MGAT4B

protein-coding

alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B, the group of Mannosyl-glycoprotein N-acetylglucosaminyltransferases|MicroRNA protein coding host genes

Gene summary

This gene encodes a key glycosyltransferase that regulates the formation of tri- and multiantennary branching structures in the Golgi apparatus. The encoded protein, in addition to the related isoenzyme A, catalyzes the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc in a beta-1,4 linkage to the Man-alpha-1,3-Man-beta-1,4-GlcNAc arm of R-Man-alpha-1,6(GlcNAc-beta-1,2-Man-alpha-1,3)Man-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1-Asn. The encoded protein may play a role in regulating the availability of serum glycoproteins, oncogenesis, and differentiation. [provided by RefSeq, Jul 2008]

MANE transcript

NM_014275.5

Inheritance

—

ClinVar variants

U:92B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr5:179,797,597-179,806,952

External References & Databases

Ensembl (ENSG00000161013)

Transcript & Mutation Effects

hg38 • Region Span ~9.4 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 MGAT4B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014275.5. 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			3 clinvar	1 clinvar		4
missense			85 clinvar	1 clinvar		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	92	2	0	94

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014275.5	RefSeq	NP_055090.1	15	MANE Select
ENST00000292591.12	Ensembl	ENSP00000292591.7	15	MANE Select
NM_054013.3	RefSeq	NP_463459.1	14	Standard
ENST00000337755.9	Ensembl	ENSP00000338487.5	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

N-Glycan biosynthesis - Homo sapiens (human)
Post-translational protein modification
N-Glycan antennae elongation
N-glycan antennae elongation in the medial/trans-Golgi
Metabolism of proteins

Biological Process

protein N-linked glycosylation
N-glycan processing

Molecular Function

alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity
metal ion binding

Cellular Component

Golgi membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337755
Coding exons: 14
Length: 9356
Individuals with no LoFs: 125695
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125737
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.31	290	360	0.806	0.0000244	3626
Missense (PolyPhen)		48	82.08	0.5848		912
Synonymous	-2.00	191	159	1.20	0.0000116	1125
Loss of Function	4.08	6	30.2	0.199	0.00000148	328

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000095	0.000092	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00058	0.00056	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Glycosyltransferase that participates in the transfer of N-acetylglucosamine (GlcNAc) to the core mannose residues of N- linked glycans. Catalyzes the formation of the GlcNAcbeta1-4 branch on the GlcNAcbeta1-2Manalpha1-3 arm of the core structure of N-linked glycans. Essential for the production of tri- and tetra-antennary N-linked sugar chains. Has lower affinities for donors or acceptors than MGAT4A, suggesting that, under physiological conditions, it is not the main contributor in N- glycan biosynthesis.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.713
RVIS EVS: 0.07
RVIS percentile EVS: 59.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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