C1GALT1

Summary

C1GALT1 (core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1, HGNC:24337) is a protein-coding gene on chromosome 7p22.1-p21.3, encoding Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 (Q9NS00). Glycosyltransferase that generates the core 1 O-glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins.

The protein encoded by this gene generates the common core 1 O-glycan structure, Gal-beta-1-3GalNAc-R, by the transfer of Gal from UDP-Gal to GalNAc-alpha-1-R. Core 1 is a precursor for many extended mucin-type O-glycans on cell surface and secreted glycoproteins. Studies in mice suggest that this gene plays a key role in thrombopoiesis and kidney homeostasis.

Source: NCBI Gene 56913 — RefSeq curated summary.

At a glance

• GWAS associations: 20
• Clinical variants (ClinVar): 72 total — 1 pathogenic
• Druggable target: yes
• MANE Select transcript: NM_020156

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24337
Approved symbol	C1GALT1
Name	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1
Location	7p22.1-p21.3
Locus type	gene with protein product
Status	Approved
Aliases	C1GALT, T-synthase
Ensembl gene	ENSG00000106392
Ensembl biotype	protein_coding
OMIM	610555
Entrez	56913

Gene structure

Transcript identifiers

Ensembl transcripts: 50 — 48 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000223122, ENST00000402468, ENST00000429911, ENST00000436587, ENST00000467716, ENST00000476068, ENST00000910742, ENST00000910743, ENST00000910744, ENST00000910745, ENST00000910746, ENST00000910747, ENST00000910748, ENST00000910749, ENST00000910750, ENST00000910751, ENST00000910752, ENST00000910753, ENST00000910754, ENST00000910755, ENST00000910756, ENST00000910757, ENST00000910758, ENST00000910759, ENST00000910760, ENST00000910761, ENST00000910762, ENST00000910763, ENST00000910764, ENST00000910765, ENST00000910766, ENST00000910767, ENST00000910768, ENST00000933051, ENST00000933052, ENST00000933053, ENST00000933054, ENST00000933055, ENST00000933056, ENST00000933057, ENST00000933058, ENST00000933059, ENST00000933060, ENST00000933061, ENST00000933062, ENST00000933063, ENST00000933064, ENST00000933065, ENST00000933066, ENST00000952097

RefSeq mRNA: 1 — MANE Select: NM_020156 NM_020156

CCDS: CCDS5355

Canonical transcript exons

ENST00000436587 — 4 exons

Exon	Start	End
ENSE00000671246	7238255	7238922
ENSE00000831717	7243524	7248616
ENSE00001552786	7234303	7234539
ENSE00001673680	7182544	7182820

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 95.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.9448 / max 397.2214, expressed in 1793 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
77176	14.1161	1778
77175	3.7491	1248
77178	1.0407	569
77173	0.6399	255
77174	0.5392	212
204347	0.4135	213
77177	0.3613	177
77172	0.0849	31

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
amniotic fluid	UBERON:0000173	95.11	gold quality
secondary oocyte	CL:0000655	94.64	gold quality
corpus callosum	UBERON:0002336	93.39	gold quality
choroid plexus epithelium	UBERON:0003911	91.78	gold quality
monocyte	CL:0000576	91.72	gold quality
pylorus	UBERON:0001166	91.72	gold quality
mononuclear cell	CL:0000842	91.32	gold quality
leukocyte	CL:0000738	91.10	gold quality
nephron tubule	UBERON:0001231	91.00	gold quality
palpebral conjunctiva	UBERON:0001812	90.88	gold quality
esophagus squamous epithelium	UBERON:0006920	90.80	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	90.62	gold quality
lower esophagus mucosa	UBERON:0035834	90.48	gold quality
oocyte	CL:0000023	90.41	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.38	gold quality
islet of Langerhans	UBERON:0000006	90.02	gold quality
eye	UBERON:0000970	89.97	gold quality
spinal cord	UBERON:0002240	89.76	gold quality
right uterine tube	UBERON:0001302	89.07	gold quality
calcaneal tendon	UBERON:0003701	89.02	gold quality
parotid gland	UBERON:0001831	89.00	gold quality
buccal mucosa cell	CL:0002336	88.99	gold quality
cardia of stomach	UBERON:0001162	88.97	gold quality
esophagus mucosa	UBERON:0002469	88.96	gold quality
rectum	UBERON:0001052	88.84	gold quality
gall bladder	UBERON:0002110	88.38	gold quality
epithelium of esophagus	UBERON:0001976	88.18	gold quality
superior surface of tongue	UBERON:0007371	88.08	gold quality
kidney epithelium	UBERON:0004819	88.05	gold quality
tendon	UBERON:0000043	87.94	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-75688	yes	534.09
E-ANND-3	yes	11.08
E-MTAB-6524	no	230.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

