Is EOGT p.Asp269= (c.807C>T) pathogenic?

EOGT p.Asp269= (c.807C>T) is classified Benign/Likely benign in EOGT (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-11-17). Rare (popmax 0.159%, sas); Associated with Adams-Oliver syndrome 4.

What condition is associated with EOGT p.Asp269= (c.807C>T)?

EOGT p.Asp269= (c.807C>T) is associated with Adams-Oliver syndrome 4 (ClinVar).

How common is EOGT p.Asp269= (c.807C>T) in the general population?

EOGT p.Asp269= (c.807C>T) is rare (popmax 0.159%, sas) (gnomAD).

EOGT p.Asp269=

c.807C>T · rs200904493 · VCV2049339

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.159%, sas)

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 -8.6	GERP -4.2
Overall
CADD	0.172	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.159% South Asian · 139/87,396 alleles

Filtering AF 0.137% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.129%

Overall 0.0123% 195/1,587,136 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.159%	629
Middle Eastern	0.0166%	6,028
Remaining individualsnot grpmax-eligible	0.013%	7,696
African / African-American	0.0122%	8,224
Admixed American	0.00531%	18,823
European (non-Finnish)	0.00292%	34,219
East Asian	0.00227%	44,022

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.Asp269=
Coding: c.807C>T
MANE Select: NM_001278689
dbSNP: rs200904493
Type: single nucleotide variant
Location: chr3:68998035 (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-asp269 (accessed [today's date]).

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