MGAT3

beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase, the group of Mannosyl-glycoprotein N-acetylglucosaminyltransferases

Basic information

Region (hg38): 22:39457012-39492194

Links

ENSG00000128268

∙ NCBI:4248 ∙ OMIM:604621 ∙ HGNC:7046 ∙ Uniprot:Q09327 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MGAT3 gene.

not_specified (54 variants)
not_provided (2 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAT3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002409.5. 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	2
missense			50 clinvar	5 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	5	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAT3	protein_coding	protein_coding	ENST00000341184	1	34851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.147	0.849	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.13	199	368	0.540	0.0000284	3388
Missense in Polyphen		18	95.943	0.18761		844
Synonymous	-0.132	181	179	1.01	0.0000156	1107
Loss of Function	2.56	4	14.5	0.276	7.75e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: It is involved in the regulation of the biosynthesis and biological function of glycoprotein oligosaccharides. Catalyzes the addition of N-acetylglucosamine in beta 1-4 linkage to the beta-linked mannose of the trimannosyl core of N-linked sugar chains. It is one of the most important enzymes involved in the regulation of the biosynthesis of glycoprotein oligosaccharides.;
Pathway: N-Glycan biosynthesis - Homo sapiens (human);Reactions specific to the hybrid N-glycan synthesis pathway;Post-translational protein modification;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;Stabilization and expansion of the E-cadherin adherens junction (Consensus)

Recessive Scores

pRec: 0.200

Intolerance Scores

loftool: 0.0378
rvis_EVS: -0.58
rvis_percentile_EVS: 18.72

Haploinsufficiency Scores

pHI: 0.199
hipred: Y
hipred_score: 0.713
ghis: 0.689

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.373

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mgat3
Phenotype: homeostasis/metabolism phenotype; cellular phenotype; neoplasm; liver/biliary system phenotype; normal phenotype;

Gene ontology

Biological process: N-acetylglucosamine metabolic process;protein N-linked glycosylation;protein localization;regulation of cell migration;cellular response to oxidative stress;amyloid-beta metabolic process;cognition;positive regulation of protein localization to early endosome;negative regulation of lysosomal protein catabolic process
Cellular component: Golgi membrane;integral component of membrane
Molecular function: beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity;transferase activity, transferring glycosyl groups