GALNT1

Summary

GALNT1 (polypeptide N-acetylgalactosaminyltransferase 1, HGNC:4123) is a protein-coding gene on chromosome 18q12.2, encoding Polypeptide N-acetylgalactosaminyltransferase 1 (Q10472). Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor.

This gene encodes a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAc-T) family of enzymes. GalNAc-Ts initiate mucin-type O-linked glycosylation in the Golgi apparatus by catalyzing the transfer of GalNAc to serine and threonine residues on target proteins. They are characterized by an N-terminal transmembrane domain, a stem region, a lumenal catalytic domain containing a GT1 motif and Gal/GalNAc transferase motif, and a C-terminal ricin/lectin-like domain. GalNAc-Ts have different, but overlapping, substrate specificities and patterns of expression. Transcript variants derived from this gene that utilize alternative polyA signals have been described in the literature.

Source: NCBI Gene 2589 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 37 total
• Druggable target: yes
• MANE Select transcript: NM_020474

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4123
Approved symbol	GALNT1
Name	polypeptide N-acetylgalactosaminyltransferase 1
Location	18q12.2
Locus type	gene with protein product
Status	Approved
Aliases	GalNAc-T1
Ensembl gene	ENSG00000141429
Ensembl biotype	protein_coding
OMIM	602273
Entrez	2589

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 26 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000269195, ENST00000586725, ENST00000589189, ENST00000590654, ENST00000591081, ENST00000591924, ENST00000909612, ENST00000909613, ENST00000909614, ENST00000909615, ENST00000935563, ENST00000935564, ENST00000935565, ENST00000935566, ENST00000935567, ENST00000935568, ENST00000935569, ENST00000935570, ENST00000971164, ENST00000971165, ENST00000971166, ENST00000971167, ENST00000971168, ENST00000971169, ENST00000971170, ENST00000971171, ENST00000971172, ENST00000971173, ENST00000971174

RefSeq mRNA: 10 — MANE Select: NM_020474 NM_001384438, NM_001384439, NM_001384440, NM_001384441, NM_001384442, NM_001384443, NM_001384444, NM_001384445, NM_001384446, NM_020474

CCDS: CCDS11915

Canonical transcript exons

ENST00000269195 — 12 exons

Exon	Start	End
ENSE00001108438	35709624	35711834
ENSE00002786001	35654560	35654801
ENSE00002964687	35581740	35581862
ENSE00003464799	35691012	35691192
ENSE00003481693	35692181	35692320
ENSE00003484758	35687016	35687186
ENSE00003513120	35689173	35689290
ENSE00003515934	35683391	35683598
ENSE00003557177	35703509	35703643
ENSE00003596824	35677591	35677757
ENSE00003620645	35702897	35702995
ENSE00003673146	35663628	35663802

Expression profiles

Bgee: expression breadth ubiquitous, 299 present calls, max score 99.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.9640 / max 110.0044, expressed in 1738 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
169942	4.7577	1484
169940	2.7619	1262
169943	1.2388	831
169941	1.0694	774
169939	0.6196	400
169938	0.5166	233

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	99.55	gold quality
esophagus squamous epithelium	UBERON:0006920	99.05	gold quality
pharyngeal mucosa	UBERON:0000355	98.74	gold quality
nipple	UBERON:0002030	98.36	gold quality
amniotic fluid	UBERON:0000173	98.31	gold quality
epithelium of esophagus	UBERON:0001976	98.21	gold quality
oral cavity	UBERON:0000167	98.02	gold quality
tibia	UBERON:0000979	97.96	gold quality
superior surface of tongue	UBERON:0007371	97.96	gold quality
mammary duct	UBERON:0001765	97.82	gold quality
pigmented layer of retina	UBERON:0001782	97.66	gold quality
retina	UBERON:0000966	97.64	gold quality
periodontal ligament	UBERON:0008266	97.64	gold quality
epithelium of mammary gland	UBERON:0003244	97.40	gold quality
squamous epithelium	UBERON:0006914	97.38	gold quality
tongue	UBERON:0001723	97.22	gold quality
jejunal mucosa	UBERON:0000399	97.18	gold quality
adrenal tissue	UBERON:0018303	96.83	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.82	gold quality
body of tongue	UBERON:0011876	96.72	gold quality
upper leg skin	UBERON:0004262	96.56	gold quality
secondary oocyte	CL:0000655	96.50	gold quality
tongue squamous epithelium	UBERON:0006919	96.43	gold quality
pylorus	UBERON:0001166	96.37	gold quality
colonic mucosa	UBERON:0000317	96.27	gold quality
duodenum	UBERON:0002114	96.19	gold quality
gingiva	UBERON:0001828	96.18	gold quality
parotid gland	UBERON:0001831	96.17	gold quality
tonsil	UBERON:0002372	96.12	gold quality
calcaneal tendon	UBERON:0003701	96.08	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-6524	no	66.32
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CREB1

miRNA regulators (miRDB)

182 targeting GALNT1, 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-6867-5P	100.00	82.21	3464
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-150-5P	99.99	66.69	1976
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
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-548N	99.98	71.94	4170

Literature-anchored findings (GeneRIF, showing 21)

• First simultaneous kinetic description of O-glycosylation events by recombinant UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase I at all putative O-glycosylation sites within human mucin MUC1 containing 5 tandem repeats. (PMID:14636048)
• The results indicated that IL-4-treated LS174T cells are able to produce mucins with a higher degree of O-glycosylation than untreated counterparts. (PMID:17916404)
• GalNAc T10 has a large and pronounced glycopeptide preference for Ser/Thr-O-GalNAc only at the +1 position from the acceptor site, whereas T1 and T2 have significantly reduced and variable preferences for Ser/Thr-O-GalNAc. (PMID:19460755)
• A direct link between miR-129 and the two putative targets GALNT1 and SOX4 in bladder cancer. (PMID:19487295)
• 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)
• the present analysis fails to replicate an earlier reported association of a GALNT1 variant with risk of ovarian cancer (PMID:20142253)
• Growth factor stimulation regulates O-glycosylation initiation in a Src-dependent fashion by GalNac-T redistribution from golgi to the endoplasmic reticulum. (PMID:20498016)
• each ppGalNAc T isoform may be uniquely sensitive to peptide sequence and overall charge, which together dictates the substrate sites that will be glycosylated (PMID:21349845)
• Utilizing unnatural glycopeptide substrates for GalNAc-T3 we demonstrated that the GalNAc-specific sugar recognition of the lectin domain regulates further glycosylation. (PMID:22042768)
• The GALNT1 is the glycosyltransferase enzyme family covering a single known glycosidic linkage. (PMID:22183981)
• High ppGalNAc T1 expresdsion is associated with bladder cancer. (PMID:23317233)
• Study demonstrates that down-regulation of GALNT1 is sufficient to suppress malignant phenotype of HCC cells by decreasing EGFR signaling. (PMID:25730904)
• appears to be responsive to the inhibition of GALNT1 and SHH signaling (PMID:26676748)
• Expression of GALNT3 was reduced in CAD patients, and down regulation of GALNT3 contributed to endothelial injury by promoting apoptosis and up-regulating the expression of MMP-2 and MMP-14 genes via p38 MAPK activation. (PMID:26714046)
• the GalNAc-T13 isoform is predicted to function similarly to GalNAc-T1 against peptide substrates in vivo, in contrast to a prior report, but is unique by being selectively expressed in the brain. (PMID:27913570)
• We have elucidated a novel miR-30-GALNT1/2 axis whose dysregulation increases the proportion of inactive proBNP secreted by the heart and impairs the compensatory actions of BNP during the progression of heart failure. (PMID:28188250)
• SNHG7 positively regulated GALNT1 level through sponging miR-216b, and played an oncogenic role in colorectal cancer progression. (PMID:29915311)
• a mechanism of Ebola GP-induced cell detachment that depends solely on ectodomain bulkiness and identify a single host-derived glycosylation enzyme, ppGalNAc-T1 (PMID:30389789)
• LAMTOR5 raises abnormal initiation of O-glycosylation in breast cancer metastasis via modulating GALNT1 activity. (PMID:31836847)
• High Expression of N-Acetylgalactosaminyl-transferase 1 (GALNT1) Associated with Invasion, Metastasis, and Proliferation in Osteosarcoma. (PMID:33284788)
• GALNT1 Enhances Malignant Phenotype of Gastric Cancer via Modulating CD44 Glycosylation to Activate the Wnt/beta-catenin Signaling Pathway. (PMID:36439876)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	galnt1	ENSDARG00000061335
mus_musculus	Galnt1	ENSMUSG00000000420
rattus_norvegicus	Galnt1	ENSRNOG00000016207

Paralogs (19): GALNT16 (ENSG00000100626), GALNTL5 (ENSG00000106648), GALNT7 (ENSG00000109586), GALNT18 (ENSG00000110328), GALNT3 (ENSG00000115339), GALNT12 (ENSG00000119514), GALNT8 (ENSG00000130035), GALNT15 (ENSG00000131386), GALNT5 (ENSG00000136542), GALNT6 (ENSG00000139629), GALNT2 (ENSG00000143641), GALNT13 (ENSG00000144278), GALNT14 (ENSG00000158089), GALNT10 (ENSG00000164574), GALNTL6 (ENSG00000174473), GALNT11 (ENSG00000178234), GALNT9 (ENSG00000182870), GALNT17 (ENSG00000185274), GALNT4 (ENSG00000257594)

Protein

Protein identifiers

Polypeptide N-acetylgalactosaminyltransferase 1 — Q10472 (reviewed: Q10472)

Alternative names: Polypeptide GalNAc transferase 1, Protein-UDP acetylgalactosaminyltransferase 1, UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1

All UniProt accessions (3): Q10472, K7EJV8, K7EK46

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Has a broad spectrum of substrates such as apomucin-, MUC5AC-, MUC1- and MUC2-derived peptides.

Subcellular location. Golgi apparatus. Golgi stack membrane Secreted.

Tissue specificity. Widely expressed. Expressed in all tissues tested.

Domain organisation. There are two conserved domains in the glycosyltransferase region: the N-terminal domain (domain A, also called GT1 motif), which is probably involved in manganese coordination and substrate binding and the C-terminal domain (domain B, also called Gal/GalNAc-T motif), which is probably involved in catalytic reaction and UDP-Gal binding. The ricin B-type lectin domain directs the glycopeptide specificity. It is required in the glycopeptide specificity of enzyme activity but not for activity with naked peptide substrates, suggesting that it triggers the catalytic domain to act on GalNAc-glycopeptide substrates.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 2 family. GalNAc-T subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q10472-1	1	yes
Q10472-2	2

RefSeq proteins (10): NP_001371367, NP_001371368, NP_001371369, NP_001371370, NP_001371371, NP_001371372, NP_001371373, NP_001371374, NP_001371375, NP_065207* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000772	Ricin_B_lectin	Domain
IPR001173	Glyco_trans_2-like	Domain
IPR029044	Nucleotide-diphossugar_trans	Homologous_superfamily
IPR035992	Ricin_B-like_lectins	Homologous_superfamily
IPR045885	GalNAc-T	Domain

Pfam: PF00535, PF00652

Enzyme classification (BRENDA):

• EC 2.4.1.41 — polypeptide N-acetylgalactosaminyltransferase (BRENDA: 21 organisms, 537 substrates, 86 inhibitors, 206 Km, 52 kcat entries)

Substrate kinetics (BRENDA)

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

Substrate	Km (mM)	Measurements
UDP-GALNAC	0.0017–16	32
UDP-N-ACETYL-D-GALACTOSAMINE	0.008–0.081	11
PTTDSTTPAPTTK	0.042–1.02	7
GTTPSPVPTTSTTSAP	0.0259–0.344	5
MUC5AC-13	0.018–0.77	5
MUC5AC-3	0.033–0.107	5
STPSTPSTPSTPSTP	0.2–0.65	5
CPPTPSATTPAPPSSSAPPETTAA	0.01–0.48	4
DSTTPAPTTK	0.07–2.19	4
GTTPSPVPTTST[GALNAC]TSAP	0.115–0.46	4
GT[GALNAC]TPSPVPTTSTTSAP	0.035–0.332	4
UDP-GAL	0.027–0.041	4
GVVPTVVPG	1.74–17.6	3
IGA HINGE	0.01–0.02	3
IGA HINGE-4GALNAC	0.12–0.81	3

Catalyzed reactions (Rhea), 2 shown:

• L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = a 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP + H(+) (RHEA:23956)
• L-threonyl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = a 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP + H(+) (RHEA:52424)

UniProt features (26 total): binding site 8, disulfide bond 5, region of interest 3, chain 2, glycosylation site 2, topological domain 2, splice variant 1, sequence variant 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q10472-F1	91.66	0.83

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 (8): 186; 209; 211; 316; 344; 347; 352; 156

Disulfide bonds (5): 106–339, 330–408, 442–459, 482–497, 523–540

Glycosylation sites (2): 95, 552

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-6811436	COPI-independent Golgi-to-ER retrograde traffic
R-HSA-913709	O-linked glycosylation of mucins
R-HSA-9683673	Maturation of protein 3a
R-HSA-9694719	Maturation of protein 3a

MSigDB gene sets: 282 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, ATACCTC_MIR202, CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_UP, REACTOME_MEMBRANE_TRAFFICKING, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, BRUECKNER_TARGETS_OF_MIRLET7A3_DN, PUJANA_CHEK2_PCC_NETWORK, chr18q12, MODULE_239, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, WAGNER_APO2_SENSITIVITY, SCHLOSSER_SERUM_RESPONSE_DN, TIEN_INTESTINE_PROBIOTICS_24HR_UP, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P

GO Biological Process (6): protein O-linked glycosylation (GO:0006493), protein O-linked glycosylation via N-acetylgalactosamine (GO:0016266), viral protein processing (GO:0019082), obsolete protein glycosylation (GO:0006486), obsolete protein O-linked glycosylation via serine (GO:0018242), obsolete protein O-linked glycosylation via threonine (GO:0018243)

GO Molecular Function (6): polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653), manganese ion binding (GO:0030145), carbohydrate binding (GO:0030246), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757), metal ion binding (GO:0046872)

GO Cellular Component (8): Golgi membrane (GO:0000139), extracellular region (GO:0005576), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), Golgi cisterna membrane (GO:0032580), endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116), perinuclear region of cytoplasm (GO:0048471), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Golgi-to-ER retrograde transport	1
O-linked glycosylation	1
Translation of Structural Proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
bounding membrane of organelle	2
organelle membrane	2
cytoplasm	2
glycoprotein biosynthetic process	1
protein O-linked glycosylation	1
viral process	1
viral gene expression	1
acetylgalactosaminyltransferase activity	1
catalytic activity, acting on a protein	1
transition metal ion binding	1
binding	1
catalytic activity	1
transferase activity	1
cation binding	1
Golgi apparatus	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
Golgi cisterna	1
endoplasmic reticulum-Golgi intermediate compartment	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

854 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GALNT1	B4GALNT1	Q00973	855
GALNT1	SDC3	O75056	648
GALNT1	MUC3A	Q02505	635
GALNT1	C1GALT1	Q9NS00	613
GALNT1	ARHGEF39	Q8N4T4	550
GALNT1	C1GALT1C1	Q96EU7	550
GALNT1	RMP24	Q32NC0	503
GALNT1	ST3GAL1	Q11201	495
GALNT1	GCNT1	Q02742	481
GALNT1	CHSY1	Q86X52	480
GALNT1	CERS2	Q96G23	472
GALNT1	ST6GAL1	P15907	438
GALNT1	B4GALT3	O60512	434
GALNT1	RPRD1A	Q96P16	431
GALNT1	SPP2	Q13103	427

IntAct

72 interactions, top by confidence:

A	B	Type	Score
TUBA1C	TXNDC9	psi-mi:“MI:0914”(association)	0.730
B3GNT3	PGRMC1	psi-mi:“MI:0914”(association)	0.670
P2RX4	FAM20B	psi-mi:“MI:0914”(association)	0.640
SLC1A1	AGPAT2	psi-mi:“MI:0914”(association)	0.640
MMP14	TIMP2	psi-mi:“MI:0914”(association)	0.560
PRSS22	PPM1A	psi-mi:“MI:0914”(association)	0.560
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
ARMC6	SLC27A2	psi-mi:“MI:0914”(association)	0.530
HFE	ADAM10	psi-mi:“MI:0914”(association)	0.530
ANKH	FAM234B	psi-mi:“MI:0914”(association)	0.530
SEC23A	GALNT1	psi-mi:“MI:0915”(physical association)	0.400
	AGPS	psi-mi:“MI:0915”(physical association)	0.400
	TK2	psi-mi:“MI:0915”(physical association)	0.400
Tgfbr1	HSPA8	psi-mi:“MI:0914”(association)	0.350
E5	ESYT2	psi-mi:“MI:0914”(association)	0.350
	ESYT2	psi-mi:“MI:0914”(association)	0.350
TNFAIP3	FZD7	psi-mi:“MI:0914”(association)	0.350
P2RX4	ORC4	psi-mi:“MI:0914”(association)	0.350
GALNT13	GALNT1	psi-mi:“MI:0914”(association)	0.350
	NBAS	psi-mi:“MI:0914”(association)	0.350
	TMEM223	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
NYX	POTEF	psi-mi:“MI:0914”(association)	0.350
OTOA	SLC27A2	psi-mi:“MI:0914”(association)	0.350

BioGRID (83): GALNT1 (Affinity Capture-RNA), GALNT1 (Affinity Capture-RNA), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-RNA), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS), GALNT1 (Affinity Capture-MS)

ESM2 similar proteins: A8Y236, H0ZAB5, O08832, O08912, O45293, O45947, O61394, O61397, P34678, P70419, Q07537, Q10471, Q10472, Q10473, Q14435, Q29121, Q49A17, Q5EA41, Q5RFJ6, Q6DJR8, Q6P6V1, Q6P9S7, Q6PB93, Q6UE39, Q6WV16, Q6WV17, Q6WV19, Q6WV20, