Is EOGT p.Lys390= (c.1170A>G) pathogenic?

EOGT p.Lys390= (c.1170A>G) is classified Benign/Likely benign in EOGT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-28). Low-frequency (popmax 4.51%, afr); Associated with Adams-Oliver syndrome 4.

What condition is associated with EOGT p.Lys390= (c.1170A>G)?

EOGT p.Lys390= (c.1170A>G) is associated with Adams-Oliver syndrome 4 (ClinVar).

How common is EOGT p.Lys390= (c.1170A>G) in the general population?

EOGT p.Lys390= (c.1170A>G) is low-frequency (popmax 4.51%, afr) (gnomAD).

EOGT p.Lys390=

c.1170A>G · rs114914860 · VCV784012

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 4.51%, afr)

Conditions

Adams-Oliver syndrome 4

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.2	GERP -4.1, phastCons 1
Overall
CADD	6.714	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.51% African / African-American · 3,359/74,498 alleles

Filtering AF 4.38% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.33%

Overall 0.234% 3,744/1,602,998 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.51%	22
Middle Eastern	0.331%	302
Remaining individualsnot grpmax-eligible	0.253%	396
Admixed American	0.244%	410
South Asian	0.0113%	8,862
European (non-Finnish)	0.0046%	21,757
Finnishnot grpmax-eligible	0.00157%	63,634

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.Lys390=
Coding: c.1170A>G
MANE Select: NM_001278689
dbSNP: rs114914860
Type: single nucleotide variant
Location: chr3:68982855 (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

Adams-Oliver syndrome 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EOGT c.1335-1G>A Pathogenic/Likely pathogenic ★★ same condition
EOGT c.311+1G>T Pathogenic/Likely pathogenic ★★ same condition
EOGT c.621-2A>T Pathogenic/Likely pathogenic ★★ same condition
EOGT p.Arg372Trp 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.Asp252Asn 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-lys390 (accessed [today's date]).

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