MOGS

mannosyl-oligosaccharide glucosidase, the group of Glycoside hydrolases

Basic information

Region (hg38): 2:74461056-74465410

Links

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

Phenotypes

GenCC

Source: genCC

• SRD5A3-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• MOGS-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• MOGS-congenital disorder of glycosylation (Moderate), 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 (Definitive), 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 (432 variants)
• Inborn genetic diseases (39 variants)
• not provided (29 variants)
• not specified (23 variants)
• MOGS-related condition (2 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.

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	121	3	125
missense		2	252	7	7	268
nonsense	8	3	6			17
start loss						0
frameshift	5	3	4			12
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region			1	3		4
non coding			2	22	1	25
Total	13	9	266	150	11

Highest pathogenic variant AF is 0.0000657

Variants in MOGS

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

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

Position	Type	Phenotype	Significance	ClinVar
2-74461276-C-A		MOGS-congenital disorder of glycosylation	Uncertain significance (Oct 28, 2019)
2-74461280-A-G		MOGS-congenital disorder of glycosylation	Uncertain significance (Jul 07, 2023)
2-74461284-T-G		MOGS-congenital disorder of glycosylation	Uncertain significance (Jul 14, 2023)
2-74461288-GC-G		MOGS-congenital disorder of glycosylation	Uncertain significance (May 03, 2022)
2-74461296-C-T		MOGS-congenital disorder of glycosylation	Likely benign (Nov 15, 2022)
2-74461313-T-C		MOGS-congenital disorder of glycosylation	Uncertain significance (Feb 15, 2018)
2-74461318-C-T		MOGS-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2022)
2-74461319-C-T		MOGS-congenital disorder of glycosylation	Uncertain significance (Dec 01, 2021)
2-74461320-G-A		MOGS-congenital disorder of glycosylation	Likely benign (Sep 26, 2022)
2-74461331-G-A		MOGS-congenital disorder of glycosylation	Uncertain significance (May 27, 2022)
2-74461345-C-T		MOGS-congenital disorder of glycosylation	Uncertain significance (Jan 20, 2022)
2-74461346-G-T		MOGS-congenital disorder of glycosylation	Likely benign (Sep 21, 2022)
2-74461353-G-A		MOGS-congenital disorder of glycosylation	Likely benign (Dec 07, 2023)
2-74461355-G-A		MOGS-congenital disorder of glycosylation • Inborn genetic diseases	Uncertain significance (Oct 17, 2022)
2-74461367-G-A		MOGS-congenital disorder of glycosylation	Uncertain significance (Jul 21, 2022)
2-74461367-G-T		MOGS-congenital disorder of glycosylation	Uncertain significance (Aug 20, 2019)
2-74461391-G-A		MOGS-congenital disorder of glycosylation	Uncertain significance (Mar 04, 2020)
2-74461395-C-T		MOGS-related disorder	Likely benign (Apr 20, 2020)
2-74461399-C-T		MOGS-congenital disorder of glycosylation	Uncertain significance (Sep 01, 2021)
2-74461400-G-A		MOGS-congenital disorder of glycosylation	Uncertain significance (Oct 28, 2021)
2-74461403-A-G		MOGS-congenital disorder of glycosylation	Uncertain significance (Sep 17, 2021)
2-74461404-T-C		MOGS-congenital disorder of glycosylation	Likely benign (Apr 28, 2021)
2-74461414-A-G		MOGS-congenital disorder of glycosylation	Uncertain significance (Dec 06, 2023)
2-74461419-G-A		MOGS-congenital disorder of glycosylation	Likely benign (Jul 20, 2021)
2-74461420-T-C		Inborn genetic diseases	Uncertain significance (Nov 07, 2023)

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
5.81e-11	0.836	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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.197
• ghis: 0.460

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

Mouse Genome Informatics

• Gene name: Mogs
• Phenotype: immune system phenotype; digestive/alimentary phenotype; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype

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