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MGAT4B

gene
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Also known as GnT-Ivb

Summary

MGAT4B (alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B, HGNC:7048) is a protein-coding gene on chromosome 5q35.3, encoding Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B (Q9UQ53). Glycosyltransferase that catalyzes 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 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.

Source: NCBI Gene 11282 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 113 total
  • MANE Select transcript: NM_014275

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:7048
Approved symbolMGAT4B
Namealpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B
Location5q35.3
Locus typegene with protein product
StatusApproved
AliasesGnT-Ivb
Ensembl geneENSG00000161013
Ensembl biotypeprotein_coding
OMIM604561
Entrez11282

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 18 protein_coding, 7 protein_coding_CDS_not_defined, 5 retained_intron, 2 nonsense_mediated_decay

ENST00000292591, ENST00000337755, ENST00000518168, ENST00000518702, ENST00000518778, ENST00000518867, ENST00000518980, ENST00000519616, ENST00000519836, ENST00000519965, ENST00000520019, ENST00000520134, ENST00000520822, ENST00000520875, ENST00000520918, ENST00000520969, ENST00000521305, ENST00000521855, ENST00000522293, ENST00000522451, ENST00000523108, ENST00000523329, ENST00000523382, ENST00000881423, ENST00000881424, ENST00000881425, ENST00000881426, ENST00000960972, ENST00000960973, ENST00000960974, ENST00000960975, ENST00000960976

RefSeq mRNA: 2 — MANE Select: NM_014275 NM_014275, NM_054013

CCDS: CCDS4448, CCDS4449

Canonical transcript exons

ENST00000292591 — 15 exons

ExonStartEnd
ENSE00002134066179806487179806866
ENSE00003466755179798928179799121
ENSE00003500380179798513179798591
ENSE00003518653179801784179801969
ENSE00003554513179799203179799310
ENSE00003577818179799506179799636
ENSE00003609512179800484179800597
ENSE00003625728179800184179800259
ENSE00003637074179801334179801467
ENSE00003662699179799954179800068
ENSE00003662761179800907179800953
ENSE00003675197179801554179801694
ENSE00003681853179798347179798434
ENSE00003786411179798165179798277
ENSE00003848865179797610179798068

Expression profiles

Bgee: expression breadth ubiquitous, 140 present calls, max score 99.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 98.9797 / max 591.8398, expressed in 1826 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
6524372.96771820
6524110.24081702
652453.74581549
652463.50421513
652482.13371219
652421.91981146
652391.3324737
652401.3062836
652441.0958814
652470.7334524

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
duodenumUBERON:000211499.29gold quality
mucosa of transverse colonUBERON:000499199.29gold quality
stromal cell of endometriumCL:000225598.99gold quality
metanephros cortexUBERON:001053398.84gold quality
rectumUBERON:000105298.82gold quality
right lobe of liverUBERON:000111498.80gold quality
apex of heartUBERON:000209898.41gold quality
small intestine Peyer’s patchUBERON:000345498.38gold quality
small intestineUBERON:000210898.37gold quality
right hemisphere of cerebellumUBERON:001489098.35gold quality
transverse colonUBERON:000115798.30gold quality
cortex of kidneyUBERON:000122598.26gold quality
left adrenal gland cortexUBERON:003582598.23gold quality
islet of LangerhansUBERON:000000698.20gold quality
cerebellar hemisphereUBERON:000224598.17gold quality
liverUBERON:000210798.15gold quality
cerebellar cortexUBERON:000212998.15gold quality
cerebellumUBERON:000203798.14gold quality
left adrenal glandUBERON:000123498.13gold quality
right adrenal glandUBERON:000123398.08gold quality
right adrenal gland cortexUBERON:003582798.06gold quality
lower esophagus mucosaUBERON:003583498.05gold quality
gall bladderUBERON:000211097.74gold quality
adult mammalian kidneyUBERON:000008297.72gold quality
body of stomachUBERON:000116197.72gold quality
adrenal glandUBERON:000236997.66gold quality
cortical plateUBERON:000534397.58gold quality
right lobe of thyroid glandUBERON:000111997.57gold quality
right uterine tubeUBERON:000130297.53gold quality
left lobe of thyroid glandUBERON:000112097.50gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting MGAT4B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4692100.0067.322066
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-451499.9967.101870
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548I99.9471.253481
HSA-MIR-548J-5P99.9471.143489
HSA-MIR-548O-5P99.9471.243488
HSA-MIR-548W99.9471.243488
HSA-MIR-548Y99.9471.283514
HSA-MIR-652-5P99.9167.49505
HSA-MIR-182599.7268.111089
HSA-MIR-58699.6570.402051

Literature-anchored findings (GeneRIF, showing 4)

  • 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)-IVb, and found that (GnT)-IVb expression was increased in HLE-cells Epirubicin resistant. (PMID:17488527)
  • UDP-galactose (SLC35A2) and UDP-N-acetylglucosamine (SLC35A3) Transporters Form Glycosylation-related Complexes with Mannoside Acetylglucosaminyltransferases (Mgats). (PMID:25944901)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomgat4bENSDARG00000004115
mus_musculusMgat4bENSMUSG00000036620
rattus_norvegicusMgat4bENSRNOG00000003235
drosophila_melanogasterMgat4aFBGN0036446
drosophila_melanogasterMgat4bFBGN0036447

Paralogs (3): MGAT4A (ENSG00000071073), MGAT4C (ENSG00000182050), MGAT4D (ENSG00000205301)

Protein

Protein identifiers

Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B — Q9UQ53 (reviewed: Q9UQ53)

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

All UniProt accessions (10): Q9UQ53, E5RFL0, E5RFS3, H0YB63, H0YB84, H0YB89, H0YC11, H0YC13, H0YC56, H0YC79

UniProt curated annotations — full annotation on UniProt →

Function. Glycosyltransferase that catalyzes 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. Prefers complex-type N-glycans over hybrid-types. Has lower affinities for donors or acceptors than MGAT4A, suggesting that, under physiological conditions, it is not the main contributor in N-glycan biosynthesis.

Subunit / interactions. Interacts with SLC35A3.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Widely expressed. Strongly overexpressed in pancreatic cancer.

Post-translational modifications. N-glycosylated.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 54 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9UQ53-11yes
Q9UQ53-22
Q9UQ53-33

RefSeq proteins (2): NP_055090, NP_463459 (=MANE)

Domains & families (InterPro)

IDNameType
IPR006759Glyco_transf_54Family
IPR056576MGAT4_A/B/C_CDomain
IPR057279MGAT4Domain

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.

SubstrateKm (mM)Measurements
UDP-N-ACETYL-D-GLUCOSAMINE0.118–0.3584
GLCNACBETA1-2(GLCNACBETA1-6)MANALPHA1-6(GLCNACBE0.532–3.352
GLCNACBETA1-2MAN1-3(GLCNACBETA1-2MANALPHA1-6)MAN1.04–6.942
GLCNACBETA1-2MANALPHA1-3(GLCNACBETA1-2MANALPHA1-0.971–5.722
GLCNACBETA1-2MANALPHA1-3(MANALPHA1-6)MANBETA1-4G3.19–10.52
PYRIDYLAMINATED ACCEPTOR SUBSTRATE3.41
UDP-N-ACETYLGLUCOSAMINE8.31

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 (11 total): topological domain 2, sequence variant 2, glycosylation site 2, splice variant 2, chain 1, transmembrane region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UQ53-F183.880.57

Functional residue map

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

Glycosylation sites (2): 87, 103

Function

Pathways and Gene Ontology

Reactome pathways

14 pathways

IDPathway
R-HSA-9694548Maturation of spike protein
R-HSA-975577N-Glycan antennae elongation
R-HSA-1643685Disease
R-HSA-392499Metabolism of proteins
R-HSA-446203Asparagine N-linked glycosylation
R-HSA-5663205Infectious disease
R-HSA-597592Post-translational protein modification
R-HSA-948021Transport to the Golgi and subsequent modification
R-HSA-9679506SARS-CoV Infections
R-HSA-9694516SARS-CoV-2 Infection
R-HSA-9694635Translation of Structural Proteins
R-HSA-975576N-glycan antennae elongation in the medial/trans-Golgi
R-HSA-9772573Late SARS-CoV-2 Infection Events
R-HSA-9824446Viral Infection Pathways

