B3GNT2

Summary

B3GNT2 (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2, HGNC:15629) is a protein-coding gene on chromosome 2p15, encoding N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 (Q9NY97). Beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine.

This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein. It prefers the substrate of lacto-N-neotetraose, and is involved in the biosynthesis of poly-N-acetyllactosamine chains. Two transcript variants encoding the same protein have been found for this gene.

Source: NCBI Gene 10678 — RefSeq curated summary.

At a glance

• Gene–disease (curated): muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 (Moderate, GenCC) — +1 more curated relationship
• GWAS associations: 14
• Clinical variants (ClinVar): 51 total — 3 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 1
• Druggable target: yes
• MANE Select transcript: NM_006577

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15629
Approved symbol	B3GNT2
Name	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2
Location	2p15
Locus type	gene with protein product
Status	Approved
Aliases	B3GNT-2, BETA3GNT, B3GN-T2, B3GN-T1
Ensembl gene	ENSG00000170340
Ensembl biotype	protein_coding
OMIM	605581
Entrez	10678

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000301998, ENST00000405767, ENST00000866702, ENST00000866703, ENST00000920407, ENST00000946315, ENST00000946316

RefSeq mRNA: 2 — MANE Select: NM_006577 NM_001319075, NM_006577

CCDS: CCDS1870

Canonical transcript exons

ENST00000301998 — 2 exons

Exon	Start	End
ENSE00001355572	62196115	62196355
ENSE00001426860	62222212	62224731

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 99.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 46.4432 / max 1199.1351, expressed in 1820 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20488	44.1304	1819
20487	2.3129	1301

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	99.90	gold quality
oocyte	CL:0000023	99.74	gold quality
visceral pleura	UBERON:0002401	96.71	gold quality
epithelium of nasopharynx	UBERON:0001951	96.19	gold quality
esophagus squamous epithelium	UBERON:0006920	96.13	gold quality
germinal epithelium of ovary	UBERON:0001304	95.89	gold quality
lower lobe of lung	UBERON:0008949	94.84	gold quality
parietal pleura	UBERON:0002400	94.74	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.41	gold quality
pleura	UBERON:0000977	94.33	gold quality
jejunal mucosa	UBERON:0000399	93.76	gold quality
epithelium of esophagus	UBERON:0001976	93.51	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.50	gold quality
colonic mucosa	UBERON:0000317	92.48	gold quality
gingival epithelium	UBERON:0001949	92.48	gold quality
duodenum	UBERON:0002114	92.26	gold quality
gingiva	UBERON:0001828	92.21	gold quality
buccal mucosa cell	CL:0002336	92.05	gold quality
gall bladder	UBERON:0002110	92.05	gold quality
bronchial epithelial cell	CL:0002328	91.95	gold quality
oral cavity	UBERON:0000167	91.64	gold quality
amniotic fluid	UBERON:0000173	91.50	gold quality
bone marrow	UBERON:0002371	91.15	gold quality
endometrium	UBERON:0001295	90.89	gold quality
parotid gland	UBERON:0001831	90.64	gold quality
heart right ventricle	UBERON:0002080	90.44	gold quality
rectum	UBERON:0001052	90.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.34	gold quality
mammary duct	UBERON:0001765	90.32	gold quality
placenta	UBERON:0001987	89.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-112	yes	20.32
E-HCAD-11	yes	18.19
E-CURD-114	yes	8.07
E-ANND-3	yes	4.39
E-MTAB-6379	no	859.55
E-CURD-10	no	641.02

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

110 targeting B3GNT2, 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-3163	100.00	77.23	8605
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
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-12133	99.92	71.82	2006

Literature-anchored findings (GeneRIF, showing 13)

