EOGT
protein-codingEGF domain specific O-linked N-acetylglucosamine transferase, the group of O-linked N-acetylglucosaminyltransferases
Gene summary
This gene encodes an enzyme that acts in the lumen of the endoplasmic reticulum to catalyze the transfer of N-acetylglucosamine to serine or threonine residues of extracellular-targeted proteins. This enzyme modifies proteins containing eukaryotic growth factor (EGF)-like domains, including the Notch receptor, thereby regulating developmental signalling. Mutations in this gene have been observed in individuals with Adams-Oliver syndrome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
- C3orf64
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~38.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014124
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014124
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0014124
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0007034
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014124
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014124
Submitter: ClinGen
*EOGT* was first reported in relation to Adams-Oliver syndrome, an autosomal recessive disorder, in 2013 (Shaheen et al, PMID: 23522784). Adams-Oliver syndrome is characterized by aplasia cutis congenita (ACC), typically affecting the vertex of the scalp, with underlying skull defects in more severe cases; transverse terminal limb defects; cutaneous vascular abnormalities such as cutis marmorata telangiectatica congenita; and, in some cases, congenital heart defects, vascular anomalies, growth impairment, and, less commonly, developmental delay or neurological abnormalities. *EOGT* encodes EGF domain-specific O-linked N-acetylglucosamine (O-GlcNAc) transferase which, in the ER, catalyzes the addition of a single O-GlcNAc residue to specific serine or threonine residues EGF-like repeats of secreted and cell-surface proteins such as NOTCH1 and other Notch receptors. Variants in EOGT have been implicated in only one condition, Adamas-Oliver syndrome 4. Ten variants (5 missense, 3 splice site, 2 frameshift) that have been reported in ten probands in six publications (Shaheen et al, 2013, PMID: 23522784; Cohen et al, 2014; PMID: 23860037; Meester et al, 2018, PMID: 29924900; Schröder et al, 2019, PMID: 31368252; Dudoignon et al, 2020, PMID: 31654484; He et al, 2026, PMID: 41959640) are included in this curation. Segregation evidence from three distantly-related families in the Bedouin population, which led to the identification of a founder frameshift variant, c.1074delA (p.Gly359AspfsTer28), was included (Cohen et al, 2014; PMID: 23860037). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism of pathogenicity appears to be loss of function. This gene-disease relationship is also supported by experimental evidence. *EOGT* was first identified as a novel OGT in Drosophila that O-GlcNAcylated the EGF repeats of Notch and Dumpy (Matsuura et al, 2008, PMID: 18948267, Sakaidani et al, 2011, PMID: 2215843). The gene was later cloned in mice and shown to rescue a posterior wing blistering phenotype resulting from RNAi knockdown of the Drosophila gene (Sakaidani et al, 2012, PMID: 22310717). O-GlcNAcylation of Notch1 enhances the binding of DLL1 and DLL4 to NOTCH1, thereby promoting downstream transcription of Notch target genes (Ogawa et al, 2015, PMID: 25488668). As the Notch signaling pathway is important in vascular development and angiogenesis, the role of EOGT is consistent with the features observed in patients with Adams-Oliver syndrome. Furthermore, the Eogt null mouse was shown to have vascular defects in the retina (Sawaguchi et al, 2017, PMID: 28395734). Of note, four of the six genes implicated in Adams-Oliver syndrome are in the Notch signaling pathway (RBPJ, NOTCH1, DLL4, EOGT (Tișa et al, 2025, PMID: 41516051). In summary, there is definitive evidence supporting the relationship between *EOGT* and Adams-Oliver syndrome 4, and autosomal recessive condition. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the ClinGen Congenital Disorders of Glycosylation GCEP on July 6, 2026 (SOP Version 12).
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Musculoskeletal
Intervention: Cardiovascular
Rationale: The condition can involve congenital cardiac anomalies, and awareness may allow early management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EOGT variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001278689.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 47 | 2 | 50 | ||
| missense | 3 | 100 | 8 | 2 | 113 | |
| nonsense | 1 | 1 | 3 | 1 | 6 | |
| start loss | 0 | |||||
| frameshift | 1 | 3 | 1 | 5 | ||
| splice donor/acceptor (+/-2bp) | 8 | 2 | 10 | |||
| Total | 5 | 12 | 107 | 56 | 4 | 184 |
Highest pathogenic variant AF is 0.000089211375
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001265618.1 | 15 | MANE Select | |
| Ensembl | ENSP00000373206.3 | 15 | MANE Select | |
| RefSeq | NP_775925.1 | 12 | Standard | |
| Ensembl | ENSP00000295571.5 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Other types of O-glycan biosynthesis - Homo sapiens (human)
Biological Process
- protein O-linked glycosylation
Molecular Function
- protein N-acetylglucosaminyltransferase activity
Cellular Component
- endoplasmic reticulum lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000295571
- Coding exons
- 12
- Length
- 38748
- Individuals with no LoFs
- 125111
- Homozygous LoFs
- 9
- Heterozygous LoFs
- 628
- Defined
- 125748
- p
- 0.00254
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0882 | 249 | 245 | 1.02 | 0.0000130 | 2951 |
| Missense (PolyPhen) | 71 | 78.307 | 0.90668 | 964 | ||
| Synonymous | -0.893 | 95 | 84.5 | 1.12 | 0.00000451 | 760 |
| Loss of Function | 1.62 | 17 | 25.9 | 0.656 | 0.00000133 | 315 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.028 | 0.028 | notable |
| Latino/Admixed American | 0.0021 | 0.0021 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00071 | 0.00065 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00042 | 0.00040 | rare |
| South Asian | 0.0017 | 0.0017 | notable |
| Other | 0.0011 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the transfer of a single N-acetylglucosamine from UDP-GlcNAc to a serine or threonine residue in extracellular proteins resulting in their modification with a beta-linked N- acetylglucosamine (O-GlcNAc). Specifically glycosylates the Thr residue located between the fifth and sixth conserved cysteines of folded EGF-like domains. {ECO:0000269|PubMed:23671640}.;
- Disease
- DISEASE: Adams-Oliver syndrome 4 (AOS4) [MIM:615297]: A form of Adams-Oliver syndrome, a disorder characterized by the congenital absence of skin (aplasia cutis congenita) in combination with transverse limb defects. Aplasia cutis congenita can be located anywhere on the body, but in the vast majority of the cases, it is present on the posterior parietal region where it is often associated with an underlying defect of the parietal bones. Limb abnormalities are typically limb truncation defects affecting the distal phalanges or entire digits (true ectrodactyly). Only rarely, metatarsals/metacarpals or more proximal limb structures are also affected. Apart from transverse limb defects, syndactyly, most commonly of second and third toes, can also be observed. The clinical features are highly variable and can also include cardiovascular malformations, brain abnormalities and vascular defects such as cutis marmorata and dilated scalp veins. {ECO:0000269|PubMed:23522784}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.0953
Intolerance Scores
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 65.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |