Is EOGT p.Tyr304= (c.912T>C) pathogenic?

EOGT p.Tyr304= (c.912T>C) is classified Benign in EOGT (ClinVar, Multiple submitters, 5 submitters; last evaluated 2024-11-26). Common (popmax 28.4%, eas) — too common for a highly-penetrant pathogenic allele; Associated with Adams-Oliver syndrome 4.

What condition is associated with EOGT p.Tyr304= (c.912T>C)?

EOGT p.Tyr304= (c.912T>C) is associated with Adams-Oliver syndrome 4 (ClinVar).

EOGT p.Tyr304=

Q: How common is EOGT p.Tyr304= (c.912T>C) in the general population?

EOGT p.Tyr304= (c.912T>C) is common (popmax 28.4%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.912T>C · rs13085120 · VCV1255384

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 28.4%, eas) — too common for a highly-penetrant pathogenic allele

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 -2.8	GERP -4.3
Overall
CADD	0.681	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 28.4% East Asian · 11,544/40,578 alleles

Filtering AF 28% ClinGen BA1/BS1 input FAF95, joint · FAF99 27.8%

Overall 18.1% 274,579/1,515,792 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	28.4%	4
South Asian	24%	4
Ashkenazi Jewishnot grpmax-eligible	23.9%	4
Middle Eastern	23%	4
Remaining individualsnot grpmax-eligible	18.3%	5
European (non-Finnish)	18.2%	5
Amishnot grpmax-eligible	17.5%	6
Admixed American	12.5%	8
Finnishnot grpmax-eligible	10.4%	10
African / African-American	9.96%	10

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.Tyr304=
Coding: c.912T>C
MANE Select: NM_001278689
dbSNP: rs13085120
Type: single nucleotide variant
Location: chr3:68988937 (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 p.Tyr304Ter Uncertain significance ★ same residue
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

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-tyr304 (accessed [today's date]).

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