• beta3Gal-T5, controlled by the intestinal homeoproteins, may play an important role in the specific function of intestinal cells by modifying the carbohydrate structure of glycoproteins (PMID:12855703)
• beta3Gal-T5 is presumed to be responsible for the synthesis of CA 19-9 in pancreatic cancer tissue. (PMID:14555842)
• beta 3Gal-T5 plays a relevant role in gastrointestinal and pancreatic tissues counteracting the glycosylation pattern associated with malignancy (PMID:14686931)
• beta1, 3-N-acetylglucosaminyltransferase is similar to a new protein, beta3-GnTL1 (PMID:15560372)
• up-regulation of beta3Gn-T8 in differentiated cells increases poly-N-acetyllactosamine chains by activating intrinsic beta3Gn-T2. (PMID:18826941)
• data reveals beta3GnT2 and polyLacNAc may be involved in the progression of the pre-malignant lesions of human the uterine cervix. (PMID:24998922)
• High B3GNT2 expression is associated with hepatocellular carcinoma. (PMID:25605193)
• Study provides evidence that mutations in B3GNT2, B4GALT2, and ST6GALNAC2 underlie aberrant glycosylation, and contribute to the pathogenesis of molecular subsets of colon and other gastrointestinal malignancies. (PMID:27004849)
• we confirmed the involvement of BGNT-1.1 in ciliated sensory neuron function and morphogenesis. BGNT-1.1 functions at the trans-Golgi network of sheath cells (glia) to influence dye-filling and cilium length, in a cell non-autonomous manner. Notably, BGNT-1.1 is the orthologue of human B3GNT1/B4GAT1, a glycosyltransferase associated with Walker-Warburg syndrome (WWS). (PMID:27508411)
• Structures and mechanism of human glycosyltransferase beta1,3-N-acetylglucosaminyltransferase 2 (B3GNT2), an important player in immune homeostasis. (PMID:33158990)
• Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites. (PMID:33229435)
• Genetic effects of B3GNT2 on ankylosing spondylitis susceptibility and clinical manifestations in Taiwanese. (PMID:34645591)
• Construction and investigation of beta3GNT2-associated regulatory network in esophageal carcinoma. (PMID:35073841)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	b3gnt2a	ENSDARG00000052376
danio_rerio	b3gnt2b	ENSDARG00000091902
mus_musculus	B3gnt2	ENSMUSG00000051650
rattus_norvegicus	B3gnt2	ENSRNOG00000009267
drosophila_melanogaster	brn	FBGN0000221
caenorhabditis_elegans		WBGENE00000270
caenorhabditis_elegans		WBGENE00007096
caenorhabditis_elegans		WBGENE00017653

Paralogs (15): B3GNT7 (ENSG00000156966), B3GALT2 (ENSG00000162630), B3GALNT2 (ENSG00000162885), B3GALNT1 (ENSG00000169255), B3GALT1 (ENSG00000172318), B3GALT6 (ENSG00000176022), B3GNT4 (ENSG00000176383), B3GNT5 (ENSG00000176597), B3GNT8 (ENSG00000177191), B3GNT3 (ENSG00000179913), B3GALT5 (ENSG00000183778), B3GNT6 (ENSG00000198488), B3GALT9 (ENSG00000214654), B3GALT4 (ENSG00000235863), B3GNT9 (ENSG00000237172)

Protein

Protein identifiers

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2 — Q9NY97 (reviewed: Q9NY97)

Alternative names: Beta-1,3-N-acetylglucosaminyltransferase 1, Beta-1,3-galactosyltransferase 7, Beta-3-Gx-T7, UDP-Gal:beta-GlcNAc beta-1,3-galactosyltransferase 7, UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2, UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase 7

All UniProt accessions (1): Q9NY97

UniProt curated annotations — full annotation on UniProt →

Function. Beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine. Catalyzes the initiation and elongation of poly-N-acetyllactosamine chains. Shows a marked preference for Gal(beta1-4)Glc(NAc)-based acceptors. Probably constitutes the main polylactosamine synthase.

Subunit / interactions. Interacts with B3GNT8; this interaction greatly increases B3GNT2 catalytic activity, independently of B3GNT8 enzymatic activity.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Ubiquitous.

Pathway. Protein modification; protein glycosylation.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the glycosyltransferase 31 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NY97-1	1	yes
Q9NY97-2	2

RefSeq proteins (2): NP_001306004, NP_006568* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002659	Glyco_trans_31	Family

Pfam: PF01762

Catalyzed reactions (Rhea), 1 shown:

• a beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + UDP-N-acetyl-alpha-D-glucosamine = an N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + UDP + H(+) (RHEA:14389)

UniProt features (47 total): helix 19, strand 11, turn 5, glycosylation site 5, topological domain 2, chain 1, mutagenesis site 1, sequence conflict 1, transmembrane region 1, splice variant 1

Structure

Experimental structures (PDB)

12 structures.

