MGAT3

protein-coding

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

Gene summary

There are believed to be over 100 different glycosyltransferases involved in the synthesis of protein-bound and lipid-bound oligosaccharides. The enzyme encoded by this gene transfers a GlcNAc residue to the beta-linked mannose of the trimannosyl core of N-linked oligosaccharides and produces a bisecting GlcNAc. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002409.5

Inheritance

—

ClinVar variants

U:58B:7

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr22:39,457,012-39,492,194

External References & Databases

Ensembl (ENSG00000128268)

Transcript & Mutation Effects

hg38 • Region Span ~35.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MGAT3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002409.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			58 clinvar	5 clinvar		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	5	2	65

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002409.5	RefSeq	NP_002400.3	1	MANE Select
ENST00000341184.7	Ensembl	ENSP00000345270.6	1	MANE Select
NM_001098270.2	RefSeq	NP_001091740.1	1	Standard
ENST00000418314.1	Ensembl	ENSP00000408075.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

N-acetylglucosamine metabolic process
protein N-linked glycosylation
protein localization
regulation of cell migration
cellular response to oxidative stress

Molecular Function

beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity
transferase activity, transferring glycosyl groups

Cellular Component

Golgi membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341184
Coding exons: 1
Length: 34851
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125747
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.13	199	368	0.540	0.0000284	3388
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.200

Intolerance Scores

LoFtool: 0.0378
RVIS EVS: -0.58
RVIS percentile EVS: 18.72

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.373

Gene Damage Prediction

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