MOGS

mannosyl-oligosaccharide glucosidase, the group of Glycoside hydrolases

Basic information

Region (hg38): 2:74461057-74465410

Links

ENSG00000115275 ∙ NCBI:7841 ∙ OMIM:601336 ∙ HGNC:24862 ∙ Uniprot:Q13724 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• MOGS-congenital disorder of glycosylation (Moderate), mode of inheritance: AR
• MOGS-congenital disorder of glycosylation (Definitive), mode of inheritance: AR
• MOGS-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• MOGS-congenital disorder of glycosylation (Supportive), mode of inheritance: AR
• MOGS-congenital disorder of glycosylation (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type IIb	AR	Hematologic	At least theoretically, awareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgery	Biochemical; Craniofacial; Gastrointestinal; Genitourinary; Hematologic; Musculoskeletal; Neurologic	10788335; 20301507; 24716661
Hepatic-metabolized agents should be avoided

ClinVar

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

• MOGS-congenital_disorder_of_glycosylation (528 variants)
• Inborn_genetic_diseases (123 variants)
• not_provided (46 variants)
• not_specified (22 variants)
• MOGS-related_disorder (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MOGS gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006302.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				184	3	187
missense	2	5	318	19	1	345
nonsense	10	5	7			22
start loss						0
frameshift	10	6	6			22
splice donor/acceptor (+/-2bp)		1	1			2
Total	22	17	332	203	4

Highest pathogenic variant AF is 0.000038412498

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MOGS	protein_coding	protein_coding	ENST00000233616	4	4354

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124707	0	111	124818	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.662	434	475	0.914	0.0000283	5267
Missense in Polyphen		149	177.32	0.84029		2040
Synonymous	-0.512	209	200	1.05	0.0000105	1907
Loss of Function	1.75	21	31.6	0.664	0.00000202	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00109	0.00102
Ashkenazi Jewish	0.00	0.00
East Asian	0.000501	0.000501
Finnish	0.000279	0.000278
European (Non-Finnish)	0.000434	0.000432
Middle Eastern	0.000501	0.000501
South Asian	0.000588	0.000588
Other	0.000991	0.000989

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves the distal alpha 1,2-linked glucose residue from the Glc(3)Man(9)GlcNAc(2) oligosaccharide precursor in a highly specific manner.
• Disease: DISEASE: Type IIb congenital disorder of glycosylation (CDGIIb) [MIM:606056]: Characterized by marked generalized hypotonia and hypomotility of the neonate, dysmorphic features, including a prominent occiput, short palpebral fissures, retrognathia, high arched palate, generalized edema, and hypoplastic genitalia. Symptoms of the infant included hepatomegaly, hypoventilation, feeding problems and seizures. The clinical course was progressive and the infant did not survive more than a few months. {ECO:0000269|PubMed:10788335}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);N-Glycan biosynthesis - Homo sapiens (human);er associated degradation (erad) pathway;Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle;N-Glycan biosynthesis (Consensus)

Intolerance Scores

• loftool: 0.891
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.29

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.652

Gene Damage Prediction

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

Gene ontology

• Biological process: protein folding;protein N-linked glycosylation;oligosaccharide metabolic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of membrane;extracellular exosome
• Molecular function: mannosyl-oligosaccharide glucosidase activity;glucosidase activity