MGAT3

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

Basic information

Region (hg38): 22:39457011-39492194

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.

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.

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					2	2
missense			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	2

Variants in MGAT3

This is a list of pathogenic ClinVar variants found in the MGAT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39487360-C-G		not specified	Uncertain significance (May 30, 2022)
22-39487378-A-G		not specified	Uncertain significance (Oct 06, 2021)
22-39487477-A-C		not specified	Uncertain significance (Nov 10, 2022)
22-39487559-G-A		not specified	Uncertain significance (Jul 13, 2021)
22-39487571-A-G		not specified	Uncertain significance (Dec 27, 2023)
22-39487735-C-A		not specified	Uncertain significance (May 14, 2024)
22-39487792-C-A		not specified	Uncertain significance (Jan 18, 2023)
22-39487795-C-G		not specified	Uncertain significance (Feb 28, 2024)
22-39487810-G-A		not specified	Likely benign (Apr 22, 2022)
22-39487823-C-G		not specified	Uncertain significance (Sep 13, 2023)
22-39487873-G-A		not specified	Uncertain significance (Sep 01, 2021)
22-39487907-T-A		not specified	Uncertain significance (Aug 10, 2021)
22-39487922-A-C		not specified	Uncertain significance (Jan 22, 2024)
22-39487969-G-A		not specified	Uncertain significance (Mar 04, 2024)
22-39488112-G-C		not specified	Uncertain significance (Mar 01, 2024)
22-39488269-C-G		not specified	Uncertain significance (Nov 07, 2022)
22-39488274-C-T			Benign (Mar 29, 2018)
22-39488352-C-G			Benign (May 31, 2018)
22-39488387-C-T		not specified	Uncertain significance (Jun 17, 2024)
22-39488431-G-A		not specified	Uncertain significance (Apr 08, 2024)
22-39488461-G-A		not specified	Likely benign (Apr 07, 2023)
22-39488526-A-C		not specified	Uncertain significance (Apr 07, 2023)
22-39488662-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
22-39488760-G-C		not specified	Uncertain significance (Sep 16, 2021)
22-39488821-G-C		not specified	Uncertain significance (Sep 16, 2021)

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