Is EOGT p.Lys84= (c.252A>G) pathogenic?

EOGT p.Lys84= (c.252A>G) is classified Likely benign in EOGT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-21). Rare (popmax 0.127%, afr); Associated with Adams-Oliver syndrome 4.

What condition is associated with EOGT p.Lys84= (c.252A>G)?

EOGT p.Lys84= (c.252A>G) is associated with Adams-Oliver syndrome 4 (ClinVar).

How common is EOGT p.Lys84= (c.252A>G) in the general population?

EOGT p.Lys84= (c.252A>G) is rare (popmax 0.127%, afr) (gnomAD).

EOGT p.Lys84=

c.252A>G · rs150080769 · VCV2078253

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.127%, 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 -0.45	GERP -2.8, phastCons 0.16
Overall
CADD	7.501	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.127% African / African-American · 95/75,046 alleles

Filtering AF 0.106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0982%

Overall 0.00644% 104/1,614,138 alleles · rare exomes 47/1,461,828 · genomes 57/152,310 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.127%	790
Remaining individualsnot grpmax-eligible	0.008%	12,501
South Asian	0.0011%	91,080
European (non-Finnish)	0.000254%	393,335

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.Lys84=
Coding: c.252A>G
MANE Select: NM_001278689
dbSNP: rs150080769
Type: single nucleotide variant
Location: chr3:69008487 (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-lys84 (accessed [today's date]).

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