MSigDB gene sets: 164 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_N_GLYCAN_PROCESSING, GOBP_PROTEIN_N_LINKED_GLYCOSYLATION, KEGG_N_GLYCAN_BIOSYNTHESIS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, SHEPARD_BMYB_MORPHOLINO_DN, YY1_02, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GROSS_HYPOXIA_VIA_ELK3_UP, GROSS_HYPOXIA_VIA_HIF1A_UP, GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN, ACTTTAT_MIR1425P, RFX1_02, DBP_Q6, GTGACTT_MIR224

GO Biological Process (5): protein N-linked glycosylation (GO:0006487), N-glycan processing (GO:0006491), glycoprotein biosynthetic process (GO:0009101), viral protein processing (GO:0019082), obsolete protein glycosylation (GO:0006486)

GO Molecular Function (6): acetylglucosaminyltransferase activity (GO:0008375), alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454), metal ion binding (GO:0046872), protein binding (GO:0005515), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (6): Golgi membrane (GO:0000139), endoplasmic reticulum (GO:0005783), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), Golgi stack (GO:0005795), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-12 pathways:

CategoryPathways
Translation of Structural Proteins1
N-glycan antennae elongation in the medial/trans-Golgi1
Post-translational protein modification1
Disease1
Metabolism of proteins1
Asparagine N-linked glycosylation1
Viral Infection Pathways1
SARS-CoV Infections1
Late SARS-CoV-2 Infection Events1
Transport to the Golgi and subsequent modification1
SARS-CoV-2 Infection1
Infectious disease1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm3
intracellular membrane-bounded organelle3
glycoprotein biosynthetic process2
endomembrane system2
protein N-linked glycosylation1
macromolecule biosynthetic process1
glycoprotein metabolic process1
carbohydrate derivative biosynthetic process1
viral process1
viral gene expression1
UDP-glycosyltransferase activity1
hexosyltransferase activity1
acetylglucosaminyltransferase activity1
catalytic activity, acting on a glycoprotein1
cation binding1
binding1
catalytic activity1
transferase activity1
Golgi apparatus1
bounding membrane of organelle1
Golgi apparatus subcompartment1
cellular anatomical structure1

Protein interactions and networks

STRING

636 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MGAT4BMGAT5BQ3V5L5928
MGAT4BMGAT5Q09328925
MGAT4BPOMGNT1Q8WZA1752
MGAT4BMGAT3Q09327709
MGAT4BMGAT2Q10469692
MGAT4BFUT8Q9BYC5663
MGAT4BGYPCP04921635
MGAT4BGCNT2Q8N0V5606
MGAT4BMGAT1P26572600
MGAT4BMAN2A2P49641581
MGAT4BB4GALT1P15291567
MGAT4BMAN2A1Q16706550
MGAT4BST3GAL4Q11206534
MGAT4BST6GAL1P15907528
MGAT4BMAN1A1P33908504
MGAT4BST3GAL3Q11203504

IntAct

33 interactions, top by confidence:

ABTypeScore
APPBP2MGAT4Bpsi-mi:“MI:0915”(physical association)0.560
OPTNMGAT4Bpsi-mi:“MI:0915”(physical association)0.560
YIPF3TMEM120Bpsi-mi:“MI:0914”(association)0.530
PLAURXRCC3psi-mi:“MI:0914”(association)0.530
TTMPTMEM223psi-mi:“MI:0914”(association)0.350
HLA-DQA1TMEM223psi-mi:“MI:0914”(association)0.350
DKKL1VWA8psi-mi:“MI:0914”(association)0.350
OPRL1METTL15psi-mi:“MI:0914”(association)0.350
SCGB2A2RTL8Cpsi-mi:“MI:0914”(association)0.350
KIR2DS3RTL8Cpsi-mi:“MI:0914”(association)0.350
SEC62GPR89Apsi-mi:“MI:0914”(association)0.350
CEACAM8PRRT4psi-mi:“MI:0914”(association)0.350
IGF2RMANBApsi-mi:“MI:0914”(association)0.350
GALNT10PLXNA2psi-mi:“MI:0914”(association)0.350
MGAT4BSLC3A2psi-mi:“MI:0914”(association)0.350
MGAT4BHSPA2psi-mi:“MI:0914”(association)0.350
SEC62IPO8psi-mi:“MI:0914”(association)0.350
CLGNTMEM131Lpsi-mi:“MI:0914”(association)0.350
CXCR4ESYT2psi-mi:“MI:0914”(association)0.350
ISLRB4GALT5psi-mi:“MI:0914”(association)0.350
SYPTMEM223psi-mi:“MI:0914”(association)0.350
TMED5DGAT1psi-mi:“MI:0914”(association)0.350
SLC30A1PSMD11psi-mi:“MI:0914”(association)0.350
SLC30A5NBASpsi-mi:“MI:0914”(association)0.350
SLC30A7ESYT2psi-mi:“MI:0914”(association)0.350
MGAT4BAPPBP2psi-mi:“MI:0915”(physical association)0.000

BioGRID (37): HBB (Affinity Capture-MS), MGAT4B (Affinity Capture-MS), MGAT4B (Affinity Capture-MS), MGAT4B (Affinity Capture-MS), HBB (Affinity Capture-MS), MGAT4B (Affinity Capture-MS), MGAT4B (Two-hybrid), MGAT4B (Affinity Capture-RNA), MGAT4B (Affinity Capture-MS), MGAT4B (Affinity Capture-MS), MGAT4B (Affinity Capture-MS), MGAT4B (Affinity Capture-MS), HBB (Affinity Capture-MS), SLC3A2 (Affinity Capture-MS), MGAT4B (Affinity Capture-MS)

ESM2 similar proteins: A0A0D3QS98, A0A0D3QS99, A4D0V7, C5H5C4, F6Q1T7, O70309, O75354, P17405, P18084, P18424, P22413, P50747, P52850, P58242, P61642, P80747, Q04519, Q0VBD0, Q0VD19, Q13219, Q52KP5, Q58CQ9, Q5QQ51, Q5STE3, Q64687, Q6DFZ6, Q6KFX9, Q6MZW2, Q6P988, Q6UWX4, Q6YGZ1, Q6ZXD2, Q71RP1, Q812F8, Q8BJQ9, Q8C1F4, Q8C419, Q8N5D6, Q8N6G5, Q8R116

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

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance81
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2645 predictions. Top by Δscore:

VariantEffectΔscore
5:179798273:GGAGC:Gacceptor_gain1.0000
5:179798276:GC:Gacceptor_gain1.0000
5:179798277:CC:Cacceptor_gain1.0000
5:179798277:CCTG:Cacceptor_loss1.0000
5:179798278:C:CCacceptor_gain1.0000
5:179798346:CCGAT:Cdonor_gain1.0000
5:179798503:CCGAA:Cdonor_gain1.0000
5:179798508:CTTA:Cdonor_loss1.0000
5:179798509:TTACG:Tdonor_loss1.0000
5:179798510:TACGT:Tdonor_loss1.0000
5:179798511:A:ACdonor_gain1.0000
5:179798511:ACGTC:Adonor_loss1.0000
5:179798512:C:CCdonor_gain1.0000
5:179798512:C:Gdonor_loss1.0000
5:179798512:CG:Cdonor_gain1.0000
5:179798512:CGT:Cdonor_gain1.0000
5:179798529:T:TAdonor_gain1.0000
5:179798922:A:ACdonor_gain1.0000
5:179798923:C:CCdonor_gain1.0000
5:179798923:CTGA:Cdonor_loss1.0000
5:179798924:TGACC:Tdonor_loss1.0000
5:179798925:GACCG:Gdonor_loss1.0000
5:179798926:A:ACdonor_gain1.0000
5:179798926:A:AGdonor_loss1.0000
5:179798927:C:CCdonor_gain1.0000
5:179798927:CCG:Cdonor_gain1.0000
5:179798927:CCGCT:Cdonor_gain1.0000
5:179799120:TC:Tacceptor_gain1.0000
5:179799121:CC:Cacceptor_gain1.0000
5:179799122:C:Aacceptor_loss1.0000