212 targeting C1GALT1, 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-5692A	100.00	74.40	6850
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-5696	99.98	72.36	4487
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787

Literature-anchored findings (GeneRIF, showing 40)

• Tn syndrome is associated with a somatic mutation in Cosmc, a gene on the X chromosome that encodes a molecular ‘chaperone’ that is required for the proper folding and hence full activity of T-synthase (PMID:16251947)
• The present study suggested that the polymorphisms of C1GALT1 gene were associated with the genetic susceptibility to IgAN in Chinese population. (PMID:17228361)
• These results suggest that the intracellular dynamics of C1GalT is controlled by its specific molecular chaperon, Cosmc, in association with core 1 synthase activity. (PMID:18061573)
• Lectin staining and blotting experiments confirmed that C1GalTA contributes to the synthesis of Gal-beta1,3-GalNAc in vivo (PMID:18985719)
• Systematic determination of the peptide acceptor preferences for the human UDP-Gal:glycoprotein-alpha-GalNac beta 3-galactosyltransferase (T synthase) are reported. (PMID:19073881)
• The 1365G allele and 1365G/G genotype of C1GalT1 seem to confer susceptibility to IgA nephropathy. (PMID:19229831)
• potential genetic interactions of C1GALT1 and ST6GALNAC2 variants influence IgA1 O-glycosylation, disease predisposition, and disease severity, and may contribute to the polygenic nature of IgA nephropathy (PMID:19357720)
• Data show that the sequences and O-glycosylation patterns direct the addition of the first and second sugar residues by ppGalNAc-T and C1GalT which act in a site directed fashion. (PMID:19524017)
• knockdown of T-synthase resulted in decreased cell surface O-glycosylation, reduced cell surface galectin-3, and increased epithelial permeability. (PMID:19556244)
• The chaperone activity of Cosmc is specific, does not require ATP in vitro, and is effective toward T-synthase but not another beta-galactosyltransferase (PMID:19923218)
• Results indicate that Cosmc mediates the co-translational activation of C1GalT and that it may prevent the unfavorable aggregation of C1GalT. (PMID:21496458)
• C1GALT1 polymorphisms influence the risk to develop IgA nephropathy and proteinuria. (PMID:22131235)
• Results show that soluble Cosmc directly interacts in a specific manner with denatured, but not native, T-synthase to form a noncovalent and reversible complex that results in the acquisition of T-synthase catalytic activity. (PMID:22416136)
• Down-regulation of C1GalT1 is correlated with breast cancer (PMID:22534569)
• our study suggested that the 1365 G/A polymorphism of the C1GALT1 gene may contribute to Henoch-Schonlein purpura nephritis development (PMID:22544166)
• using RNA interfering system targeting the core 1 ss1,3-galactosyltransferase to explore the role of mucin-type carbohydrates in apical endocytic trafficking in human corneal keratinocytes (PMID:22574202)
• Data show that the Golgi docking of vesicular complexes (VCs) use different golgins for docking: C2GnT-M-carrying VC (C2GnT-M-VC) utilizes Giantin, whereas C1GalT1-VC employs GM130-GRASP65 complex. (PMID:22988244)
• The MDR analysis showed a potential interaction of C1GALT1-330G/T (rs1008898) and IL5RA31+197A/G (rs340833) on the susceptibility of IgAN (P<0.001). Gene-gene interaction may have some influence on the susceptibility to IgA nephropathy. (PMID:23190752)
• Suppression of core 1 Gal-transferase is associated with reduction of TF and reciprocal increase of Tn, sialyl-Tn and Core 3 glycans in human colon cancer cells. (PMID:23536887)
• Variations in the C1GALT1 gene were found to be associated with Henoch-Schonlein purpura risk. (PMID:23624553)
• High C1GALT1 enhances proliferation of hepatocellular carcinoma cells via modulating MET glycosylation and dimerization. (PMID:23832667)
• Il-6 and Il-4 reduced galactosylation of the O-glycan substrate directly via decreased expression of the galactosyltransferase C1GalT1 and, indirectly, via increased expression of the sialyltransferase ST6GalNAc-II (PMID:24398680)
