EOGT

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

Basic information

Region (hg38): 3:68975216-69013684

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 (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 (119 variants)
• not provided (79 variants)
• Inborn genetic diseases (30 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	27	6	34
missense	1		60	6	2	69
nonsense	1		3			4
start loss						0
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)	2	3				5
splice region			2	10	1	13
non coding			1	38	39	78
Total	6	3	65	71	47

Highest pathogenic variant AF is 0.0000788

Variants in EOGT

This is a list of pathogenic ClinVar variants found in the EOGT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-68977324-CA-C			Likely benign (Aug 31, 2019)
3-68977324-CAA-C			Benign (Aug 15, 2019)
3-68977435-T-C			Benign (Apr 10, 2019)
3-68977627-A-C		Adams-Oliver syndrome 4 • Inborn genetic diseases	Uncertain significance (Oct 19, 2022)
3-68977647-G-C		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
3-68977668-C-T		Adams-Oliver syndrome 4	Uncertain significance (Apr 11, 2022)
3-68977671-G-A		Adams-Oliver syndrome 4	Uncertain significance (Nov 13, 2023)
3-68977678-A-G		Adams-Oliver syndrome 4	Likely benign (Oct 03, 2022)
3-68977704-C-T		EOGT-related disorder	Uncertain significance (Dec 08, 2023)
3-68977711-A-G			Likely benign (Apr 17, 2018)
3-68977714-G-A		Adams-Oliver syndrome 4	Likely benign (Oct 13, 2023)
3-68977735-C-T		Adams-Oliver syndrome 4	Likely benign (Jul 25, 2023)
3-68977736-G-A		Inborn genetic diseases	Uncertain significance (Apr 08, 2022)
3-68977742-T-C		Adams-Oliver syndrome 4 • Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
3-68977744-C-T		Adams-Oliver syndrome 4	Likely benign (Aug 22, 2022)
3-68977747-C-G		Adams-Oliver syndrome 4	Likely benign (Jan 05, 2024)
3-68977756-A-G		Adams-Oliver syndrome 4	Likely benign (Aug 10, 2022)
3-68977759-G-T		Adams-Oliver syndrome 4	Uncertain significance (Jan 28, 2022)
3-68977760-T-C		Adams-Oliver syndrome 4 • Inborn genetic diseases	Uncertain significance (Dec 05, 2022)
3-68977761-GG-AA		Adams-Oliver syndrome 4	Uncertain significance (Dec 11, 2023)
3-68977762-G-A		Adams-Oliver syndrome 4	Likely benign (Sep 26, 2023)
3-68978155-T-C			Likely benign (Mar 14, 2020)
3-68978318-G-C		Adams-Oliver syndrome 4	Likely benign (Nov 08, 2022)
3-68978322-T-C		Adams-Oliver syndrome 4	Likely benign (Apr 25, 2023)
3-68978358-T-C		Adams-Oliver syndrome 4	Uncertain significance (May 03, 2022)

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

• 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 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