MGAT4A

alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A, the group of Mannosyl-glycoprotein N-acetylglucosaminyltransferases

Basic information

Region (hg38): 2:98619105-98731132

Links

ENSG00000071073 ∙ NCBI:11320 ∙ OMIM:604623 ∙ HGNC:7047 ∙ Uniprot:Q9UM21 ∙ 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 MGAT4A gene.

• Inborn genetic diseases (20 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGAT4A 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			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	2

Variants in MGAT4A

This is a list of pathogenic ClinVar variants found in the MGAT4A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-98625758-T-A		not specified	Uncertain significance (May 23, 2023)
2-98635248-C-T		not specified	Uncertain significance (May 25, 2022)
2-98636542-G-C		not specified	Uncertain significance (Apr 18, 2023)
2-98636588-A-G		not specified	Uncertain significance (Apr 22, 2022)
2-98639845-T-A		not specified	Uncertain significance (Jul 05, 2023)
2-98639845-T-C		not specified	Uncertain significance (Jan 17, 2024)
2-98639913-T-G		not specified	Uncertain significance (Nov 09, 2023)
2-98639948-C-T			Benign (Dec 13, 2017)
2-98639953-G-A		not specified	Uncertain significance (Jul 14, 2021)
2-98639989-T-C		not specified	Uncertain significance (May 03, 2023)
2-98643964-G-C		not specified	Uncertain significance (May 10, 2022)
2-98644038-G-A		not specified	Uncertain significance (Oct 12, 2021)
2-98655513-T-C			Benign (Apr 02, 2018)
2-98658230-T-C		not specified	Uncertain significance (Dec 13, 2022)
2-98658239-A-C		not specified	Uncertain significance (Jun 30, 2022)
2-98663099-T-G		not specified	Uncertain significance (Dec 21, 2022)
2-98675052-C-T		not specified	Uncertain significance (Jan 10, 2022)
2-98675089-T-C		not specified	Uncertain significance (Oct 25, 2023)
2-98675136-T-A		not specified	Uncertain significance (Mar 01, 2023)
2-98675167-G-C		not specified	Uncertain significance (Dec 01, 2022)
2-98678355-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-98678362-C-G		not specified	Uncertain significance (Nov 18, 2022)
2-98678370-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-98678420-C-T		not specified	Uncertain significance (May 31, 2023)
2-98678438-G-A		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGAT4A	protein_coding	protein_coding	ENST00000264968	15	112021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000445	1.00	125719	0	26	125745	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	203	273	0.744	0.0000136	3513
Missense in Polyphen		19	59.34	0.32019		758
Synonymous	0.0906	94	95.1	0.988	0.00000485	974
Loss of Function	3.12	13	32.1	0.405	0.00000170	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000277	0.000270
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000141	0.000139
European (Non-Finnish)	0.0000988	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.000101	0.0000980
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. Involved in glucose transport by mediating SLC2A2/GLUT2 glycosylation, thereby controlling cell-surface expression of SLC2A2 in pancreatic beta cells.
• Pathway: N-Glycan biosynthesis - Homo sapiens (human);Post-translational protein phosphorylation;Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;N-Glycan biosynthesis (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.710
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.342
• hipred: Y
• hipred_score: 0.558
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Mgat4a
• Phenotype: liver/biliary system phenotype; cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: protein N-linked glycosylation;N-glycan processing;post-translational protein modification;cellular protein metabolic process
• Cellular component: Golgi membrane;endoplasmic reticulum lumen;integral component of membrane;extracellular exosome
• Molecular function: alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity;metal ion binding