MGAT2

alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase, the group of Mannosyl-glycoprotein N-acetylglucosaminyltransferases

Basic information

Region (hg38): 14:49620799-49623481

Links

ENSG00000168282 ∙ NCBI:4247 ∙ OMIM:602616 ∙ HGNC:7045 ∙ Uniprot:Q10469 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• MGAT2-congenital disorder of glycosylation (Definitive), mode of inheritance: AR
• MGAT2-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• MGAT2-congenital disorder of glycosylation (Moderate), mode of inheritance: AR
• MGAT2-congenital disorder of glycosylation (Supportive), mode of inheritance: AR
• MGAT2-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 IIa	AR	Hematologic	Awareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgery	Audiologic/Otolaryngologic; Biochemical; Craniofacial; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic	7944531; 8808595; 11228641; 19419693; 20684000; 22105986; 23023920
Hepatic-metabolized agents should be avoided

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MGAT2 gene.

• MGAT2-congenital_disorder_of_glycosylation (75 variants)
• Inborn_genetic_diseases (51 variants)
• not_provided (18 variants)
• not_specified (15 variants)
• MGAT2-related_disorder (7 variants)
• Congenital_disorder_of_glycosylation (3 variants)
• Primary_ciliary_dyskinesia (1 variants)
• Abnormal_facial_shape (1 variants)
• Abnormal_glycosylation (1 variants)
• Global_developmental_delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002408.4. 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			5	23	2	30
missense	3	1	81	2		87
nonsense	2	2				4
start loss						0
frameshift	1	3	2			6
splice donor/acceptor (+/-2bp)						0
Total	6	6	88	25	2

Highest pathogenic variant AF is 0.00000372196

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAT2	protein_coding	protein_coding	ENST00000305386	1	2710

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0342	0.958	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.515	214	236	0.906	0.0000115	2924
Missense in Polyphen		62	87.085	0.71195		1149
Synonymous	-0.398	107	102	1.05	0.00000511	894
Loss of Function	2.34	5	14.7	0.341	7.15e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes an essential step in the conversion of oligo- mannose to complex N-glycans.
• Disease: DISEASE: Congenital disorder of glycosylation 2A (CDG2A) [MIM:212066]: A multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N- glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:11228641, ECO:0000269|PubMed:8808595}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Reactions specific to the complex N-glycan synthesis pathway;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Intolerance Scores

• loftool: 0.122
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.580
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.400

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgat2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; muscle phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); craniofacial phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; renal/urinary system phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: oligosaccharide biosynthetic process;protein N-linked glycosylation via asparagine
• Cellular component: Golgi membrane;Golgi apparatus;Golgi stack;membrane;integral component of membrane
• Molecular function: alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity;manganese ion binding;carbohydrate binding;protein homodimerization activity