PDB	Method	Resolution (Å)
6WMM	X-RAY DIFFRACTION	1.55
6WMO	X-RAY DIFFRACTION	1.85
7JHO	X-RAY DIFFRACTION	1.85
6WMN	X-RAY DIFFRACTION	2.04
7JHM	X-RAY DIFFRACTION	2.19
7JHN	X-RAY DIFFRACTION	2.2
8TJC	X-RAY DIFFRACTION	2.2
7JHL	X-RAY DIFFRACTION	2.26
8SZ3	X-RAY DIFFRACTION	2.32
7JHK	X-RAY DIFFRACTION	2.34
7JHI	X-RAY DIFFRACTION	2.5
8TIC	X-RAY DIFFRACTION	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NY97-F1	91.41	0.80

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 (5): 79, 89, 127, 173, 219

Mutagenesis-validated functional residues (1):

Position	Phenotype
245	loss of enzymatic activity, no loss of b3gnt8-binding.

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-2022854	Keratan sulfate biosynthesis
R-HSA-913709	O-linked glycosylation of mucins
R-HSA-1430728	Metabolism
R-HSA-1630316	Glycosaminoglycan metabolism
R-HSA-1638074	Keratan sulfate/keratin metabolism
R-HSA-392499	Metabolism of proteins
R-HSA-5173105	O-linked glycosylation
R-HSA-597592	Post-translational protein modification
R-HSA-71387	Metabolism of carbohydrates and carbohydrate derivatives

MSigDB gene sets: 316 (showing top): GSE45365_NK_CELL_VS_BCELL_UP, SHEPARD_CRASH_AND_BURN_MUTANT_UP, SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_AMINOGLYCAN_BIOSYNTHETIC_PROCESS, SHAFFER_IRF4_TARGETS_IN_PLASMA_CELL_VS_MATURE_B_LYMPHOCYTE, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, MODULE_239, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_AMINOGLYCAN_METABOLIC_PROCESS, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, KUNINGER_IGF1_VS_PDGFB_TARGETS_DN, SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL, CUI_TCF21_TARGETS_2_DN, SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP

GO Biological Process (8): protein O-linked glycosylation (GO:0006493), axon guidance (GO:0007411), sensory perception of smell (GO:0007608), keratan sulfate proteoglycan biosynthetic process (GO:0018146), poly-N-acetyllactosamine biosynthetic process (GO:0030311), cellular response to leukemia inhibitory factor (GO:1990830), obsolete protein glycosylation (GO:0006486), protein O-linked glycosylation via N-acetylgalactosamine (GO:0016266)

GO Molecular Function (6): N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532), protein binding (GO:0005515), N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity (GO:0008499), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757), hexosyltransferase activity (GO:0016758)

GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
Keratan sulfate/keratin metabolism	1
O-linked glycosylation	1
Metabolism of carbohydrates and carbohydrate derivatives	1
Glycosaminoglycan metabolism	1
Post-translational protein modification	1
Metabolism of proteins	1
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
glycoprotein biosynthetic process	1
axonogenesis	1
neuron projection guidance	1
sensory perception of chemical stimulus	1
proteoglycan biosynthetic process	1
keratan sulfate proteoglycan metabolic process	1
aminoglycan biosynthetic process	1
poly-N-acetyllactosamine metabolic process	1
cellular response to cytokine stimulus	1
response to leukemia inhibitory factor	1
protein O-linked glycosylation	1
acetylglucosaminyltransferase activity	1
binding	1
UDP-galactosyltransferase activity	1
beta-1,3-galactosyltransferase activity	1
catalytic activity	1
transferase activity	1
glycosyltransferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1046 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
B3GNT2	GCNT2	Q8N0V5	876
B3GNT2	B4GALT1	P15291	672
B3GNT2	B4GALT2	O60909	611
B3GNT2	C1GALT1	Q9NS00	604
B3GNT2	MGAT5	Q09328	598
B3GNT2	COMMD1	Q8N668	597
B3GNT2	TMEM17	Q86X19	587
B3GNT2	ST6GAL1	P15907	582
B3GNT2	SPPL3	Q8TCT6	564
B3GNT2	B4GALT4	O60513	544
B3GNT2	ST3GAL3	Q11203	532
B3GNT2	B4GALT5	O43286	529
B3GNT2	FUT8	Q9BYC5	520
B3GNT2	ST3GAL1	Q11201	513
B3GNT2	MGAT1	P26572	501

IntAct

64 interactions, top by confidence:

A	B	Type	Score
IFT27	IFT56	psi-mi:“MI:0914”(association)	0.690
B3GNT3	PGRMC1	psi-mi:“MI:0914”(association)	0.670
B3GNT2	B3GNT8	psi-mi:“MI:0915”(physical association)	0.660
B3GNT2	B3GNT8	psi-mi:“MI:0559”(glycosylation reaction)	0.660
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
ITGB8	GET1	psi-mi:“MI:0914”(association)	0.530
OS9	AGRN	psi-mi:“MI:0914”(association)	0.530
SLC1A5	GPR89A	psi-mi:“MI:0914”(association)	0.530
	B3GNT2	psi-mi:“MI:0559”(glycosylation reaction)	0.440
B3GNT2	B3gnt8	psi-mi:“MI:0559”(glycosylation reaction)	0.440
PGAP4	B3GNT2	psi-mi:“MI:0915”(physical association)	0.370
CANX	HLA-A	psi-mi:“MI:0914”(association)	0.350
PDGFRA	GXYLT2	psi-mi:“MI:0914”(association)	0.350
PSCA	METTL15	psi-mi:“MI:0914”(association)	0.350
SCGB2A2	RTL8C	psi-mi:“MI:0914”(association)	0.350
EDEM2	HACD1	psi-mi:“MI:0914”(association)	0.350
TMEM59	GPR89A	psi-mi:“MI:0914”(association)	0.350
CST9L	QSOX1	psi-mi:“MI:0914”(association)	0.350
CD79B	GOLIM4	psi-mi:“MI:0914”(association)	0.350
C1orf54	AGRN	psi-mi:“MI:0914”(association)	0.350
CIB2	PLD2	psi-mi:“MI:0914”(association)	0.350
LCN6	COCH	psi-mi:“MI:0914”(association)	0.350
NRG1	CHST10	psi-mi:“MI:0914”(association)	0.350
B3GNT8	GSDME	psi-mi:“MI:0914”(association)	0.350
B3GNT2	NDUFA10	psi-mi:“MI:0914”(association)	0.350
APOM	ESYT2	psi-mi:“MI:0914”(association)	0.350
TMEM106A	TMEM131L	psi-mi:“MI:0914”(association)	0.350
BTNL2	TMEM131L	psi-mi:“MI:0914”(association)	0.350
SFTPC	TMEM131L	psi-mi:“MI:0914”(association)	0.350
ASIC4	TMEM131L	psi-mi:“MI:0914”(association)	0.350

BioGRID (599): B3GNT2 (Affinity Capture-MS), TUBB8 (Affinity Capture-MS), C1GALT1C1 (Affinity Capture-MS), TOR3A (Affinity Capture-MS), TMTC3 (Affinity Capture-MS), LDLR (Affinity Capture-MS), TUBA4A (Affinity Capture-MS), PAM (Affinity Capture-MS), ADAM10 (Affinity Capture-MS), NDUFA10 (Affinity Capture-MS), PON2 (Affinity Capture-MS), FAM3A (Affinity Capture-MS), CAPN2 (Affinity Capture-MS), ITGA7 (Affinity Capture-MS), FAM3C (Affinity Capture-MS)

ESM2 similar proteins: A0A2C9JXL4, O43825, O54904, O54905, O75752, O93403, P79948, P79949, Q08BL3, Q0VC84, Q24342, Q5F3G7, Q5HZL5, Q5R5Y3, Q5RAL7, Q5XJP0, Q5YB40, Q66H69, Q6AY39, Q6DE15, Q6GNL1, Q6P3P5, Q6QMG1, Q76EC5, Q793U7, Q7JK24, Q7JK25, Q7JK26, Q7K237, Q7SYI5, Q7T3S5, Q864U6, Q864U8, Q8BGY6, Q8K0J2, Q8NFL0, Q920V1, Q99NB2, Q9BYG0, Q9JI67

Diamond homologs: O43825, O54904, O54905, O75752, O88178, Q1RLK6, Q3USF0, Q5HZL5, Q5R5Y3, Q5RAL7, Q5XJP0, Q66H69, Q6AY39, Q6DE15, Q6P3P5, Q6ZMB0, Q793U7, Q7JK24, Q7JK25, Q7JK26, Q7T3S5, Q7Z7M8, Q864U6, Q864U8, Q8BGY6, Q8K0J2, Q8NFL0, Q8R3I9, Q920V1, Q99NB2, Q9BYG0, Q9C0J1, Q9JI67, Q9MYM7, Q9N293, Q9N294, Q9N295, Q9NY97, Q9Y2C3, Q9Y5Z6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 90 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
ERAD pathway	6	13.3×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	1
Uncertain significance	35
Likely benign	6
Benign	4

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
154940	GRCh38/hg38 2p16.1-15(chr2:58031916-63611810)x1	Pathogenic
57148	GRCh38/hg38 2p16.1-15(chr2:59658846-62336083)x1	Pathogenic
60179	GRCh38/hg38 2p15(chr2:61515438-62305848)x1	Pathogenic
545283	Single allele	Likely pathogenic

SpliceAI

358 predictions. Top by Δscore:

Variant	Effect	Δscore
2:62222206:TTCCA:T	acceptor_loss	1.0000
2:62222207:TCCAG:T	acceptor_loss	1.0000
2:62222209:CAG:C	acceptor_loss	1.0000
2:62222210:A:AT	acceptor_loss	1.0000
2:62222211:G:GT	acceptor_loss	1.0000
2:62222211:GATAT:G	acceptor_gain	1.0000
2:62196351:ACAAG:A	donor_loss	0.9900
2:62196352:CAAG:C	donor_loss	0.9900
2:62196353:AAG:A	donor_loss	0.9900
2:62196357:T:A	donor_loss	0.9900
2:62222205:A:AG	acceptor_gain	0.9900
2:62222210:A:AG	acceptor_gain	0.9900
2:62222211:G:GC	acceptor_gain	0.9900
2:62222211:GA:G	acceptor_gain	0.9900
2:62222211:GAT:G	acceptor_gain	0.9900
2:62222211:GATA:G	acceptor_gain	0.9900
2:62222290:ATTAT:A	acceptor_gain	0.9900
2:62222294:T:TA	acceptor_gain	0.9800
2:62209763:TTGTA:T	donor_gain	0.9600
2:62222206:T:G	acceptor_gain	0.9500
2:62222290:A:AG	acceptor_gain	0.9500
2:62196356:G:GG	donor_gain	0.9300
2:62222293:AT:A	acceptor_gain	0.9300
2:62222198:C:G	acceptor_gain	0.9200
2:62222294:T:G	acceptor_gain	0.9200
2:62197408:A:G	donor_gain	0.9000
2:62222295:G:A	acceptor_gain	0.8900
2:62197408:A:AG	donor_gain	0.8800
2:62222197:A:AG	acceptor_gain	0.8800
2:62222291:T:G	acceptor_gain	0.8200

AlphaMissense

2652 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:62222693:G:C	R158T	1.000
2:62222693:G:T	R158M	1.000
2:62222694:G:C	R158S	1.000
2:62222694:G:T	R158S	1.000
2:62222954:A:T	D245V	1.000
2:62223085:T:C	Y289H	1.000
2:62223215:A:T	D332V	1.000
2:62223217:G:C	D333H	1.000
2:62223217:G:T	D333Y	1.000
2:62223218:A:C	D333A	1.000
2:62223218:A:G	D333G	1.000
2:62223218:A:T	D333V	1.000
2:62223219:C:A	D333E	1.000
2:62223219:C:G	D333E	1.000
2:62222665:A:G	K149E	0.999
2:62222667:G:C	K149N	0.999
2:62222667:G:T	K149N	0.999
2:62222705:G:C	R162P	0.999
2:62222713:T:A	W165R	0.999
2:62222713:T:C	W165R	0.999
2:62222715:G:C	W165C	0.999
2:62222715:G:T	W165C	0.999
2:62222758:T:C	F180L	0.999
2:62222759:T:C	F180S	0.999
2:62222759:T:G	F180C	0.999
2:62222760:C:A	F180L	0.999
2:62222760:C:G	F180L	0.999
2:62222839:G:C	D207H	0.999
2:62222840:A:C	D207A	0.999
2:62222840:A:T	D207V	0.999

dbSNP variants (sampled 300 via entrez): RS1000026275 (2:62214248 G>A), RS1000065201 (2:62213040 G>C), RS1000087316 (2:62220543 A>G), RS1000103210 (2:62221937 T>C), RS1000148909 (2:62209182 A>G), RS1000195682 (2:62194174 C>T), RS1000196177 (2:62204246 G>A), RS1000199972 (2:62200059 T>C,G), RS1000426373 (2:62203553 A>G), RS1000461524 (2:62214508 G>T), RS1000563204 (2:62211220 G>A,T), RS1000617239 (2:62210883 G>A,T), RS1000761226 (2:62203901 C>A,T), RS1000762313 (2:62205001 AG>A), RS1000791547 (2:62205742 G>C)

Disease associations

OMIM: gene MIM:605581 | disease phenotypes: MIM:181500

GenCC curated gene-disease

Disease	Classification	Inheritance
muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13	Moderate	Autosomal recessive
muscular dystrophy-dystroglycanopathy	Moderate	Autosomal recessive

Mondo (3): schizophrenia (MONDO:0005090), muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 (MONDO:0014120), muscular dystrophy-dystroglycanopathy (MONDO:0018276)

Orphanet (1): NON RARE IN EUROPE: Schizophrenia (Orphanet:3140)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0100753	Schizophrenia

GWAS associations

14 associations (top):

Study	Trait	p-value
GCST000563_4	Ankylosing spondylitis	2.000000e-19
GCST001241_12	Bipolar disorder	2.000000e-07
GCST001454_5	Rheumatoid arthritis	1.000000e-08
GCST002318_169	Rheumatoid arthritis	9.000000e-07
GCST002874_19	Psoriasis	7.000000e-07
GCST003268_12	Psoriasis vulgaris	9.000000e-12
GCST004571_25	Iron status biomarkers (total iron binding capacity)	7.000000e-08
GCST004572_6	Iron status biomarkers (transferrin saturation)	7.000000e-08
GCST005527_24	Psoriasis	5.000000e-10
GCST005992_28	Mean corpuscular hemoglobin concentration	3.000000e-08
GCST006011_94	Mean corpuscular volume	5.000000e-08
GCST006585_2700	Blood protein levels	1.000000e-06
GCST006959_179	Rheumatoid arthritis	3.000000e-06
GCST011116_3	Coronary artery disease in type 1 diabetes	5.000000e-07

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:1001494	psoriasis vulgaris
EFO:0006334	total iron binding capacity
EFO:0004528	mean corpuscular hemoglobin concentration

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5465363 (SINGLE PROTEIN)

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

ChEMBL bioactivities

40 potent at pChembl≥5 of 41 total, top 40 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.10	IC50	8	nM	CHEMBL5418011
8.05	IC50	9	nM	CHEMBL5410549
7.89	IC50	13	nM	CHEMBL5398949
7.62	IC50	24	nM	CHEMBL5433694
7.62	IC50	24	nM	CHEMBL5417333
7.58	IC50	26	nM	CHEMBL5418761
7.55	IC50	28	nM	CHEMBL5410730
7.54	IC50	29	nM	CHEMBL5437335
7.52	IC50	30	nM	CHEMBL5402041
7.41	IC50	39	nM	CHEMBL5419626
7.28	IC50	53	nM	CHEMBL5415169
7.26	IC50	55	nM	CHEMBL5413800
7.22	IC50	60	nM	CHEMBL5432994
7.18	IC50	66	nM	CHEMBL5404438
7.16	IC50	70	nM	CHEMBL5410194
7.16	IC50	69	nM	CHEMBL5434394
7.12	IC50	76	nM	CHEMBL5405463
7.09	IC50	82	nM	CHEMBL5420091
7.03	IC50	93	nM	CHEMBL5399837
7.02	IC50	96	nM	CHEMBL5431279
7.00	IC50	100	nM	CHEMBL5406719
6.92	IC50	120	nM	CHEMBL5407611
6.70	IC50	200	nM	CHEMBL5432221
6.64	IC50	230	nM	CHEMBL5413528
6.64	IC50	230	nM	CHEMBL5417424
6.58	IC50	260	nM	CHEMBL5430292
6.54	IC50	290	nM	CHEMBL5397909
6.43	IC50	370	nM	CHEMBL5402738
6.37	IC50	430	nM	CHEMBL5439813
6.29	IC50	510	nM	CHEMBL5403458
6.22	IC50	600	nM	CHEMBL5424059
6.21	IC50	610	nM	CHEMBL5413076
6.09	IC50	820	nM	CHEMBL5432738
6.08	IC50	840	nM	CHEMBL5401480
6.05	IC50	890	nM	CHEMBL5414987
6.05	IC50	900	nM	CHEMBL5436441
6.00	IC50	1010	nM	CHEMBL5416652
5.57	IC50	2720	nM	CHEMBL5410773
5.54	IC50	2900	nM	CHEMBL5414599
5.04	IC50	9100	nM	CHEMBL5423813

PubChem BioAssay actives

40 with measured affinity, of 42 total; 40 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(4S)-4-methyl-5-oxo-4-[6-(trifluoromethyl)-3-pyridinyl]-1H-imidazol-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0080	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(4S)-4-methyl-5-oxo-4-[2-(trifluoromethyl)pyrimidin-5-yl]-1H-imidazol-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0090	uM
5-[(2S)-2-benzyl-5-oxo-2-[2-(trifluoromethyl)pyrimidin-5-yl]-1H-imidazol-4-yl]-3-[(2R)-3,3-dimethylbutan-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0130	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(2S)-2-methyl-5-oxo-2-[2-(trifluoromethyl)pyrimidin-5-yl]-1H-imidazol-4-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0240	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(4S)-4-methyl-4-(2-methylpyrimidin-5-yl)-5-oxo-1H-imidazol-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0240	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(2S)-5-oxo-2-pyridin-3-yl-2-(1H-1,2,4-triazol-5-yl)-1H-imidazol-4-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0260	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(5S)-5-methyl-2-oxo-5-[2-(trifluoromethyl)pyrimidin-5-yl]furan-3-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0280	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(4S)-4-methyl-4-(6-methyl-3-pyridinyl)-5-oxo-1H-imidazol-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0290	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(4S)-4-methyl-5-oxo-4-[5-(trifluoromethyl)-2-pyridinyl]-1H-imidazol-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0300	uM
5-[(2R)-2-(6-chloro-3-pyridinyl)-5-oxo-2-pyridin-2-yl-1H-imidazol-4-yl]-3-[(2R)-3,3-dimethylbutan-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0390	uM
(3S)-6-bromo-4’-[3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazol-5-yl]spiro[1,2-dihydroindene-3,2’-1H-imidazole]-5’-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0530	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(2S)-2-(1H-indol-2-yl)-2-methyl-5-oxo-1H-imidazol-4-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0550	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-N-(2,3-dimethyl-1H-indol-6-yl)-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0600	uM
5-[(4S)-4-(5-chloro-2-pyridinyl)-4-methyl-5-oxo-1H-imidazol-2-yl]-3-[(2R)-3,3-dimethylbutan-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0660	uM
5-[(2S)-2-(5-chloro-2-pyridinyl)-2-methyl-5-oxo-1H-imidazol-4-yl]-3-[(2R)-3,3-dimethylbutan-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0690	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-N-[(1S)-1-[2-(trifluoromethyl)pyrimidin-5-yl]ethyl]-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0700	uM
N-[(1S)-1-(2-chloropyrimidin-5-yl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0760	uM
5-[(4S)-4-(5-chloropyrimidin-2-yl)-4-methyl-5-oxo-1H-imidazol-2-yl]-3-[(2R)-3,3-dimethylbutan-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0820	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-N-[(1S)-1-(5-methyl-2-pyridinyl)ethyl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0930	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(4S)-4-methyl-4-(5-methyl-2-pyridinyl)-5-oxo-1H-imidazol-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.0960	uM
N-[(1S)-1-(5-bromo-2-pyridinyl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.1000	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-N-[(1S)-1-(2-methylpyrimidin-5-yl)ethyl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.1200	uM
5-[2,2-bis(5-chloro-2-pyridinyl)-5-oxo-1H-imidazol-4-yl]-3-[(2R)-3,3-dimethylbutan-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.2000	uM
N-[(1S)-1-(5-chloro-2-pyridinyl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.2300	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-N-[(1S)-1-[5-(trifluoromethyl)-2-pyridinyl]ethyl]-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.2300	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxylic acid	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.2600	uM
N-[(1S)-1-(4-chlorophenyl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.2900	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(2S)-2-imidazo[1,2-a]pyridin-6-yl-2-methyl-5-oxo-1H-imidazol-4-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.3700	uM
N-[(1S)-1-(5-chloropyrimidin-2-yl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.4300	uM
5-[(4R)-4-(5-chloro-2-pyridinyl)-4-methyl-5-oxo-1H-imidazol-2-yl]-3-[(2R)-3,3-dimethylbutan-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.5100	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(4S)-4-methyl-5-oxo-4-phenyl-1H-imidazol-2-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.6000	uM
N-[(4-chlorophenyl)methyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.6100	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-N-phenyl-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.8200	uM
N-[2-(4-chlorophenyl)propan-2-yl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.8400	uM
N-[(1S)-1-(5-chloropyrazin-2-yl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.8900	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-(5-methyl-5-phenyl-2H-1,2,4-oxadiazol-3-yl)-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	0.9000	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-5-[(2S)-2-(2,3-dimethyl-1H-indol-5-yl)-2-methyl-5-oxo-1H-imidazol-4-yl]-1H-benzimidazol-2-one	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	1.0100	uM
N-[(1R)-1-(4-chlorophenyl)ethyl]-3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	2.7200	uM
3-[(2R)-3,3-dimethylbutan-2-yl]-2-oxo-N-propan-2-yl-1H-benzimidazole-5-carboxamide	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	2.9000	uM
3-(2-methylpropyl)-2-oxo-1H-benzimidazole-5-carboxylic acid	1992415: Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	ic50	9.1000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression, affects methylation	3
methylmercuric chloride	decreases expression	2
trichostatin A	affects cotreatment, increases expression	2
Valproic Acid	affects expression, increases expression	2
Cyclosporine	decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
bisphenol A	decreases expression	1
arsenite	affects expression	1
afimoxifene	increases expression	1
ochratoxin A	decreases expression	1
cupric chloride	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
(+)-JQ1 compound	increases expression	1
MT19c compound	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Bortezomib	decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Glyphosate	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Calcitriol	increases expression, affects cotreatment	1
Cisplatin	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5345418	Binding	Inhibition of B3GNT2 (unknown origin) using N-acetyl-lactosamine and UDP-GlcNAc as substrate incubated for 1.5 to 2 hrs by UDP-Glo based analysis	Imidazolone as an Amide Bioisostere in the Development of β-1,3-N-Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors. — J Med Chem

Cellosaurus cell lines

8 cell lines: 8 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D7J4	Ubigene A-375 B3GNT2 KO	Cancer cell line	Female
CVCL_D8HU	Ubigene HCT 116 B3GNT2 KO	Cancer cell line	Male
CVCL_D9YD	Ubigene HeLa B3GNT2 KO	Cancer cell line	Female
CVCL_JA11	VACO 915	Cancer cell line	Female
CVCL_JA12	VACO 920	Cancer cell line	Male
CVCL_JA19	VACO 964	Cancer cell line	Male
CVCL_SE46	HAP1 B3GNT1 (-) 1	Cancer cell line	Male
CVCL_SE47	HAP1 B3GNT1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00000374	PHASE4	COMPLETED	Treatment for First-Episode Schizophrenia
NCT00001656	PHASE4	COMPLETED	Comparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774	PHASE4	COMPLETED	To Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001	PHASE4	COMPLETED	CATIE- Schizophrenia Trial
NCT00018668	PHASE4	COMPLETED	Antipsychotic Response in Schizophrenia
NCT00034801	PHASE4	COMPLETED	Olanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905	PHASE4	COMPLETED	A Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088	PHASE4	COMPLETED	Olanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187	PHASE4	COMPLETED	The Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655	PHASE4	COMPLETED	Switching Medication to Treat Schizophrenia
NCT00048828	PHASE4	COMPLETED	Treating Drug-Resistant Childhood Schizophrenia
NCT00053703	PHASE4	COMPLETED	Treatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498	PHASE4	COMPLETED	Risperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802	PHASE4	COMPLETED	Efficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327	PHASE4	COMPLETED	Study of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049	PHASE4	COMPLETED	Study of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012	PHASE4	COMPLETED	Comparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776	PHASE4	COMPLETED	Efficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571	PHASE4	COMPLETED	Olanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368	PHASE4	COMPLETED	The Effects of Risperidone and Olanzapine on Thinking
NCT00114595	PHASE4	COMPLETED	Ethyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923	PHASE4	COMPLETED	Risperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020	PHASE4	COMPLETED	Clinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166	PHASE4	COMPLETED	Treatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847	PHASE4	COMPLETED	Naltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564	PHASE4	COMPLETED	Energy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715	PHASE4	COMPLETED	Efficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223	PHASE4	COMPLETED	Effectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081	PHASE4	COMPLETED	One Year Drug Treatment in First-Episode Schizophrenia
NCT00159120	PHASE4	COMPLETED	Maintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133	PHASE4	COMPLETED	Prodrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757	PHASE4	TERMINATED	12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817	PHASE4	COMPLETED	Effect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026	PHASE4	TERMINATED	Alcoholism and Schizophrenia: Effects of Clozapine
NCT00169039	PHASE4	TERMINATED	Clozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065	PHASE4	COMPLETED	Effectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091	PHASE4	TERMINATED	Clozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423	PHASE4	COMPLETED	Efficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436	PHASE4	COMPLETED	Atomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008	PHASE4	COMPLETED	Aripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety