MGAT4A

Summary

MGAT4A (alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A, HGNC:7047) is a protein-coding gene on chromosome 2q11.2, encoding Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A (Q9UM21). Glycosyltransferase that catalyze the transfer of GlcNAc from UDP-GlcNAc to the GlcNAcbeta1-2Manalpha1-3 arm of the core structure of N-linked glycans through a beta1-4 linkage and participates in the production of tri- and tetra-antennary N-linked sugar chains.

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 B, 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.

Source: NCBI Gene 11320 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 80 total
• MANE Select transcript: NM_012214

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7047
Approved symbol	MGAT4A
Name	alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A
Location	2q11.2
Locus type	gene with protein product
Status	Approved
Aliases	GnT-Iva, GnT-4a
Ensembl gene	ENSG00000071073
Ensembl biotype	protein_coding
OMIM	604623
Entrez	11320

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 14 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000264968, ENST00000393487, ENST00000409391, ENST00000414521, ENST00000460768, ENST00000461884, ENST00000484936, ENST00000492163, ENST00000495056, ENST00000877290, ENST00000877291, ENST00000877292, ENST00000877293, ENST00000877294, ENST00000968678, ENST00000968679, ENST00000968680, ENST00000968681

RefSeq mRNA: 2 — MANE Select: NM_012214 NM_001160154, NM_012214

CCDS: CCDS2036, CCDS54380

Canonical transcript exons

ENST00000393487 — 16 exons

Exon	Start	End
ENSE00001515507	98731048	98731132
ENSE00003493049	98726239	98726567
ENSE00003539987	98656352	98656465
ENSE00003541885	98675035	98675175
ENSE00003544893	98658218	98658264
ENSE00003572772	98663046	98663179
ENSE00003576424	98655445	98655520
ENSE00003636932	98678304	98678471
ENSE00003889757	98639808	98640001
ENSE00003889820	98636517	98636595
ENSE00003891235	98625723	98625835
ENSE00003892024	98640121	98640228
ENSE00003892822	98643923	98644053
ENSE00003892993	98645428	98645542
ENSE00003893009	98619106	98625592
ENSE00003895599	98635222	98635288

Expression profiles

Bgee: expression breadth ubiquitous, 266 present calls, max score 96.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.0499 / max 347.2952, expressed in 1031 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29853	10.7764	1030
29846	0.6348	79
29849	0.2539	63
29847	0.2002	56
29848	0.1095	50
29852	0.0751	35

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
jejunal mucosa	UBERON:0000399	96.95	gold quality
colonic mucosa	UBERON:0000317	94.28	gold quality
renal medulla	UBERON:0000362	94.18	gold quality
mucosa of sigmoid colon	UBERON:0004993	94.02	gold quality
body of pancreas	UBERON:0001150	93.25	gold quality
islet of Langerhans	UBERON:0000006	93.13	gold quality
tibia	UBERON:0000979	93.08	gold quality
visceral pleura	UBERON:0002401	92.47	gold quality
pancreas	UBERON:0001264	92.12	gold quality
rectum	UBERON:0001052	91.98	gold quality
duodenum	UBERON:0002114	91.51	gold quality
secondary oocyte	CL:0000655	91.44	gold quality
parotid gland	UBERON:0001831	90.88	gold quality
tonsil	UBERON:0002372	90.68	gold quality
Brodmann (1909) area 23	UBERON:0013554	90.34	gold quality
granulocyte	CL:0000094	90.33	gold quality
bone marrow	UBERON:0002371	90.23	gold quality
middle temporal gyrus	UBERON:0002771	90.15	gold quality
mucosa of transverse colon	UBERON:0004991	90.10	gold quality
small intestine Peyer’s patch	UBERON:0003454	89.19	gold quality
cerebellar vermis	UBERON:0004720	89.13	gold quality
palpebral conjunctiva	UBERON:0001812	88.99	gold quality
endothelial cell	CL:0000115	88.86	gold quality
small intestine	UBERON:0002108	88.69	gold quality
postcentral gyrus	UBERON:0002581	88.29	gold quality
colonic epithelium	UBERON:0000397	88.14	gold quality
cerebellar cortex	UBERON:0002129	87.98	gold quality
epithelium of nasopharynx	UBERON:0001951	87.97	gold quality
nasopharynx	UBERON:0001728	87.95	gold quality
cerebellar hemisphere	UBERON:0002245	87.95	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-CURD-88	yes	45.54
E-HCAD-35	yes	29.19
E-CURD-46	yes	23.15
E-ANND-3	yes	7.20
E-MTAB-10137	no	188.64
E-MTAB-5061	no	4.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

351 targeting MGAT4A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928

Literature-anchored findings (GeneRIF, showing 10)

• upregulation of mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetyl-glucosaminyl-transferase is associated with metastatic colorectal carcinoma (PMID:15688387)
• analysis of expression of N-acetylglucosaminyltransferase-IVa and IVb (GnT-IVa and b) in pancreatic cancer (PMID:16434023)
• GnT-IVa is more active than GnT-IVb under physiological conditions and it primarily contributes to the biosynthesis of N-glycans. (PMID:17006639)
• We investigated mRNA levels of glycosyltransferases, namely, N-acetylglucosaminyltransferase a (GnT)-IVa, and found that (GnT)-IVa expression was decreased in HLE-cells Epirubicin resistant. (PMID:17488527)
• The results of this work suggest that in T2D subjects, high levels of glucose and triglycerides are accompanied by an increase on MGAT4A mRNA levels and WBC count; condition that suggests a pro-inflammatory state due to a chronic metabolic stress. (PMID:17953760)
• GNT-IV genetic variation is not associated with gastric cancer. (PMID:19751437)
• Findings suggest that GnT-IVa is involved in regulating invasion of choriocarcinoma through modifications of the oligosaccharide chains of beta1 integrin. (PMID:23169300)
• Data suggest microRNA-424 regulates expression of MGAT4A (mannoside beta-1,4-N-acetylglucosaminyltransferase A), OGT (O-linked N-acetylglucosamine transferase), and GALNT13 (polypeptide N-acetylgalactosaminyltransferase 13) in mammary epithelium. (PMID:26589799)
• GnT-IVa may contribute to the malignancy of choriocarcinoma by promoting cell adhesion, migration and invasion through glycosylation of integrin beta1 and LAMP-2. (PMID:28534963)
• N-glycosylation by N-acetylglucosaminyltransferase IVa enhances the interaction of integrin beta1 with vimentin and promotes hepatocellular carcinoma cell motility. (PMID:37295747)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	mgat4a	ENSDARG00000063330
mus_musculus	Mgat4a	ENSMUSG00000026110
rattus_norvegicus	Mgat4a	ENSRNOG00000018276
rattus_norvegicus		ENSRNOG00000069701
drosophila_melanogaster	Mgat4a	FBGN0036446
drosophila_melanogaster	Mgat4b	FBGN0036447

Paralogs (3): MGAT4B (ENSG00000161013), MGAT4C (ENSG00000182050), MGAT4D (ENSG00000205301)

Protein

Protein identifiers

Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A — Q9UM21 (reviewed: Q9UM21)

Alternative names: N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase IVa, UDP-N-acetylglucosamine: alpha-1,3-D-mannoside beta-1,4-N-acetylglucosaminyltransferase IVa

All UniProt accessions (2): Q9UM21, U3KPT4

UniProt curated annotations — full annotation on UniProt →

Function. Glycosyltransferase that catalyze the transfer of GlcNAc from UDP-GlcNAc to the GlcNAcbeta1-2Manalpha1-3 arm of the core structure of N-linked glycans through a beta1-4 linkage and participates in 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.

Subcellular location. Golgi apparatus membrane Secreted.

Tissue specificity. Expressed in pancreas, spleen, thymus, prostate, small intestine, peripheral blood leukocytes and lymph node. Strongly overexpressed in choriocarcinoma cancer cell lines. Down-regulated in pancreatic cancer.

Post-translational modifications. N-glycosylated.

Activity regulation. Inhibited by UDP.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 54 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UM21-1	1	yes
Q9UM21-2	2

RefSeq proteins (2): NP_001153626, NP_036346* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006759	Glyco_transf_54	Family
IPR056576	MGAT4_A/B/C_C	Domain
IPR057279	MGAT4	Domain

Pfam: PF04666, PF23524

Enzyme classification (BRENDA):

• EC 2.4.1.145 — alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase (BRENDA: 6 organisms, 27 substrates, 5 inhibitors, 14 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

7 substrates with measured Km, best-characterized 7. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
UDP-N-ACETYL-D-GLUCOSAMINE	0.118–0.358	4
GLCNACBETA1-2(GLCNACBETA1-6)MANALPHA1-6(GLCNACBE	0.532–3.35	2
GLCNACBETA1-2MAN1-3(GLCNACBETA1-2MANALPHA1-6)MAN	1.04–6.94	2
GLCNACBETA1-2MANALPHA1-3(GLCNACBETA1-2MANALPHA1-	0.971–5.72	2
GLCNACBETA1-2MANALPHA1-3(MANALPHA1-6)MANBETA1-4G	3.19–10.5	2
PYRIDYLAMINATED ACCEPTOR SUBSTRATE	3.4	1
UDP-N-ACETYLGLUCOSAMINE	8.3	1

Catalyzed reactions (Rhea), 7 shown:

• N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP + H(+) (RHEA:16057)
• an N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = an N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP + H(+) (RHEA:69615)
• an N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = an N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP + H(+) (RHEA:69619)
• an N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-[alpha-L-Fuc-(1->6)]-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-[alpha-L-Fuc-(1->6)]-beta-D-GlcNAc}-asparaginyl-[protein] + UDP + H(+) (RHEA:69623)
• an N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = an N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-[beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + UDP + H(+) (RHEA:69627)
• N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-{alpha-D-Man-(1->6)}-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-{alpha-D-Man-(1->6)}-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-asparaginyl-[protein] + UDP + H(+) (RHEA:69631)
• N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = N(4)-{beta-D-GlcNAc-(1->2)-[beta-D-GlcNAc-(1->4)]-alpha-D-Man-(1->3)-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-asparaginyl-[protein] + UDP + H(+) (RHEA:69635)

UniProt features (25 total): strand 9, splice variant 3, helix 3, chain 2, topological domain 2, glycosylation site 2, sequence conflict 1, transmembrane region 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7XTL	X-RAY DIFFRACTION	1.97

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UM21-F1	85.32	0.53

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 474

Glycosylation sites (2): 77, 458

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

ID	Pathway
R-HSA-381426	Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-HSA-8957275	Post-translational protein phosphorylation
R-HSA-9694548	Maturation of spike protein
R-HSA-975577	N-Glycan antennae elongation
R-HSA-1643685	Disease
R-HSA-392499	Metabolism of proteins
R-HSA-446203	Asparagine N-linked glycosylation
R-HSA-5663205	Infectious disease
R-HSA-597592	Post-translational protein modification
R-HSA-948021	Transport to the Golgi and subsequent modification
R-HSA-9679506	SARS-CoV Infections
R-HSA-9694516	SARS-CoV-2 Infection
R-HSA-9694635	Translation of Structural Proteins
R-HSA-975576	N-glycan antennae elongation in the medial/trans-Golgi
R-HSA-9772573	Late SARS-CoV-2 Infection Events
R-HSA-9824446	Viral Infection Pathways

MSigDB gene sets: 348 (showing top): GOBP_N_GLYCAN_PROCESSING, ACTACCT_MIR196A_MIR196B, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_PROTEIN_N_LINKED_GLYCOSYLATION, KEGG_N_GLYCAN_BIOSYNTHESIS, TATTATA_MIR374, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, AAAYRNCTG_UNKNOWN, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, PATIL_LIVER_CANCER, GTGCCTT_MIR506, FOSTER_TOLERANT_MACROPHAGE_UP, NF1_Q6_01, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_GLYOXYLATE_METABOLIC_PROCESS

GO Biological Process (6): protein N-linked glycosylation (GO:0006487), N-glycan processing (GO:0006491), glycoprotein biosynthetic process (GO:0009101), viral protein processing (GO:0019082), glyoxylate metabolic process (GO:0046487), obsolete protein glycosylation (GO:0006486)

GO Molecular Function (7): acetylglucosaminyltransferase activity (GO:0008375), L-alanine:glyoxylate transaminase activity (GO:0008453), alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454), protein homodimerization activity (GO:0042803), metal ion binding (GO:0046872), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (10): Golgi membrane (GO:0000139), peroxisome (GO:0005777), endoplasmic reticulum (GO:0005783), endoplasmic reticulum lumen (GO:0005788), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), Golgi stack (GO:0005795), extracellular exosome (GO:0070062), extracellular region (GO:0005576), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-12 pathways:

Category	Pathways
Metabolism of proteins	2
Post-translational protein modification	2
Translation of Structural Proteins	1
N-glycan antennae elongation in the medial/trans-Golgi	1
Disease	1
Asparagine N-linked glycosylation	1
Viral Infection Pathways	1
SARS-CoV Infections	1
Late SARS-CoV-2 Infection Events	1
Transport to the Golgi and subsequent modification	1
SARS-CoV-2 Infection	1
Infectious disease	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	3
intracellular membrane-bounded organelle	3
glycoprotein biosynthetic process	2
endomembrane system	2
cellular anatomical structure	2
protein N-linked glycosylation	1
macromolecule biosynthetic process	1
glycoprotein metabolic process	1
carbohydrate derivative biosynthetic process	1
viral process	1
viral gene expression	1
aldehyde metabolic process	1
monocarboxylic acid metabolic process	1
UDP-glycosyltransferase activity	1
hexosyltransferase activity	1
L-alanine:oxo-acid transaminase activity	1
acetylglucosaminyltransferase activity	1
catalytic activity, acting on a glycoprotein	1
identical protein binding	1
protein dimerization activity	1
cation binding	1
catalytic activity	1
transferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
microbody	1
endoplasmic reticulum	1
intracellular organelle lumen	1
Golgi apparatus subcompartment	1
extracellular vesicle	1

Protein interactions and networks

STRING

512 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MGAT4A	MGAT5	Q09328	917
MGAT4A	MGAT5B	Q3V5L5	906
MGAT4A	POMGNT1	Q8WZA1	720
MGAT4A	SLC2A2	P11168	704
MGAT4A	MGAT3	Q09327	695
MGAT4A	MGAT2	Q10469	692
MGAT4A	GCNT2	Q8N0V5	616
MGAT4A	FUT8	Q9BYC5	612
MGAT4A	GYPC	P04921	607
MGAT4A	MGAT1	P26572	576
MGAT4A	B4GALT4	O60513	550
MGAT4A	ST6GAL1	P15907	515
MGAT4A	MAN2A2	P49641	488
MGAT4A	ST3GAL3	Q11203	451
MGAT4A	C1GALT1	Q9NS00	449

IntAct

4 interactions, top by confidence:

A	B	Type	Score
WASHC3	WASH3P	psi-mi:“MI:0914”(association)	0.530
SLC30A5	NBAS	psi-mi:“MI:0914”(association)	0.350

BioGRID (3): MGAT4A (Affinity Capture-MS), MGAT4A (Affinity Capture-MS), MGAT4A (Affinity Capture-MS)

ESM2 similar proteins: A4IID1, A5D7I4, A9X1C8, O77836, O95461, O95803, P38649, P97464, Q13822, Q16394, Q4R854, Q5F407, Q5IGR8, Q5M854, Q5RBC3, Q5REP8, Q5U4X8, Q659X0, Q66PG2, Q66PG3, Q6EV76, Q6EV77, Q6GMK0, Q6GQI7, Q6GQK9, Q6IS24, Q6KFX9, Q6UW63, Q7TT15, Q812F8, Q812G0, Q86X52, Q8BJQ9, Q8HY56, Q8HYB2, Q8IYK4, Q8N6G5, Q8SPR2, Q8TDX6, Q9BYC5

Diamond homologs: A4IID1, A6NG13, O77836, Q4R4A8, Q4R854, Q4V8F8, Q5F407, Q5M854, Q5REP8, Q5U3T0, Q6GMK0, Q6GQI7, Q6ITT3, Q812F8, Q812G0, Q9D306, Q9D4R2, Q9DGD1, Q9UBM8, Q9UM21, Q9UQ53, A6H684

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

80 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2848 predictions. Top by Δscore:

Variant	Effect	Δscore
2:98625513:A:C	donor_gain	1.0000
2:98625717:GCTTA:G	donor_loss	1.0000
2:98625718:CTTAC:C	donor_loss	1.0000
2:98625719:TTA:T	donor_loss	1.0000
2:98625720:TAC:T	donor_loss	1.0000
2:98635285:CACT:C	acceptor_gain	1.0000
2:98635287:CT:C	acceptor_gain	1.0000
2:98635289:C:CC	acceptor_gain	1.0000
2:98636511:TCATA:T	donor_loss	1.0000
2:98636512:CATA:C	donor_loss	1.0000
2:98636513:ATAC:A	donor_loss	1.0000
2:98636514:TA:T	donor_loss	1.0000
2:98636515:ACCTT:A	donor_loss	1.0000
2:98636533:T:TA	donor_gain	1.0000
2:98636591:AATAA:A	acceptor_gain	1.0000
2:98636592:ATAA:A	acceptor_gain	1.0000
2:98636593:TAA:T	acceptor_gain	1.0000
2:98636594:AA:A	acceptor_gain	1.0000
2:98636596:C:CC	acceptor_gain	1.0000
2:98639803:CCAA:C	donor_loss	1.0000
2:98639805:AAC:A	donor_loss	1.0000
2:98639806:AC:A	donor_loss	1.0000
2:98640002:CTGG:C	acceptor_loss	1.0000
2:98640003:T:C	acceptor_loss	1.0000
2:98643894:C:CA	donor_gain	1.0000
2:98643921:A:AC	donor_gain	1.0000
2:98643922:C:CC	donor_gain	1.0000
2:98643922:CTG:C	donor_gain	1.0000
2:98655440:CTTA:C	donor_loss	1.0000
2:98655441:TTACC:T	donor_loss	1.0000

AlphaMissense

3533 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:98625740:A:G	W522R	1.000
2:98625740:A:T	W522R	1.000
2:98625769:C:G	R512P	1.000
2:98639875:A:G	W419R	1.000
2:98639875:A:T	W419R	1.000
2:98640146:A:G	L368P	1.000
2:98640161:C:T	G363D	1.000
2:98640162:C:G	G363R	1.000
2:98640166:A:C	H361Q	1.000
2:98640166:A:T	H361Q	1.000
2:98640167:T:C	H361R	1.000
2:98640168:G:C	H361D	1.000
2:98640168:G:T	H361N	1.000
2:98640220:A:C	C343W	1.000
2:98640221:C:A	C343F	1.000
2:98640221:C:G	C343S	1.000
2:98640221:C:T	C343Y	1.000
2:98640222:A:G	C343R	1.000
2:98640222:A:T	C343S	1.000
2:98643941:G:C	C334W	1.000
2:98643942:C:A	C334F	1.000
2:98643942:C:G	C334S	1.000
2:98643942:C:T	C334Y	1.000
2:98643943:A:G	C334R	1.000
2:98643943:A:T	C334S	1.000
2:98643972:A:G	L324P	1.000
2:98643974:C:A	W323C	1.000
2:98643974:C:G	W323C	1.000
2:98643976:A:G	W323R	1.000
2:98643976:A:T	W323R	1.000

dbSNP variants (sampled 300 via entrez): RS1000002721 (2:98691229 G>T), RS1000013081 (2:98666633 C>A,T), RS1000078595 (2:98672459 C>T), RS1000138557 (2:98698222 C>T), RS1000143992 (2:98728786 T>C), RS1000155624 (2:98729095 T>C), RS1000158733 (2:98721180 G>A), RS1000203069 (2:98639959 T>C), RS1000220545 (2:98636336 A>C), RS1000232714 (2:98720842 A>C,G), RS1000262718 (2:98640043 T>A), RS1000283955 (2:98679161 C>T), RS1000311171 (2:98633252 C>A), RS1000317561 (2:98678640 T>C,G), RS1000365241 (2:98633557 A>C)

Disease associations

OMIM: gene MIM:604623 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001135_2	Bipolar disorder	1.000000e-06
GCST001241_13	Bipolar disorder	3.000000e-06
GCST003057_1	Progression free survival in metastatic colorectal cancer (chemotherapy interaction)	2.000000e-08
GCST004719_14	Left ventricular obstructive tract defect (inherited effect)	1.000000e-07
GCST006051_6	Idiopathic inflammatory myopathy	3.000000e-06
GCST008103_118	Bipolar disorder	5.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004920	progression free survival
EFO:0007682	response to cetuximab
EFO:0007683	response to CAPOX-B
EFO:1001480	metastatic colorectal cancer

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

2 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs885036	Efficacy	3	bevacizumab;capecitabine;oxaliplatin	Colorectal Neoplasms
rs885036	Efficacy	3	bevacizumab;capecitabine;cetuximab;oxaliplatin	Colorectal Neoplasms

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs885036	MGAT4A	3	2.25	2	bevacizumab;capecitabine;cetuximab;oxaliplatin;bevacizumab;capecitabine;oxaliplatin

CTD chemical–gene interactions

43 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	decreases expression, increases expression, affects cotreatment	3
Valproic Acid	increases methylation, affects expression, increases expression	3
sodium arsenite	decreases expression, increases expression	2
cobaltous chloride	decreases expression, increases expression	2
Estradiol	decreases expression, affects cotreatment	2
Lipopolysaccharides	decreases expression, affects cotreatment	2
Nickel	increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tretinoin	increases expression	2
Cyclosporine	decreases expression, increases methylation	2
Aflatoxin B1	decreases expression, increases methylation	2
GSK-J4	increases expression	1
FR900359	decreases phosphorylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
benzo(e)pyrene	decreases methylation	1
potassium chromate(VI)	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
(+)-JQ1 compound	increases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, affects expression	1
Amiodarone	increases expression	1

Cellosaurus cell lines

8 cell lines: 7 transformed cell line, 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_C8NY	Jar-GnT4a	Cancer cell line	Male
CVCL_VT64	CHO IM4/IV	Transformed cell line	Female
CVCL_VT67	CHO IM4/V/IV	Transformed cell line	Female
CVCL_VT68	CHO IM4/V/IV-G1	Transformed cell line	Female
CVCL_VT69	CHO IM4/V/IV-G2	Transformed cell line	Female
CVCL_VT70	CHO IM4/V/IV-G3	Transformed cell line	Female
CVCL_VT71	CHO IM4/V/IV-G4	Transformed cell line	Female
CVCL_VT72	CHO IM4/V/IV-G5	Transformed cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.