EOGT

EGF domain specific O-linked N-acetylglucosamine transferase, the group of O-linked N-acetylglucosaminyltransferases

Basic information

Region (hg38): 3:68975217-69013684

Previous symbols: [ "C3orf64" ]

Links

ENSG00000163378

∙ NCBI:285203 ∙ OMIM:614789 ∙ HGNC:28526 ∙ Uniprot:Q5NDL2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Adams-Oliver syndrome (Supportive), mode of inheritance: AD
Adams-Oliver syndrome 4 (Definitive), mode of inheritance: AR
Adams-Oliver syndrome 4 (Moderate), mode of inheritance: AR
Adams-Oliver syndrome 4 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Adams-Oliver syndrome 4	AR	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Musculoskeletal	23522784

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EOGT gene.

Adams-Oliver_syndrome_4 (128 variants)
Inborn_genetic_diseases (63 variants)
not_provided (46 variants)
EOGT-related_disorder (6 variants)
not_specified (1 variants)
Adams-Oliver_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EOGT gene is commonly pathogenic or not. These statistics are base on transcript: NM_001278689.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	38 clinvar	3 clinvar	43
missense	3 clinvar		87 clinvar	8 clinvar	2 clinvar	100
nonsense	1 clinvar		3 clinvar	1 clinvar		5
start loss						0
frameshift	1 clinvar	2 clinvar	1 clinvar			4
splice donor/acceptor (+/-2bp)	2 clinvar	3 clinvar				5
Total	7	5	93	47	5

Highest pathogenic variant AF is 0.000089211375

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EOGT	protein_coding	protein_coding	ENST00000295571	12	38748

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.04e-9	0.838	125111	9	628	125748	0.00254

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0882	249	245	1.02	0.0000130	2951
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0301	0.0299
Ashkenazi Jewish	0.00	0.00
East Asian	0.000706	0.000653
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000416	0.000396
Middle Eastern	0.000706	0.000653
South Asian	0.00173	0.00170
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

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.;
Pathway: Other types of O-glycan biosynthesis - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.0953

Intolerance Scores

loftool
rvis_EVS: 0.17
rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

pHI: 0.518
hipred: N
hipred_score: 0.289
ghis: 0.515

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Eogt
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype;

Gene ontology

Biological process: protein O-linked glycosylation
Cellular component: endoplasmic reticulum lumen
Molecular function: protein N-acetylglucosaminyltransferase activity