• Data indicate that cytotoxin associated gene A protein (CagA) promoted the underglycosylation of IgA1, which at least partly attributed to the downregulation of beta1,3-galactosyltransferase (C1GALT1) and its chaperone Cosmc. (PMID:24462875)
• C1GALT1 overexpression modifies O-glycans on FGFR2 and enhances its phosphorylation to promote the invasive behavior and cancer stem-like property in colon cancer cells. (PMID:24758762)
• Using qRT-PCR, sialyl-Tn expression was found to be associated with an increase in alpha2,6-sialyltransferase gene (ST6GALNAC1) and a decrease in core 1 synthase gene (C1GALT1) in LS174T cells. (PMID:24840470)
• C1GALT1 promotes invasive phenotypes of hepatocellular carcinoma cells by modulating integrin beta1 glycosylation and activity. (PMID:25089569)
• Overexpression of C1GALT1 enhanced breast cancer cell growth, migration, and invasion in vitro as well as tumor growth in vivo. (PMID:25762620)
• Cosmc and T-synthase are transcriptionally regulated at a basal level by the specificity protein/Kruppel-like transcription factor family of members. (PMID:26063800)
• Polymorphisms in the C1GALT1 gene were associated with genetic susceptibility to Uyghur Immunoglobulin A (IgA) nephropathy. (PMID:26125729)
• There was no statistically significant difference between the two groups (P > 0.05). The rs1047763 SNP of the C1GALT1 gene probably has no correlation with genetic susceptibility to IgAN in Xinjiang Uyghur people. (PMID:26782518)
• Polymorphisms near C1galt1 (rs10486157) and its molecular chaperone, Cosmc (rs4825729), were associated with altered composition of the colonic mucosal microbiota in Crohn’s disease patients. (PMID:27874308)
• The terminal glycosylation of secreted IgA1 was altered in response to TGFbeta1. TGFbeta1 stimulation significantly decreased the mRNA levels of C1GalT1 and Cosmc. TGFbeta1 may be key in controlling the glycosylation of IgA1, in part via the downregulation of C1GalT1 and Cosmc. (PMID:28035353)
• Data indicate that mRNA levels of both core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 (C1GALT1) and C1GALT1-specific chaperone 1 protein (C1GALT1C1) determine the rate of secretion of galactose-deficient IgA1 (Gd-IgA1) in IgA1-producing cells. (PMID:28187132)
• These findings demonstrate that common variation at C1GALT1 influences Gd-IgA1 level in the population, which independently associates with risk of progressive IgA nephropathy, and that the pathogenic importance of changes in IgA1 O-glycosylation may vary between white and Chinese patients with IgA nephropathy (PMID:28209808)
• C1GALT1 modifies O-glycan expression and enhances malignant behaviors in ovarian cancer cells, suggesting that C1GALT1 plays a role in the pathogenesis of ovarian cancer. (PMID:28498248)
• There was no relationship between rs1047763 and rs1008898 C1GALT1 polymorphisms and susceptibility to IgA nephropathy. (Meta-analysis) (PMID:28636500)
• C1GALT1 predicts poor prognosis and is a potential therapeutic target in head and neck cancer. (PMID:29930379)
• findings indicate that T-synthase deficiency in colorectal cancer cells not only is responsible for aberrant O-glycosylation, but also triggers the molecular process of EMT pathway, which may translate to increased invasiveness and metastasis in cancers (PMID:30035127)
• In addition, we found that Tn-expressing colorectal cancers (CRC) cell lines had either loss-of-function mutations in Cosmc or reversible Tn antigen expression, which was not caused by the deficiency of T-synthase activity (PMID:30115016)
• GM130 expression was significantly decreased in tonsil tissues and peripheral blood mononuclear cells of IgA nephropathy (IgAN) patients. Downregulation of GM130 can increase IgA1 O-glycosylation deficiency, which is thought to reduce C1GALT1 expression but not affect the expression of ST6GalNAC2. GM130 plays an important role in IgA1 O-glycans deficiency in IgAN patients, by negatively regulating C1GALT1 expression. (PMID:30917363)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
mus_musculus	C1galt1	ENSMUSG00000042460
rattus_norvegicus	C1galt1	ENSRNOG00000007804
drosophila_melanogaster	tgy	FBGN0030984
drosophila_melanogaster	CG18558	FBGN0031469
drosophila_melanogaster	CG2983	FBGN0031472
drosophila_melanogaster	CG34057	FBGN0054057
caenorhabditis_elegans		WBGENE00008019

Paralogs (2): C1GALT1C1 (ENSG00000171155), C1GALT1C1L (ENSG00000223658)

Protein

Protein identifiers

Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 — Q9NS00 (reviewed: Q9NS00)

Alternative names: B3Gal-T8, Core 1 O-glycan T-synthase, Core 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase 1, Core 1 beta1,3-galactosyltransferase 1

All UniProt accessions (3): Q9NS00, A0A024RA32, C9K0C8

UniProt curated annotations — full annotation on UniProt →

Function. Glycosyltransferase that generates the core 1 O-glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins. Plays a central role in many processes, such as angiogenesis, thrombopoiesis and kidney homeostasis development.

Subunit / interactions. Homodimer; disulfide-linked. Interacts with the C1GALT1C1 chaperone; required for galactosyltransferase activity.

Subcellular location. Membrane.

Tissue specificity. Widely expressed. Highly expressed in kidney, heart, placenta and liver.

Pathway. Protein modification; protein glycosylation.

Miscellaneous. Aberrant O-galactosylation of IgA1 molecules plays a role in the development and progression of IgA nephropathy (IgAN). Genetic interactions of C1GALT1 and ST6GALNAC2 variants influence IgA1 O-glycosylation, disease predisposition, and disease severity, and may contribute to the polygenic nature of IgAN.

Similarity. Belongs to the glycosyltransferase 31 family. Beta3-Gal-T subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NS00-1	1	yes
Q9NS00-2	2

RefSeq proteins (1): NP_064541* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003378	Fringe-like_glycosylTrfase	Domain
IPR026050	C1GALT1/C1GALT1_chp1	Family

Pfam: PF02434

Enzyme classification (BRENDA):

• EC 2.4.1.122 — N-acetylgalactosaminide beta-1,3-galactosyltransferase (BRENDA: 10 organisms, 63 substrates, 10 inhibitors, 10 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

6 substrates with measured Km, best-characterized 6. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
UDP-GALACTOSE	0.02–0.63	3
ASIALO-MUCIN OF COWPER’S GLAND	0.0003–0.09	2
A-P-(N-ACETYL-D-GALACTOSAMINYL)T-S-S-A	0.55	1
ASIALO OVINE SUBMAXILLARY MUCIN	5	1
N-ACETYL-ALPHA-D-GALACTOSAMINYL-BENZYL	1.7	1
N-ACETYL-ALPHA-D-GALACTOSAMINYL-PHENYL	0.76	1

Catalyzed reactions (Rhea), 3 shown:

• an N-acetyl-alpha-D-galactosaminyl derivative + UDP-alpha-D-galactose = a beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl derivative + UDP + H(+) (RHEA:15621)
• a 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-alpha-D-galactose = a 3-O-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP + H(+) (RHEA:56196)
• a 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-alpha-D-galactose = a 3-O-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP + H(+) (RHEA:56200)

UniProt features (30 total): binding site 12, mutagenesis site 6, disulfide bond 3, topological domain 2, compositionally biased region 2, chain 1, modified residue 1, transmembrane region 1, splice variant 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NS00-F1	88.43	0.67

Functional residue map

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

Ligand- & substrate-binding residues (12): 140; 146; 169; 169; 171; 285; 309; 309; 310; 94; 138; 139

Post-translational modifications (1): 235

Disulfide bonds (3): 91–115, 232–246, 300–301

Mutagenesis-validated functional residues (6):

Position	Phenotype
140	reduced activity.
201	reduced activity.
206	reduced activity.
240	inactive.
285	inactive.
310	reduced activity.

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-5083632	Defective C1GALT1C1 causes TNPS
R-HSA-913709	O-linked glycosylation of mucins
R-HSA-1643685	Disease
R-HSA-3781865	Diseases of glycosylation
R-HSA-3906995	Diseases associated with O-glycosylation of proteins
R-HSA-392499	Metabolism of proteins
R-HSA-5173105	O-linked glycosylation
R-HSA-5668914	Diseases of metabolism
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 179 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_EPITHELIAL_CELL_DEVELOPMENT, FISCHER_G1_S_CELL_CYCLE, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, chr7p22, GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT, JIANG_TIP30_TARGETS_UP, GOBP_INTESTINAL_EPITHELIAL_CELL_DEVELOPMENT, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_BLOOD_VESSEL_MORPHOGENESIS, ACATTCC_MIR1_MIR206, GOBP_INTESTINAL_EPITHELIAL_CELL_DIFFERENTIATION

GO Biological Process (6): angiogenesis (GO:0001525), kidney development (GO:0001822), protein O-linked glycosylation (GO:0006493), intestinal epithelial cell development (GO:0060576), obsolete protein glycosylation (GO:0006486), cell differentiation (GO:0030154)

GO Molecular Function (6): nucleotide binding (GO:0000166), N-acetylgalactosaminide beta-1,3-galactosyltransferase activity (GO:0016263), metal ion binding (GO:0046872), protein binding (GO:0005515), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (2): Golgi membrane (GO:0000139), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
Diseases associated with O-glycosylation of proteins	1
O-linked glycosylation	1
Diseases of metabolism	1
Diseases of glycosylation	1
Post-translational protein modification	1
Disease	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
blood vessel morphogenesis	1
anatomical structure formation involved in morphogenesis	1
animal organ development	1
renal system development	1
glycoprotein biosynthetic process	1
columnar/cuboidal epithelial cell development	1
intestinal epithelial cell differentiation	1
cellular developmental process	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
UDP-galactosyltransferase activity	1
beta-1,3-galactosyltransferase activity	1
catalytic activity, acting on a glycoprotein	1
cation binding	1
binding	1
catalytic activity	1
transferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

936 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1GALT1	B3GALT5	Q9Y2C3	944
C1GALT1	B3GALT1	Q9Y5Z6	877
C1GALT1	B4GALT2	O60909	861
C1GALT1	B3GALT2	O43825	846
C1GALT1	ST6GALNAC1	Q9NSC7	817
C1GALT1	ST3GAL1	Q11201	748
C1GALT1	GALNT2	Q10471	747
C1GALT1	GCNT1	Q02742	742
C1GALT1	B3GNT6	Q6ZMB0	739
C1GALT1	GALNT6	Q8NCL4	738
C1GALT1	ST6GALNAC2	Q9UJ37	737
C1GALT1	GCNT3	O95395	720
C1GALT1	GCNT4	Q9P109	701
C1GALT1	EEF1A2	P54266	669
C1GALT1	B4GALT4	O60513	621

IntAct

29 interactions, top by confidence:

A	B	Type	Score
CD27	TCAF2	psi-mi:“MI:0914”(association)	0.640
LRRC15	TCAF2	psi-mi:“MI:0914”(association)	0.560
DPEP1	ILVBL	psi-mi:“MI:0914”(association)	0.530
CRP	QSOX1	psi-mi:“MI:0914”(association)	0.530
HFE	ADAM10	psi-mi:“MI:0914”(association)	0.530
C1GALT1	C1GALT1C1	psi-mi:“MI:0407”(direct interaction)	0.440
C1GALT1C1	C1GALT1	psi-mi:“MI:0407”(direct interaction)	0.440
C1GALT1	HSP90B1	psi-mi:“MI:0915”(physical association)	0.400
DYRK1A	TEX13D	psi-mi:“MI:0914”(association)	0.350
CHRNB2	TMEM131L	psi-mi:“MI:0914”(association)	0.350
CCL3	KRBA1	psi-mi:“MI:0914”(association)	0.350
NPPB	TCAF2	psi-mi:“MI:0914”(association)	0.350
ST14	LIPT2	psi-mi:“MI:0914”(association)	0.350
CX3CL1	FAM171A2	psi-mi:“MI:0914”(association)	0.350
CSPG5	TCAF2	psi-mi:“MI:0914”(association)	0.350
TMPRSS13	TOR1A	psi-mi:“MI:0914”(association)	0.350
HPN	TOR1A	psi-mi:“MI:0914”(association)	0.350
C1orf54	QSOX1	psi-mi:“MI:0914”(association)	0.350
C1QTNF9B	DNASE2	psi-mi:“MI:0914”(association)	0.350
CX3CL1	ANKRD13A	psi-mi:“MI:0914”(association)	0.350
FAM20B	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
GDPD5	TMEM120B	psi-mi:“MI:0914”(association)	0.350
POMGNT2	FAM83G	psi-mi:“MI:0914”(association)	0.350
TNFSF13	FADS1	psi-mi:“MI:0914”(association)	0.350
SLC37A4	PGRMC1	psi-mi:“MI:0914”(association)	0.350

BioGRID (59): C1GALT1 (Affinity Capture-MS), C1GALT1 (Affinity Capture-MS), C1GALT1 (Affinity Capture-MS), C1GALT1 (Affinity Capture-MS), C1GALT1 (Affinity Capture-MS), C1GALT1 (Affinity Capture-MS), C1GALT1 (Two-hybrid), C1GALT1 (Two-hybrid), C1GALT1 (Two-hybrid), SLC1A1 (Two-hybrid), GPRC5D (Two-hybrid), ELOVL4 (Two-hybrid), GJA8 (Two-hybrid), FAM210B (Two-hybrid), FAM209A (Two-hybrid)

ESM2 similar proteins: A0A2C9JXL4, E9Q649, O95395, P0DN25, P97402, Q08BL3, Q0VC84, Q18515, Q24342, Q3SX46, Q499P3, Q5F3G7, Q5HZL5, Q5U258, Q5XJP0, Q5YB40, Q66GS2, Q6A1G2, Q6DE15, Q6DJR8, Q6GNL1, Q6P3P5, Q6P6V1, Q6WV16, Q6Y288, Q7K237, Q7SYI5, Q7T3S5, Q7Z1Z1, Q864U8, Q866Z5, Q8BGY6, Q8BHT6, Q8L7M1, Q8LPF8, Q8N0V5, Q8NCW6, Q96EU7, Q99NB2, Q9BYG0

Diamond homologs: A0A2C9JXL4, Q08BL3, Q0VC84, Q18515, Q5F3G7, Q6GNL1, Q7K237, Q7SYI5, Q9JJ05, Q9JJ06, Q9NS00, Q3SX46, Q499P3, Q66GS2, Q96EU7, Q9JMG2, Q5DTK1, Q70JA7, Q86X52, Q7Z1Z1, Q6KFX9, Q6ZQ11, Q76KP1, Q8BJQ9, Q8C1F4, Q8N6G5, Q8TDX6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	51
Likely benign	11
Benign	2

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
57254	GRCh38/hg38 7p22.1-21.3(chr7:6106402-11012657)x1	Pathogenic

SpliceAI

1464 predictions. Top by Δscore:

Variant	Effect	Δscore
7:7234537:AAGGT:A	donor_loss	1.0000
7:7234538:AGGT:A	donor_loss	1.0000
7:7234539:GGT:G	donor_loss	1.0000
7:7234540:GTATG:G	donor_loss	1.0000
7:7234541:T:G	donor_loss	1.0000
7:7235068:T:G	donor_gain	0.9900
7:7238253:A:AG	acceptor_gain	0.9900
7:7238254:G:GG	acceptor_gain	0.9900
7:7237504:T:TA	acceptor_gain	0.9800
7:7238249:TAATA:T	acceptor_loss	0.9800
7:7238250:AATAG:A	acceptor_loss	0.9800
7:7238251:ATAG:A	acceptor_loss	0.9800
7:7238252:TAGAT:T	acceptor_loss	0.9800
7:7238253:A:T	acceptor_loss	0.9800
7:7238254:G:GA	acceptor_loss	0.9800
7:7238254:GAT:G	acceptor_gain	0.9800
7:7238254:GATGA:G	acceptor_gain	0.9800
7:7238920:GAG:G	donor_gain	0.9800
7:7238923:G:GG	donor_gain	0.9800
7:7185471:GAT:G	donor_gain	0.9700
7:7234301:A:AG	acceptor_gain	0.9700
7:7234302:G:GG	acceptor_gain	0.9700
7:7234302:GA:G	acceptor_gain	0.9700
7:7234302:GAA:G	acceptor_gain	0.9700
7:7234540:G:GG	donor_gain	0.9700
7:7237529:A:AG	acceptor_gain	0.9700
7:7238921:AGGT:A	donor_loss	0.9700
7:7238922:GGT:G	donor_loss	0.9700
7:7238923:G:T	donor_loss	0.9700
7:7238924:T:A	donor_loss	0.9700

AlphaMissense

2411 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:7238365:T:A	W111R	1.000
7:7238365:T:C	W111R	1.000
7:7238535:A:C	K167N	1.000
7:7238535:A:T	K167N	1.000
7:7238546:A:T	D171V	1.000
7:7243560:C:G	H309D	1.000
7:7238305:T:C	C91R	0.999
7:7238307:C:G	C91W	0.999
7:7238308:T:A	W92R	0.999
7:7238308:T:C	W92R	0.999
7:7238367:G:C	W111C	0.999
7:7238367:G:T	W111C	0.999
7:7238471:A:T	K146I	0.999
7:7238472:A:C	K146N	0.999
7:7238472:A:T	K146N	0.999
7:7238524:T:A	W164R	0.999
7:7238524:T:C	W164R	0.999
7:7238539:G:C	D169H	0.999
7:7238540:A:T	D169V	0.999
7:7238542:G:C	D170H	0.999
7:7238543:A:T	D170V	0.999
7:7238545:G:C	D171H	0.999
7:7238546:A:C	D171A	0.999
7:7238546:A:G	D171G	0.999
7:7238617:G:T	G195W	0.999
7:7238618:G:A	G195E	0.999
7:7238656:A:C	S208R	0.999
7:7238658:T:A	S208R	0.999
7:7238658:T:G	S208R	0.999
7:7238660:G:A	G209E	0.999

dbSNP variants (sampled 300 via entrez): RS1000019287 (7:7159176 A>T), RS1000070691 (7:7187417 T>C), RS1000094874 (7:7189793 A>T), RS1000125738 (7:7177211 G>T), RS1000127700 (7:7168516 C>G), RS1000173015 (7:7214558 G>A), RS1000195289 (7:7207922 C>A), RS1000285588 (7:7174482 G>A,T), RS1000292464 (7:7207753 G>A,C), RS1000332152 (7:7207568 T>G), RS1000378350 (7:7196525 C>T), RS1000459437 (7:7169900 A>G), RS1000459887 (7:7182883 C>A,G,T), RS1000471909 (7:7196342 CT>C), RS1000570250 (7:7204694 A>G)

Disease associations

OMIM: gene MIM:610555 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

20 associations (top):

Study	Trait	p-value
GCST000266_4	Multiple sclerosis (severity)	4.000000e-06
GCST001523_27	Visceral adipose tissue adjusted for BMI	4.000000e-06
GCST002361_23	Smooth-surface caries	6.000000e-06
GCST003518_32	Daytime sleep phenotypes	2.000000e-06
GCST003542_173	Night sleep phenotypes	8.000000e-06
GCST003670_4	Systolic blood pressure	3.000000e-06
GCST004159_1	Serum galactose-deficient IgA1 levels	8.000000e-07
GCST004159_3	Serum galactose-deficient IgA1 levels	5.000000e-08
GCST004185_1	Lung function (FEV1/FVC)	2.000000e-08
GCST005194_227	Coronary artery disease	2.000000e-06
GCST006218_57	Erosive tooth wear (severe vs non-severe)	7.000000e-08
GCST006627_28	Diastolic blood pressure	3.000000e-12
GCST007430_111	Peak expiratory flow	1.000000e-07
GCST007431_147	Lung function (FEV1/FVC)	9.000000e-13
GCST007432_176	FEV1	5.000000e-08
GCST007611_1	Chronic obstructive pulmonary disease or high blood pressure (pleiotropy)	7.000000e-18
GCST007930_136	Medication use (agents acting on the renin-angiotensin system)	4.000000e-11
GCST010002_342	Refractive error	2.000000e-17
GCST90011884_1	Serum galactose-deficient IgA1 levels in IgA nephropathy	1.000000e-09
GCST90011899_140	Aspartate aminotransferase levels	2.000000e-11

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0007828	daytime rest measurement
EFO:0006335	systolic blood pressure
EFO:0004713	FEV/FVC ratio
EFO:0006336	diastolic blood pressure
EFO:0009718	peak expiratory flow
EFO:0004314	forced expiratory volume
EFO:0009931	Agents acting on the renin-angiotensin system use measurement
EFO:0004736	aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2321633 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, affects cotreatment, increases expression	6
Panobinostat	affects cotreatment, increases expression	2
Air Pollutants	decreases expression, increases abundance	2
Nickel	increases expression	2
Phenylmercuric Acetate	increases expression, affects cotreatment	2
Smoke	increases abundance, decreases expression	2
Cadmium Chloride	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	increases expression	1
trichostatin A	increases expression	1
sodium arsenite	affects expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
K 7174	increases expression	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
jinfukang	decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Coal	decreases expression, increases abundance	1
Demecolcine	decreases expression	1
Ivermectin	decreases expression	1
Ketoconazole	decreases expression	1
Quercetin	decreases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	increases 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
CHEMBL2329325	Binding	Inhibition of human C1GalT GlcNAc-transferase using GlcNAcalpha-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

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D9AE	Ubigene HEK293 C1GALT1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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