AlphaMissense

3577 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:179798180:C:AW536C1.000
5:179798180:C:GW536C1.000
5:179798182:A:GW536R1.000
5:179798182:A:TW536R1.000
5:179798211:C:GR526P1.000
5:179798982:G:TP430H1.000
5:179798993:C:AW426C1.000
5:179798993:C:GW426C1.000
5:179798995:A:GW426R1.000
5:179798995:A:TW426R1.000
5:179799110:A:CF387L1.000
5:179799110:A:TF387L1.000
5:179799112:A:GF387L1.000
5:179799228:A:GL375P1.000
5:179799234:G:AS373F1.000
5:179799244:C:GG370R1.000
5:179799248:G:CH368Q1.000
5:179799248:G:TH368Q1.000
5:179799249:T:CH368R1.000
5:179799250:G:CH368D1.000
5:179799250:G:TH368N1.000
5:179799255:A:GF366S1.000
5:179799302:A:CC350W1.000
5:179799303:C:AC350F1.000
5:179799303:C:GC350S1.000
5:179799303:C:TC350Y1.000
5:179799304:A:GC350R1.000
5:179799304:A:TC350S1.000
5:179799524:G:CC341W1.000
5:179799525:C:AC341F1.000

dbSNP variants (sampled 300 via entrez): RS1000000759 (5:179798720 C>A,G,T), RS1000170620 (5:179808338 AG>A), RS1000365167 (5:179808583 C>T), RS1000610493 (5:179802194 C>G,T), RS1000699365 (5:179807616 C>T), RS1000750225 (5:179807707 C>T), RS1000961466 (5:179801987 G>A,C), RS1001054875 (5:179805010 T>G), RS1001480403 (5:179806295 G>A,C), RS1001787162 (5:179806139 C>G), RS1002471535 (5:179805967 C>T), RS1002884173 (5:179802379 A>C,G), RS1003063387 (5:179807000 C>G,T), RS1003213597 (5:179804886 C>A,T), RS1003217721 (5:179803594 C>T)

Disease associations

OMIM: gene MIM:604561 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST006041_29Major depressive disorder6.000000e-07
GCST006585_1648Blood protein levels3.000000e-62
GCST90002393_111Monocyte count3.000000e-14
GCST90002400_658Plateletcrit1.000000e-10

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005091monocyte count
EFO:0007985platelet crit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs730012LTC4S, MGAT4B34.502aspirin;montelukast

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
methylmercuric chlorideincreases expression, affects cotreatment4
Valproic Acidincreases expression, increases methylation3
Phenylmercuric Acetateaffects cotreatment, increases expression2
Particulate Matterincreases abundance, affects cotreatment, increases expression, decreases expression2
aristolochic acid Iincreases expression1
GSK-J4increases expression1
bisphenol Aaffects expression1
beta-lapachonedecreases expression, increases expression1
ochratoxin Adecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
coumarindecreases phosphorylation1
diallyl trisulfideincreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
S 1 (combination)increases response to substance1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangincreases expression1
(+)-JQ1 compounddecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Arsenic Trioxidedecreases response to substance1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Atrazineincreases expression1
Benzo(a)pyreneaffects methylation1
Cadmiumincreases abundance, increases expression1
Coumestrolaffects cotreatment, decreases expression1
Bucladesineaffects cotreatment, increases expression1
Diurondecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot