chr3:69004435 (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

Similar variants

EOGT p.Lys188Ter Conflicting classifications of pathogenicity ★ same residue
EOGT p.Lys188Leu Benign ★★ same residue
EOGT c.1335-1G>A Pathogenic/Likely pathogenic ★★ same type
EOGT c.311+1G>T Pathogenic/Likely pathogenic ★★ same type
EOGT c.621-2A>T Pathogenic/Likely pathogenic ★★ same type
EOGT p.Arg149His Uncertain significance ★★ ⚠ same type
EOGT p.Arg372Trp Uncertain significance ★★ ⚠ same type
EOGT p.Arg377Trp Uncertain significance ★★ ⚠ same type

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-lys188ile (accessed [today's date]).

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