GCNT1

Summary

GCNT1 (glucosaminyl (N-acetyl) transferase 1, HGNC:4203) is a protein-coding gene on chromosome 9q21.13, encoding Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase (Q02742). Glycosyltransferase that catalyzes the transfer of an N-acetylglucosamine (GlcNAc) moiety in beta1-6 linkage from UDP-GlcNAc onto mucin-type core 1 O-glycan to form the branched mucin-type core 2 O-glycan.

This gene is a member of the beta-1,6-N-acetylglucosaminyltransferase gene family. It is essential to the formation of Gal beta 1-3(GlcNAc beta 1-6)GalNAc structures and the core 2 O-glycan branch. The gene coding this enzyme was originally mapped to 9q21, but was later localized to 9q13. Multiple alternatively spliced variants, encoding the same protein, have been identified.

Source: NCBI Gene 2650 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 71 total
• Druggable target: yes
• MANE Select transcript: NM_001490

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4203
Approved symbol	GCNT1
Name	glucosaminyl (N-acetyl) transferase 1
Location	9q21.13
Locus type	gene with protein product
Status	Approved
Aliases	C2GNT, NAGCT2
Ensembl gene	ENSG00000187210
Ensembl biotype	protein_coding
OMIM	600391
Entrez	2650

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 25 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000376730, ENST00000442371, ENST00000444201, ENST00000480311, ENST00000488136, ENST00000648797, ENST00000889367, ENST00000889368, ENST00000889369, ENST00000889370, ENST00000889371, ENST00000889372, ENST00000889373, ENST00000889374, ENST00000935213, ENST00000935214, ENST00000935215, ENST00000935216, ENST00000935217, ENST00000935218, ENST00000935219, ENST00000935220, ENST00000935221, ENST00000935222, ENST00000935223, ENST00000935224, ENST00000960788, ENST00000960789

RefSeq mRNA: 9 — MANE Select: NM_001490 NM_001097633, NM_001097634, NM_001097635, NM_001097636, NM_001407181, NM_001407182, NM_001407183, NM_001407184, NM_001490

CCDS: CCDS6653

Canonical transcript exons

ENST00000376730 — 4 exons

Exon	Start	End
ENSE00001024010	76500916	76501061
ENSE00001283007	76460060	76460177
ENSE00001888816	76502239	76507416
ENSE00001949480	76459182	76459305

Expression profiles

Bgee: expression breadth ubiquitous, 211 present calls, max score 92.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.2108 / max 165.9154, expressed in 1467 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96997	8.8968	1455
96998	0.2734	136
96996	0.0407	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
duodenum	UBERON:0002114	92.25	gold quality
jejunal mucosa	UBERON:0000399	87.59	gold quality
islet of Langerhans	UBERON:0000006	86.28	gold quality
amniotic fluid	UBERON:0000173	85.64	gold quality
calcaneal tendon	UBERON:0003701	85.49	gold quality
mucosa of sigmoid colon	UBERON:0004993	85.27	gold quality
secondary oocyte	CL:0000655	84.61	gold quality
rectum	UBERON:0001052	84.52	gold quality
colonic mucosa	UBERON:0000317	83.71	gold quality
ileal mucosa	UBERON:0000331	83.44	gold quality
monocyte	CL:0000576	82.92	gold quality
oocyte	CL:0000023	82.61	gold quality
mononuclear cell	CL:0000842	82.41	gold quality
leukocyte	CL:0000738	82.28	gold quality
tendon	UBERON:0000043	81.58	gold quality
stomach	UBERON:0000945	80.98	gold quality
right lobe of thyroid gland	UBERON:0001119	80.62	gold quality
body of stomach	UBERON:0001161	80.30	gold quality
left lobe of thyroid gland	UBERON:0001120	80.24	gold quality
thyroid gland	UBERON:0002046	79.99	gold quality
sperm	CL:0000019	79.90	gold quality
bone marrow	UBERON:0002371	79.43	gold quality
small intestine	UBERON:0002108	79.42	gold quality
mucosa of transverse colon	UBERON:0004991	79.35	gold quality
cartilage tissue	UBERON:0002418	79.05	gold quality
granulocyte	CL:0000094	78.97	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.55	gold quality
endometrium	UBERON:0001295	78.54	gold quality
stromal cell of endometrium	CL:0002255	78.40	gold quality
small intestine Peyer’s patch	UBERON:0003454	77.88	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-111727	yes	116.89
E-GEOD-36552	yes	91.93
E-ANND-3	yes	5.82

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SP1

miRNA regulators (miRDB)

189 targeting GCNT1, 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-3646	100.00	73.56	5283
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163

Literature-anchored findings (GeneRIF, showing 31)

• EGF suppressed C2GnT activity in a time- and dose-dependent fashion, and also suppressed core 4 beta1,6 N-acetylglucosaminyltransferase (C4GnT) activity (PMID:12600830)
• presence of multiple tissue-specific promoters for the C2GnT I gene (PMID:12626388)
• elevated glucose increases the activity of core 2 GlcNAc-T and adhesion of human leukocytes to retinal capillary endothelial cells, in a dose-dependent manner, through diabetes-activated serine/threonine protein kinase C beta2-dependent phosphorylation (PMID:12765965)
• core 2 beta1-6-N-glucosaminyltransferase and dimerization of P-selectin glycoprotein ligand-1 have roles in rolling on P-selectin (PMID:15026421)
• C2GnT-1 regulates sLeX expression level during differentiation of pre-B cells (PMID:15483269)
• upregulated by all-trans retinoic acid (RA) and by IL-4 and IL-13 in the H292 airway epithelial cell line (PMID:15591039)
• A/G polymorphism in enzyme is associated with the susceptibility to prostate cancer in a Japanese population (PMID:15882971)
• A differential functional impact of N-glycosylation on C2GnT-1 and FucT-VII and disclose that a strongly reduced FucT-VII activity retains the ability to fucosylate PSGL-1 on the core2-based binding site(s) for the three selectins. (PMID:15926890)
• Core2GnT is an extremely useful prognostic marker for prostate cancer progression. Acquiring Core2GnT in prostate carcinoma cells facilitates adhesion to type IV collagen and laminin causing aggressive tumor formation by prostate cancer cells. (PMID:15932919)
• C2GnT-1 regulates selectin ligand expression; downregulation of the selectin ligand expression level inhibits tissue infiltration of BCP-leukemia cells (PMID:16179912)
• glycosyltransferase haploinsufficiency results in altered cellular glycosylation and resistance to cell death, identifying a new survival mechanism for T-lymphoma cells (PMID:16778138)
• 2 beta1,6 N-acetylglucosaminyltransferase-I transcription is regulated by Sp1 in lymphocytes and epithelial cells (PMID:17530395)
• regulation of O-glycosylation controls sLe(x) expression, and also suggest that O-glycans may have a function in dendritic cells migration (PMID:17947642)
• Pancreas carcinoma antigen, C2GnT, fused to invariant chain elicits T-cell response and tumor growth inhibition. (PMID:18815556)
• 15-fold increase in C2GnT1 mRNA levels in colorectal adenocarcinomas compared to normal colorectal tissues (PMID:19267921)
• Data show that a short glycopeptide Galbeta1-3GalNAcalpha-TAGV was identified as an efficient C2GnT substrate. (PMID:19524017)
• Overexpression of C2GnT-1 enhances the metastatic potential of testicular germ cell tumor. (PMID:20017138)
• Core2 O-glycan structure is essential for expression of SI and DDP-IV during intestinal cell differentiation. (PMID:20841351)
• Data show that the reconstituted membrane system in cells expressing C2GnT-I led to the lipid vesicles exhibiting an enzyme activity 11 times higher than that found in microsomal membranes. (PMID:21081110)
• In C2GnT-expressing bladder tumour cells galectin-3 bound the NKG2D-binding site of MICA, reducing the affinity of MICA for NKG2D on natural killer cells and hence severely impairing natural killer cell activation. (PMID:21712812)
• The X-ray crystal structure (2.3 A resolution) of a mutant form of C2GnT-L (C217S) in complex with UDP was solved. C2GnT-L exists in an “open” conformation and a “closed” conformation. (PMID:22056345)
• Down-regulation of C2GnT1 is correlated with breast cancer (PMID:22534569)
• GOLPH3 can regulate cell-cell interaction by controlling Golgi retention of C2GnT1. (PMID:23027862)
• C2GnT-expressing prostate cancer cells evade NK cell immunity and survive longer in the host blood circulation, thereby resulting in the promotion of prostate cancer metastasis. (PMID:23165940)
• Immunohistochemical expression of core 2 beta1,6-N-acetylglucosaminyl transferase 1 (C2GnT1) in endometrioid-type endometrial carcinoma may be a novel potential prognostic factor. (PMID:23617619)
• NMIIA is the master regulator of Golgi fragmentation induced by heat shock or inhibition/depletion of HSP70/90 through interaction with gylosyltransferases. (PMID:23990450)
• GCNT1 is over-expressed in prostate cancer and is associated with higher levels of core 2 O-sLe(x) in PSA, PAP and MUC1 proteins. (PMID:24854630)
• Results show that ST3Gal1 uses GM130-GRASP65 and giantin, whereas C2GnT-L uses only giantin for Golgi targeting and defective giantin dimerization in PC-3 and DU145 prostate cancer cells causes fragmentation of the Golgi and prevents its targeting. (PMID:25086069)
• GCNT1 expression in prostate cancer positively correlates with cancer progression and prostate-specific antigen recurrence. (PMID:26390303)
• GCNT1 expression in prostate biopsy specimen is a significant and independent predictor of recurrence after radical prostatectomy, which can be used in pre-treatment decision making for the patient. (PMID:26768364)
• The role of GCNT1 mediated O-glycosylation in aggressive prostate cancer. (PMID:37813880)

Cross-species orthologs

21 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gcnt1	ENSMUSG00000038843
rattus_norvegicus	Gcnt1	ENSRNOG00000062686
drosophila_melanogaster	oxt	FBGN0015360
drosophila_melanogaster	CG9164	FBGN0030634
caenorhabditis_elegans	gly-15	WBGENE00001640
caenorhabditis_elegans	gly-16	WBGENE00001641
caenorhabditis_elegans	gly-17	WBGENE00001642
caenorhabditis_elegans	gly-18	WBGENE00001643
caenorhabditis_elegans	gly-19	WBGENE00001644
caenorhabditis_elegans		WBGENE00005024
caenorhabditis_elegans		WBGENE00009148
caenorhabditis_elegans	F30A10.4	WBGENE00009263
caenorhabditis_elegans		WBGENE00011090
caenorhabditis_elegans	T09E11.6	WBGENE00011655
caenorhabditis_elegans	T09E11.9	WBGENE00011658
caenorhabditis_elegans	T27F6.1	WBGENE00012102
caenorhabditis_elegans		WBGENE00012135
caenorhabditis_elegans		WBGENE00013119
caenorhabditis_elegans	ZK1225.2	WBGENE00014236
caenorhabditis_elegans		WBGENE00019270
caenorhabditis_elegans		WBGENE00019919

Paralogs (8): XYLT2 (ENSG00000015532), WSCD2 (ENSG00000075035), XYLT1 (ENSG00000103489), GCNT2 (ENSG00000111846), GCNT7 (ENSG00000124091), GCNT3 (ENSG00000140297), GCNT4 (ENSG00000176928), WSCD1 (ENSG00000179314)

Protein

Protein identifiers

Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase — Q02742 (reviewed: Q02742)

Alternative names: Core 2 beta-1,6-N-acetylglucosaminyltransferase, Core 2-branching enzyme, Core2-GlcNAc-transferase, Leukocyte type core 2 beta-1,6-N-acetylglucosaminyltransferase

All UniProt accessions (1): Q02742

UniProt curated annotations — full annotation on UniProt →

Function. Glycosyltransferase that catalyzes the transfer of an N-acetylglucosamine (GlcNAc) moiety in beta1-6 linkage from UDP-GlcNAc onto mucin-type core 1 O-glycan to form the branched mucin-type core 2 O-glycan. The catalysis is metal ion-independent and occurs with inversion of the anomeric configuration of sugar donor. Selectively involved in synthesis of mucin-type core 2 O-glycans that serve as scaffolds for the display of selectin ligand sialyl Lewis X epitope by myeloid cells, with an impact on homeostasis and recruitment to inflammatory sites. Can also act on glycolipid substrates. Transfers GlcNAc moiety to GalGb4Cer globosides in a reaction step to the synthesis of stage-specific embryonic antigen 1 (SSEA-1) determinant. Can use Galbeta1-3GalNAcalpha1- and Galbeta1-3GalNAcbeta1- oligosaccharide derivatives as acceptor substrates.

Subunit / interactions. Interacts with GOLPH3; may control GCNT1 retention in the Golgi.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Highly expressed in activated T-lymphocytes and myeloid cells.

Pathway. Protein modification; protein glycosylation. Glycolipid biosynthesis.

Similarity. Belongs to the glycosyltransferase 14 family.

RefSeq proteins (9): NP_001091102, NP_001091103, NP_001091104, NP_001091105, NP_001394110, NP_001394111, NP_001394112, NP_001394113, NP_001481* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003406	Glyco_trans_14	Family

Pfam: PF02485

Enzyme classification (BRENDA):

• EC 2.4.1.102 — beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase (BRENDA: 13 organisms, 110 substrates, 35 inhibitors, 50 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

19 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
UDP-N-ACETYL-D-GLUCOSAMINE	0.0063–5.6	9
BETA-D-GALACTOSYL-1,3-N-ACETYL-ALPHA-D-GALACTOSA	0.77–2	7
3-DEOXY-BETA-D-GALACTOSYL-1,3-N-ACETYL-D-GALACTO	2–5.5	5
4-DEOXY-BETA-D-GALACTOSYL-1,3-N-ACETYL-D-GALACTO	3.1–10	5
BETA-D-GALACTOSYL-1,3-(6-DEOXY)-N-ACETYL-D-GALAC	12–37	4
GALBETA(1-3)GALNACALPHA-P-NITROPHENOL	0.11–1.6	4
BETA-D-GALACTOSYL-1,3-N-ACETYL-ALPHA-D-GALACTOSA	0.52–0.92	2
BETA-D-GALACTOSYL-1,3-N-ACETYL-D-GALACTOSAMINYL-	0.36–0.43	2
ANTIFREEZE GLYCOPROTEIN POLYPEPTIDE	23	1
ASIALO-BLOOD GROUP A NEGATIVE PSM	5.2	1
BETA-D-GALACTOSYL-1,3-N-ACETYL-ALPHA-D-GALACTOSA	1.2	1
BETA-D-GALACTOSYL-1,3-N-ACETYL-ALPHA-D-GALACTOSA	0.86	1
BETA-D-GALACTOSYL-1,3-N-ACETYL-ALPHA-D-GALACTOSA	4.2	1
BETA-D-GALACTOSYL-1,3-N-ACETYL-BETA-D-GALACTOSAM	0.92	1

Catalyzed reactions (Rhea), 4 shown:

• a 3-O-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + UDP + H(+) (RHEA:56212)
• a 3-O-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = a 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + UDP + H(+) (RHEA:56216)
• a globoside GalGb4Cer + UDP-N-acetyl-alpha-D-glucosamine = a globoside GlcNAc-(beta1->6)-GalGb4Cer + UDP + H(+) (RHEA:56900)
• a ganglioside GA1 + UDP-N-acetyl-alpha-D-glucosamine = a ganglioside beta-D-GlcNAc-(1->6)-GA1 + UDP + H(+) (RHEA:69691)

UniProt features (29 total): binding site 11, disulfide bond 4, region of interest 3, topological domain 2, glycosylation site 2, sequence variant 2, mutagenesis site 2, chain 1, transmembrane region 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q02742-F1	93.07	0.84

Functional residue map

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

Catalytic / active sites (1): 320 (nucleophile)

Ligand- & substrate-binding residues (11): 187; 243; 251; 254; 320; 341; 358; 378; 401; 128–130; 155–157

Disulfide bonds (4): 59–413, 100–172, 151–199, 372–381

Glycosylation sites (2): 58, 95

Mutagenesis-validated functional residues (2):

Position	Phenotype
5–6	loss of interaction with golph3 and loss of localization to the golgi.
7–9	loss of interaction with golph3 and loss of localization to the golgi.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-913709	O-linked glycosylation of mucins

MSigDB gene sets: 341 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_MATURE_CELL, CROONQUIST_NRAS_SIGNALING_UP, GOBP_REGULATION_OF_LEUKOCYTE_MIGRATION, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GOBP_CELL_CELL_ADHESION, GOBP_CELLULAR_EXTRAVASATION, GOBP_LEUKOCYTE_MIGRATION, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOCC_TRANS_GOLGI_NETWORK, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_REGULATION_OF_CELLULAR_EXTRAVASATION, GOBP_LEUKOCYTE_ADHESION_TO_VASCULAR_ENDOTHELIAL_CELL

GO Biological Process (10): glycoprotein biosynthetic process (GO:0009101), protein O-linked glycosylation via N-acetylgalactosamine (GO:0016266), response to insulin (GO:0032868), tissue morphogenesis (GO:0048729), leukocyte tethering or rolling (GO:0050901), cell adhesion molecule production (GO:0060352), kidney morphogenesis (GO:0060993), positive regulation of leukocyte tethering or rolling (GO:1903238), obsolete protein glycosylation (GO:0006486), obsolete core 2 O-glycan biosynthetic process (GO:0016268)

GO Molecular Function (5): beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829), protein binding (GO:0005515), UDP-glycosyltransferase activity (GO:0008194), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (6): Golgi membrane (GO:0000139), obsolete extracellular space (GO:0005615), trans-Golgi network (GO:0005802), membrane (GO:0016020), Golgi cisterna (GO:0031985), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
O-linked glycosylation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
Golgi apparatus subcompartment	2
macromolecule biosynthetic process	1
glycoprotein metabolic process	1
carbohydrate derivative biosynthetic process	1
protein O-linked glycosylation	1
response to peptide hormone	1
anatomical structure morphogenesis	1
tissue development	1
cellular extravasation	1
leukocyte adhesion to vascular endothelial cell	1
cellular process	1
kidney development	1
animal organ morphogenesis	1
leukocyte tethering or rolling	1
regulation of leukocyte tethering or rolling	1
positive regulation of leukocyte adhesion to vascular endothelial cell	1
acetylglucosaminyltransferase activity	1
catalytic activity, acting on a glycoprotein	1
binding	1
glycosyltransferase activity	1
catalytic activity	1
transferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cellular anatomical structure	1
Golgi stack	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

686 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GCNT1	C1GALT1	Q9NS00	742
GCNT1	ST3GAL4	Q11206	728
GCNT1	ST3GAL1	Q11201	727
GCNT1	FUT7	Q11130	714
GCNT1	B3GNT6	Q6ZMB0	693
GCNT1	ST6GALNAC1	Q9NSC7	655
GCNT1	C1GALT1C1	Q96EU7	654
GCNT1	GALNT12	Q8IXK2	649
GCNT1	POMGNT1	Q8WZA1	606
GCNT1	ST6GAL1	P15907	605
GCNT1	B4GALT5	O43286	605
GCNT1	MGAT5	Q09328	601
GCNT1	ST6GALNAC2	Q9UJ37	592
GCNT1	ST3GAL6	Q9Y274	587
GCNT1	CHST4	Q8NCG5	586

IntAct

50 interactions, top by confidence:

A	B	Type	Score
GCNT1	GOLPH3	psi-mi:“MI:0915”(physical association)	0.610
GOLPH3	GCNT1	psi-mi:“MI:0915”(physical association)	0.610
GOLPH3	GCNT1	psi-mi:“MI:0403”(colocalization)	0.610
GOLPH3	GCNT1	psi-mi:“MI:0407”(direct interaction)	0.610
GCNT1	UBA52	psi-mi:“MI:0914”(association)	0.530
TOR1AIP2	TMEM223	psi-mi:“MI:0914”(association)	0.530
ISLR	BCKDK	psi-mi:“MI:0914”(association)	0.530
CLGN	NPC1	psi-mi:“MI:0914”(association)	0.530
GCNT1	CLTC	psi-mi:“MI:0915”(physical association)	0.370
SEC24D	GCNT1	psi-mi:“MI:0915”(physical association)	0.370
GCNT1	VPS36	psi-mi:“MI:0915”(physical association)	0.370
PARVA	GCNT1	psi-mi:“MI:0915”(physical association)	0.370
GCNT1	STMN2	psi-mi:“MI:0915”(physical association)	0.370
GCNT1	CCT7	psi-mi:“MI:0915”(physical association)	0.370
HSPA14	GCNT1	psi-mi:“MI:0915”(physical association)	0.370
CCDC80	GCNT1	psi-mi:“MI:0915”(physical association)	0.370
LAP3	GCNT1	psi-mi:“MI:0915”(physical association)	0.370
GCNT1	OSBPL1A	psi-mi:“MI:0915”(physical association)	0.370
RSU1	GCNT1	psi-mi:“MI:0915”(physical association)	0.370
SCGB2A2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
ISLR	DDX11L8	psi-mi:“MI:0914”(association)	0.350
PTCH1	PLXNB2	psi-mi:“MI:0914”(association)	0.350
PDGFRA	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CLEC12B	GXYLT2	psi-mi:“MI:0914”(association)	0.350
SCGB2A1	RAP1BL	psi-mi:“MI:0914”(association)	0.350
PSCA	METTL15	psi-mi:“MI:0914”(association)	0.350
KLRC1	METTL15	psi-mi:“MI:0914”(association)	0.350
ST14	LIPT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (49): GCNT1 (Affinity Capture-MS), GCNT1 (Affinity Capture-MS), UBA52 (Affinity Capture-MS), TTC19 (Affinity Capture-MS), GCNT1 (Affinity Capture-MS), GCNT1 (Affinity Capture-MS), GCNT1 (Affinity Capture-MS), SLC25A46 (Affinity Capture-MS), LRP1 (Affinity Capture-MS), GCNT1 (Affinity Capture-MS), GCNT1 (Affinity Capture-RNA), GCNT1 (Affinity Capture-MS), GCNT1 (Affinity Capture-MS), GCNT1 (Affinity Capture-MS), GCNT1 (Affinity Capture-MS)

ESM2 similar proteins: A2AJQ3, A2AUQ7, A5GFW8, A6NG13, A7RX69, D3ZNQ3, E1BPQ3, E9PU17, E9PX95, E9Q649, G3V9Q9, O15466, P0DN25, P23336, P27473, P38566, P38567, P48794, P61646, P97402, Q02742, Q09324, Q21389, Q2NKH9, Q2YDM8, Q3L7M0, Q3SX46, Q499P3, Q4R5T7, Q4V8F8, Q53G44, Q5U258, Q5ZLK4, Q6ZNI0, Q6ZXC8, Q71SG7, Q7Z388, Q7Z4J2, Q812F3, Q8BV66

Diamond homologs: A5GFW8, E9Q649, O95395, P97402, Q02742, Q09324, Q1M0V6, Q3V3K7, Q5JCT0, Q5U258, Q6ZNI0, Q71SG7, Q7YQE1, Q805R1, Q80RC7, Q866Z4, Q866Z5, Q866Z6, Q8CH87, Q8N0V5, Q92180, Q99CW3, Q9IZK2, Q9P109, Q5QQ53, Q7KVA1, Q5QQ54, Q5QQ55

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2743 predictions. Top by Δscore:

Variant	Effect	Δscore
9:76501009:G:GT	donor_gain	1.0000
9:76501026:GCAC:G	donor_gain	1.0000
9:76501029:C:CG	donor_gain	1.0000
9:76501029:C:G	donor_gain	1.0000
9:76501033:G:GG	donor_gain	1.0000
9:76614596:CAATA:C	acceptor_gain	1.0000
9:76614599:TA:T	acceptor_gain	1.0000
9:76614601:C:CC	acceptor_gain	1.0000
9:76636465:CTGTA:C	donor_loss	1.0000
9:76636466:TGTAC:T	donor_loss	1.0000
9:76636467:GTAC:G	donor_loss	1.0000
9:76636468:TAC:T	donor_loss	1.0000
9:76636469:A:C	donor_loss	1.0000
9:76636470:C:G	donor_loss	1.0000
9:76636553:TCAAC:T	acceptor_gain	1.0000
9:76636554:CAAC:C	acceptor_gain	1.0000
9:76636554:CAACC:C	acceptor_gain	1.0000
9:76636555:AAC:A	acceptor_gain	1.0000
9:76636556:AC:A	acceptor_gain	1.0000
9:76636556:ACCT:A	acceptor_loss	1.0000
9:76636557:CC:C	acceptor_gain	1.0000
9:76636558:C:CC	acceptor_gain	1.0000
9:76636559:T:A	acceptor_loss	1.0000
9:76636563:T:C	acceptor_gain	1.0000
9:76636563:T:TC	acceptor_gain	1.0000
9:76637417:CCGT:C	donor_gain	1.0000
9:76637545:CATAT:C	acceptor_gain	1.0000
9:76638182:TCA:T	donor_loss	1.0000
9:76638183:CA:C	donor_loss	1.0000
9:76638184:A:AC	donor_gain	1.0000

AlphaMissense

2862 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:76503449:G:C	W356C	0.997
9:76503449:G:T	W356C	0.997
9:76503522:T:A	C381S	0.997
9:76503523:G:C	C381S	0.997
9:76503348:T:A	W323R	0.996
9:76503348:T:C	W323R	0.996
9:76503523:G:A	C381Y	0.996
9:76502978:C:G	C199W	0.995
9:76503039:G:C	D220H	0.995
9:76503447:T:A	W356R	0.995
9:76503447:T:C	W356R	0.995
9:76503495:T:A	C372S	0.995
9:76503496:G:A	C372Y	0.995
9:76503496:G:C	C372S	0.995
9:76503522:T:C	C381R	0.995
9:76503524:C:G	C381W	0.995
9:76502825:T:A	N148K	0.994
9:76502825:T:G	N148K	0.994
9:76503009:T:A	W210R	0.994
9:76503009:T:C	W210R	0.994
9:76503584:G:C	K401N	0.994
9:76503584:G:T	K401N	0.994
9:76502834:C:G	C151W	0.993
9:76503523:G:T	C381F	0.993
9:76503497:C:G	C372W	0.992
9:76503577:C:A	A399D	0.992
9:76503582:A:G	K401E	0.992
9:76502752:C:A	A124E	0.991
9:76502754:T:G	Y125D	0.991
9:76502977:G:A	C199Y	0.991

dbSNP variants (sampled 300 via entrez): RS1000160736 (9:76488802 C>T), RS1000254164 (9:76466462 T>A), RS1000318647 (9:76484159 T>C), RS1000470981 (9:76449382 C>T), RS1000545214 (9:76442620 G>A,T), RS1000600236 (9:76472360 T>C), RS1000648717 (9:76467815 G>A), RS1000684172 (9:76506180 T>C), RS1000786987 (9:76499880 T>C), RS1000806385 (9:76461867 C>T), RS1000829050 (9:76487671 C>CT), RS1000838316 (9:76500173 T>C), RS1000890038 (9:76450554 A>C), RS1000901054 (9:76497798 T>G), RS1000937519 (9:76455832 A>G)

Disease associations

OMIM: gene MIM:600391 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001066_11	Dialysis-related mortality	7.000000e-06
GCST003265_319	Post bronchodilator FEV1/FVC ratio in COPD	2.000000e-06
GCST003941_14	Acute graft versus host disease in bone marrow transplantation (recipient effect)	2.000000e-07
GCST012139_4	D-dimer levels in HIV infection	2.000000e-08
GCST90002393_377	Monocyte count	5.000000e-10

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004713	FEV/FVC ratio
EFO:0004599	acute graft vs. host disease
EFO:0004507	D dimer measurement
EFO:0005091	monocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2321632 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	6
trichostatin A	affects cotreatment, decreases expression	3
Progesterone	affects cotreatment, decreases expression, increases expression	3
methylmercuric chloride	decreases expression	2
sodium arsenite	increases expression	2
mercuric bromide	decreases expression, affects cotreatment	2
Vorinostat	affects cotreatment, decreases expression	2
Nickel	increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
bisphenol A	decreases expression	1
lead acetate	increases expression	1
decabromobiphenyl ether	decreases expression	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
potassium chromate(VI)	decreases expression, affects cotreatment	1
cupric chloride	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
seocalcitol	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Zoledronic Acid	decreases expression	1
Ethanol	affects cotreatment, increases expression	1
Cadmium	increases abundance, increases expression	1
Calcitriol	decreases 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
CHEMBL2329324	Binding	Inhibition of human C2GnT1 using Galbeta3GalNAcalpha-Bn as substrate at 0.5 mM after 1 hr in presence of phosphatidylcholine	Selective inhibition of glycosyltransferases by bivalent imidazolium salts. — Bioorg Med Chem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_HG14	T47D-E2J	Cancer cell line	Female
CVCL_HG16	T47D-StN	Cancer cell line	Female

Clinical trials (associated diseases)

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