MGAT4B

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

Basic information

Region (hg38): 5:179797597-179806952

Links

ENSG00000161013 ∙ NCBI:11282 ∙ OMIM:604561 ∙ HGNC:7048 ∙ Uniprot:Q9UQ53 ∙ 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 MGAT4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAT4B 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				1		1
missense			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	39	1	0

Variants in MGAT4B

This is a list of pathogenic ClinVar variants found in the MGAT4B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-179798050-C-T		not specified	Uncertain significance (Jan 17, 2023)
5-179798370-C-T		not specified	Uncertain significance (Dec 27, 2023)
5-179798383-G-A		not specified	Uncertain significance (Sep 05, 2024)
5-179798424-G-A		not specified	Uncertain significance (Jun 04, 2024)
5-179798515-C-T		not specified	Uncertain significance (Jul 26, 2024)
5-179798580-C-T		not specified	Uncertain significance (Dec 17, 2021)
5-179798929-G-A		not specified	Uncertain significance (Feb 27, 2024)
5-179798976-G-A		not specified	Uncertain significance (Apr 15, 2024)
5-179799009-C-T		not specified	Uncertain significance (Apr 20, 2024)
5-179799015-T-C		not specified	Uncertain significance (Dec 13, 2023)
5-179799093-C-T		not specified	Uncertain significance (Sep 20, 2023)
5-179799094-G-A		not specified	Uncertain significance (Aug 14, 2024)
5-179799514-T-C		not specified	Uncertain significance (Dec 11, 2023)
5-179799971-G-C		not specified	Uncertain significance (Jul 14, 2022)
5-179800031-C-T		not specified	Uncertain significance (Feb 17, 2022)
5-179800049-G-A		not specified	Uncertain significance (Feb 17, 2024)
5-179800053-C-T		not specified	Uncertain significance (May 03, 2023)
5-179800545-G-C		not specified	Uncertain significance (Jun 22, 2023)
5-179800548-G-A		not specified	Uncertain significance (Mar 07, 2024)
5-179800564-C-T			Likely benign (Nov 01, 2022)
5-179800934-G-A		not specified	Uncertain significance (Oct 05, 2023)
5-179801359-G-A		not specified	Uncertain significance (Jun 16, 2023)
5-179801556-C-T		not specified	Uncertain significance (May 06, 2024)
5-179801563-G-A		not specified	Uncertain significance (Dec 14, 2023)
5-179801572-C-T		not specified	Uncertain significance (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAT4B	protein_coding	protein_coding	ENST00000337755	14	9356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.691	0.309	125695	0	42	125737	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	290	360	0.806	0.0000244	3626
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000396	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000947	0.0000924
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.00	0.00
South Asian	0.000578	0.000555
Other	0.00	0.00

dbNSFP

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.
• Pathway: 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;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.713
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.11

Haploinsufficiency Scores

• pHI: 0.124
• hipred: Y
• hipred_score: 0.613
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgat4b
• Phenotype: immune system phenotype; hematopoietic system phenotype; normal phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein N-linked glycosylation;N-glycan processing
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity;metal ion binding