B3GNT3

Summary

B3GNT3 (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3, HGNC:13528) is a protein-coding gene on chromosome 19p13.11, encoding N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 3 (Q9Y2A9). 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 and contains a signal anchor that is not cleaved. It prefers the substrates of lacto-N-tetraose and lacto-N-neotetraose, and is involved in the biosynthesis of poly-N-acetyllactosamine chains and the biosynthesis of the backbone structure of dimeric sialyl Lewis a. It plays dominant roles in L-selectin ligand biosynthesis, lymphocyte homing and lymphocyte trafficking.

Source: NCBI Gene 10331 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 61 total
• Druggable target: yes
• MANE Select transcript: NM_014256

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13528
Approved symbol	B3GNT3
Name	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	B3GN-T3, beta3Gn-T3, HP10328, B3GNT-3
Ensembl gene	ENSG00000179913
Ensembl biotype	protein_coding
OMIM	605863
Entrez	10331

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 9 protein_coding

ENST00000318683, ENST00000595387, ENST00000599265, ENST00000600777, ENST00000858455, ENST00000858456, ENST00000858457, ENST00000929613, ENST00000944332

RefSeq mRNA: 1 — MANE Select: NM_014256 NM_014256

CCDS: CCDS12364

Canonical transcript exons

ENST00000318683 — 3 exons

Exon	Start	End
ENSE00001219609	17807758	17808374
ENSE00001323238	17811571	17813576
ENSE00001512667	17795138	17795206

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 94.01.

FANTOM5 (CAGE): breadth broad, TPM avg 7.1321 / max 587.3852, expressed in 445 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174550	6.8356	435
174549	0.2964	126

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	94.01	gold quality
rectum	UBERON:0001052	92.88	gold quality
lower esophagus mucosa	UBERON:0035834	92.06	gold quality
gall bladder	UBERON:0002110	89.29	gold quality
colonic mucosa	UBERON:0000317	88.45	gold quality
mucosa of sigmoid colon	UBERON:0004993	87.97	gold quality
duodenum	UBERON:0002114	85.63	gold quality
esophagus squamous epithelium	UBERON:0006920	85.12	gold quality
epithelium of esophagus	UBERON:0001976	85.06	gold quality
nasal cavity epithelium	UBERON:0005384	84.05	gold quality
minor salivary gland	UBERON:0001830	83.78	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	83.47	gold quality
transverse colon	UBERON:0001157	82.36	gold quality
saliva-secreting gland	UBERON:0001044	82.31	gold quality
body of stomach	UBERON:0001161	82.13	gold quality
esophagus mucosa	UBERON:0002469	81.57	gold quality
stomach	UBERON:0000945	80.84	gold quality
jejunal mucosa	UBERON:0000399	80.48	gold quality
mouth mucosa	UBERON:0003729	79.54	gold quality
palpebral conjunctiva	UBERON:0001812	79.45	gold quality
amniotic fluid	UBERON:0000173	79.36	gold quality
islet of Langerhans	UBERON:0000006	79.20	gold quality
small intestine Peyer’s patch	UBERON:0003454	78.82	gold quality
parotid gland	UBERON:0001831	78.74	gold quality
ileal mucosa	UBERON:0000331	78.54	gold quality
small intestine	UBERON:0002108	78.43	gold quality
triceps brachii	UBERON:0001509	78.14	gold quality
placenta	UBERON:0001987	77.85	gold quality
endometrium epithelium	UBERON:0004811	77.61	gold quality
tongue squamous epithelium	UBERON:0006919	77.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

55 targeting B3GNT3, 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-4673	100.00	66.64	1490
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-2113	99.58	71.22	1521
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4727-5P	99.23	67.55	1154
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-6510-5P	99.14	66.59	1081
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-4764-5P	98.88	65.53	894
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126

Literature-anchored findings (GeneRIF, showing 8)

• B3GNT3 predicts a favorable cancer behavior of neuroblastoma and suppresses malignant phenotypes by modulating mucin-type O-glycosylation and signaling in neuroblastoma cells. (PMID:24118321)
• This study demonstrated that elevated B3GNT3 expression is associated with pelvic lymph node metastasis and poor outcome in early-stage cervical cancer patients. (PMID:26709519)
• These results indicate that elevated GALNT3 and B3GNT3 expression in PCSCs regulate stemness through modulating CSC markers. (PMID:30466404)
• B3GNT3 overexpression promotes tumor progression and inhibits infiltration of CD8(+) T cells in pancreatic cancer. (PMID:33316775)
• B3GNT3 acts as a carcinogenic factor in endometrial cancer via facilitating cell growth, invasion and migration through regulating RhoA/RAC1 pathway-associated markers. (PMID:33683574)
• Study on the Expression of beta-1,3-N-acetylglucosaminyltransferase 3 in Gastric Cancer and the Mechanism Promoting Gastric Cancer Progression Based on the Extraction Method of Nanomagnetic Beads. (PMID:35715910)
• Upregulation of B3GNT3 is associated with immune infiltration and activation of NF-kappaB pathway in gynecologic cancers. (PMID:35777165)
• The role of B3GNT3 as an oncogene in the growth, invasion and migration of esophageal cancer cells. (PMID:36995820)

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
danio_rerio	b3gnt3.1	ENSDARG00000043482
danio_rerio	b3gnt3.2	ENSDARG00000054373
danio_rerio	b3gnt3.4	ENSDARG00000058100
danio_rerio	b3gnt3.3	ENSDARG00000093521
mus_musculus	B3gnt3	ENSMUSG00000031803
rattus_norvegicus	B3gnt3	ENSRNOG00000018764
drosophila_melanogaster	brn	FBGN0000221
caenorhabditis_elegans		WBGENE00000270
caenorhabditis_elegans		WBGENE00007096
caenorhabditis_elegans		WBGENE00017653

Paralogs (15): B3GNT7 (ENSG00000156966), B3GALT2 (ENSG00000162630), B3GALNT2 (ENSG00000162885), B3GALNT1 (ENSG00000169255), B3GNT2 (ENSG00000170340), B3GALT1 (ENSG00000172318), B3GALT6 (ENSG00000176022), B3GNT4 (ENSG00000176383), B3GNT5 (ENSG00000176597), B3GNT8 (ENSG00000177191), B3GALT5 (ENSG00000183778), B3GNT6 (ENSG00000198488), B3GALT9 (ENSG00000214654), B3GALT4 (ENSG00000235863), B3GNT9 (ENSG00000237172)

Protein

Protein identifiers

N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 3 — Q9Y2A9 (reviewed: Q9Y2A9)

Alternative names: Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase, Beta-1,3-galactosyltransferase 8, Beta-3-Gx-T8, Core 1 extending beta-1,3-N-acetylglucosaminyltransferase, Core1-beta3GlcNAcT, Transmembrane protein 3, UDP-Gal:beta-GlcNAc beta-1,3-galactosyltransferase 8, UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3, UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase 8

All UniProt accessions (3): Q9Y2A9, M0QX58, M0R199

UniProt curated annotations — full annotation on UniProt →

Function. Beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine. Has activity for type 2 oligosaccharides. Also acts as a core1-1,3-N-acetylglucosaminyltransferase (Core1-beta3GlcNAcT) to form the 6-sulfo sialyl Lewis x on extended core1 O-glycans.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Expressed in colon, jejunum, stomach, esophagus, placenta and trachea.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 31 family.

RefSeq proteins (1): NP_055071* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002659	Glyco_trans_31	Family

Pfam: PF01762

Enzyme classification (BRENDA):

• EC 2.4.1.146 — beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase (BRENDA: 6 organisms, 17 substrates, 1 inhibitors, 4 Km, 0 kcat entries)
• EC 2.4.1.149 — N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase (BRENDA: 6 organisms, 107 substrates, 59 inhibitors, 27 Km, 1 kcat entries)
• EC 2.4.99.6 — N-acetyllactosaminide alpha-2,3-sialyltransferase (BRENDA: 0 organisms, 0 substrates, 0 inhibitors, 0 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

14 substrates with measured Km, best-characterized 14. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
UDP-N-ACETYL-D-GLUCOSAMINE	0.129–15.97	11
N-ACETYLLACTOSAMINE	2.2–19.6	4
LACTOSE	5.2–29.8	3
GALBETA(1-4)GLCNACBETA(1-4)GLCNAC-2-AMINOPYRIDIN	0.44–0.9	2
BETA-D-GALACTOSYL-1,3-(N-ACETYL-D-GLUCOSAMINYL-1	1.2	1
BETA-D-GALACTOSYL-1,3-(N-ACETYL-D-GLUCOSAMINYL-1	0.9	1
METHYL 9-[[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOP	0.13	1
UDP-N-ACETYL-D-GLUCOSAMINE	1.6	1
ASIALO-ALPHA1-ACID GLYCOPROTEIN	0.6	1
GALBETA(1->4)GLCNACBETA(1->3)GALBETA(1->4)GLCNAC	1	1
GALBETA1,4(SO3-,6)-GLCNACBETA1,3-GALBETA1,4(SO3-	0.36	1
LACTONEOTETRAOSYLCERAMIDE	0.19	1
LACTONORHEXAOSYLCERAMIDE	0.19	1
NEOLACTOTETRAOSYLCERAMIDE	0.09	1

Catalyzed reactions (Rhea), 3 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)
• 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-{beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->3)-[beta-D-GlcNAc-(1->6)]-alpha-D-GalNAc}-L-seryl-[protein] + UDP + H(+) (RHEA:56220)
• a 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-{beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->3)-[beta-D-GlcNAc-(1->6)]-alpha-D-GalNAc}-L-threonyl-[protein] + UDP + H(+) (RHEA:56224)

UniProt features (13 total): glycosylation site 5, topological domain 2, sequence variant 2, sequence conflict 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2A9-F1	88.47	0.78

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): 64, 184, 202, 362, 367

Function

Pathways and Gene Ontology

Reactome pathways

10 pathways

ID	Pathway
R-HSA-2022854	Keratan sulfate biosynthesis
R-HSA-913709	O-linked glycosylation of mucins
R-HSA-9931295	PD-L1(CD274) glycosylation and translocation to plasma membrane
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: 135 (showing top): REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_AMINOGLYCAN_BIOSYNTHETIC_PROCESS, MODULE_379, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_AMINOGLYCAN_METABOLIC_PROCESS, MODULE_242, MODULE_207, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION_VIA_N_ACETYL_GALACTOSAMINE, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION, MODULE_342, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, REACTOME_METABOLISM_OF_CARBOHYDRATES_AND_CARBOHYDRATE_DERIVATIVES, MODULE_104, KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES

GO Biological Process (6): protein O-linked glycosylation (GO:0006493), protein O-linked glycosylation via N-acetylgalactosamine (GO:0016266), keratan sulfate proteoglycan biosynthetic process (GO:0018146), poly-N-acetyllactosamine biosynthetic process (GO:0030311), obsolete protein glycosylation (GO:0006486), carbohydrate derivative biosynthetic process (GO:1901137)

GO Molecular Function (7): N-acetyl-beta-D-glucosaminide beta-(1,3)-galactosyltransferase activity (GO:0008499), N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532), beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223), protein binding (GO:0005515), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757), hexosyltransferase activity (GO:0016758)

GO Cellular Component (4): Golgi membrane (GO:0000139), plasma membrane (GO:0005886), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-8 pathways:

Category	Pathways
Keratan sulfate/keratin metabolism	1
O-linked glycosylation	1
Regulation of PD-L1(CD274) Post-translational modification	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
acetylglucosaminyltransferase activity	2
glycoprotein biosynthetic process	1
protein O-linked glycosylation	1
proteoglycan biosynthetic process	1
keratan sulfate proteoglycan metabolic process	1
aminoglycan biosynthetic process	1
poly-N-acetyllactosamine metabolic process	1
biosynthetic process	1
carbohydrate derivative metabolic process	1
UDP-galactosyltransferase activity	1
beta-1,3-galactosyltransferase activity	1
catalytic activity, acting on a glycoprotein	1
binding	1
catalytic activity	1
transferase activity	1
glycosyltransferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
membrane	1
cell periphery	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

784 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
B3GNT3	LRRTM3	Q86VH5	877
B3GNT3	IFITM3	Q01628	728
B3GNT3	CHST4	Q8NCG5	578
B3GNT3	GCNT1	Q02742	574
B3GNT3	ST3GAL6	Q9Y274	567
B3GNT3	GCNT3	O95395	556
B3GNT3	GCNT2	Q8N0V5	538
B3GNT3	ABHD16A	O95870	532
B3GNT3	B4GALT4	O60513	530
B3GNT3	CTNNA3	Q9UI47	530
B3GNT3	ST3GAL1	Q11201	519
B3GNT3	C1GALT1	Q9NS00	519
B3GNT3	GALNT3	Q14435	517
B3GNT3	PLAU	P00749	493
B3GNT3	FUT2	Q10981	492

IntAct

13 interactions, top by confidence:

A	B	Type	Score
B3GNT3	PGRMC1	psi-mi:“MI:0914”(association)	0.670
PGRMC1	B3GNT3	psi-mi:“MI:0915”(physical association)	0.670
CD19	POLR2M	psi-mi:“MI:0914”(association)	0.350
CD19	MYZAP	psi-mi:“MI:0914”(association)	0.350
SFTPC	TMEM131L	psi-mi:“MI:0914”(association)	0.350
NRG1	TMEM131L	psi-mi:“MI:0914”(association)	0.350
PDGFRA	QSOX1	psi-mi:“MI:0914”(association)	0.350
CRLF1	MANBA	psi-mi:“MI:0914”(association)	0.350
C1QB	MANBA	psi-mi:“MI:0914”(association)	0.350
SLURP1	MAN2B1	psi-mi:“MI:0914”(association)	0.350
CLEC2B	ADAM10	psi-mi:“MI:0914”(association)	0.350

BioGRID (103): MBOAT7 (Affinity Capture-MS), KDELC1 (Affinity Capture-MS), SLC30A5 (Affinity Capture-MS), PIGU (Affinity Capture-MS), GHITM (Affinity Capture-MS), GALNT12 (Affinity Capture-MS), TUBB8 (Affinity Capture-MS), CSGALNACT2 (Affinity Capture-MS), SLC30A6 (Affinity Capture-MS), DSTYK (Affinity Capture-MS), SLC30A7 (Affinity Capture-MS), FECH (Affinity Capture-MS), PIGK (Affinity Capture-MS), AMIGO1 (Affinity Capture-MS), SEPN1 (Affinity Capture-MS)

ESM2 similar proteins: O14792, O35310, O43529, O54702, P21709, P51690, P51839, Q08BL3, Q08BN9, Q14BT6, Q16WU7, Q29G54, Q5E9W5, Q5EA41, Q5RBZ6, Q5U2X4, Q5U3T0, Q5YB40, Q5ZIE4, Q60750, Q60HH5, Q66H69, Q6AXM1, Q6GNS1, Q6PGK7, Q6W3E9, Q6W3F0, Q6XQH0, Q7Q297, Q7T3S5, Q80V53, Q8BSL4, Q8IZT8, Q8K0J2, Q8NCG5, Q8NCH0, Q8NCL4, Q92035, Q92179, Q96SM3

Diamond homologs: A8MXE2, O43825, O54904, O54905, O75752, O88178, O96024, Q1RLK6, Q5HZL5, Q5JCS9, Q5R5Y3, Q5RAL7, Q66H69, Q6AY39, Q6DE15, Q6P3P5, Q793U7, Q7JK24, Q7JK25, Q7JK26, Q7T3S5, Q864U6, Q864U8, Q8BGY6, Q8R3I9, Q920V1, Q95US5, Q99NB2, Q9BYG0, Q9C0J1, Q9JI67, Q9MYM7, Q9N293, Q9N294, Q9N295, Q9Y2A9, Q9Y2C3, Q9Y5Z6, Q9Z0F0, Q24157

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
B3GNT3	“up-regulates activity”	CD274	glycosylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 16 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.

Reactome pathways:

Pathway	Partners	Fold	FDR
Neutrophil degranulation	5	9.6×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	9
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

588 predictions. Top by Δscore:

Variant	Effect	Δscore
19:17807753:CACA:C	acceptor_loss	0.9900
19:17807756:A:AG	acceptor_gain	0.9900
19:17807756:AG:A	acceptor_gain	0.9900
19:17807756:AGG:A	acceptor_loss	0.9900
19:17807757:G:GA	acceptor_gain	0.9900
19:17807757:G:T	acceptor_loss	0.9900
19:17807757:GG:G	acceptor_gain	0.9900
19:17807757:GGA:G	acceptor_gain	0.9900
19:17808370:AGCAG:A	donor_loss	0.9900
19:17808371:GCAG:G	donor_gain	0.9900
19:17808372:C:T	donor_gain	0.9900
19:17808372:CAG:C	donor_loss	0.9900
19:17808373:AG:A	donor_loss	0.9900
19:17808374:GGT:G	donor_loss	0.9900
19:17808375:G:C	donor_loss	0.9900
19:17808376:T:A	donor_loss	0.9900
19:17811568:CA:C	acceptor_loss	0.9900
19:17811569:A:AC	acceptor_loss	0.9900
19:17811570:G:GT	acceptor_loss	0.9900
19:17807757:GGAGC:G	acceptor_gain	0.9800
19:17795203:GGGG:G	donor_gain	0.9700
19:17795204:GGGG:G	donor_gain	0.9700
19:17807755:CAGG:C	acceptor_gain	0.9700
19:17807756:AGGA:A	acceptor_gain	0.9700
19:17807757:GGAG:G	acceptor_gain	0.9700
19:17811569:A:AG	acceptor_gain	0.9700
19:17811570:G:GG	acceptor_gain	0.9700
19:17797854:A:AG	acceptor_gain	0.9600
19:17807754:ACAG:A	acceptor_gain	0.9600
19:17795204:GGG:G	donor_gain	0.9500

AlphaMissense

2411 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:17808174:C:A	R123S	0.994
19:17808371:G:C	K188N	0.992
19:17808371:G:T	K188N	0.992
19:17811616:T:C	F205L	0.989
19:17811618:C:A	F205L	0.989
19:17811618:C:G	F205L	0.989
19:17811588:G:C	W195C	0.987
19:17811588:G:T	W195C	0.987
19:17808339:T:C	F178L	0.986
19:17808341:C:A	F178L	0.986
19:17808341:C:G	F178L	0.986
19:17808151:C:T	S115F	0.985
19:17808240:T:C	F145L	0.985
19:17808242:C:A	F145L	0.985
19:17808242:C:G	F145L	0.985
19:17811893:A:T	D297V	0.984
19:17808333:T:A	W176R	0.983
19:17808333:T:C	W176R	0.983
19:17811894:T:A	D297E	0.983
19:17811894:T:G	D297E	0.983
19:17808149:G:C	K114N	0.981
19:17808149:G:T	K114N	0.981
19:17808241:T:C	F145S	0.981
19:17808197:G:C	W130C	0.980
19:17808197:G:T	W130C	0.980
19:17808322:A:T	D172V	0.980
19:17811898:T:C	F299L	0.980
19:17811900:C:A	F299L	0.980
19:17811900:C:G	F299L	0.980
19:17811912:T:G	C303W	0.979

dbSNP variants (sampled 300 via entrez): RS1000149153 (19:17795651 G>A), RS1000182016 (19:17795938 G>C,T), RS1000418679 (19:17813016 C>T), RS1000477609 (19:17794248 C>A,G), RS1000867466 (19:17807104 T>C), RS1000932889 (19:17813622 C>G,T), RS1000969526 (19:17794508 T>C), RS1001026359 (19:17795295 C>A), RS1001053891 (19:17800852 T>A,C), RS1001351694 (19:17813333 C>A), RS1001430242 (19:17800521 C>T), RS1001465385 (19:17801558 A>G), RS1001752075 (19:17795019 A>G), RS1001764328 (19:17807555 C>T), RS1001943887 (19:17799963 C>T)

Disease associations

OMIM: gene MIM:605863 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001808_6	Tumor biomarkers	1.000000e-13
GCST009648_3	Serum cancer antigen 19.9 levels	3.000000e-13
GCST90000255_20	Severe COVID-19 infection with respiratory failure (analysis I)	4.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005127	cancer biomarker measurement
EFO:0010584	cancer antigen 19.9 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3325305 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression, increases methylation	4
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	3
methyleugenol	increases expression	1
lead acetate	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
4-nonylphenol	affects cotreatment, increases expression	1
4-tert-octylphenol	affects cotreatment, increases expression	1
azaspiracid	increases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	decreases response to substance	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases expression, increases abundance	1
Cisplatin	affects cotreatment, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Hydrogen Peroxide	affects expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Methotrexate	affects response to substance	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Sodium Dodecyl Sulfate	increases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	increases expression	1
Lactic Acid	decreases expression	1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3376891	Binding	Competitive inhibition of human N-terminally His6-tagged N-acetylglucosaminyltransferase 3 expressed in HEK293T cells assessed as GN-GnGnbi-PAs molar ratio level at 100 to 500 uM incubated for 4 hrs using GnGnbi-PA acceptor substrate and UD	Synthesis of N-glycan units for assessment of substrate structural requirements of N-acetylglucosaminyltransferase III. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

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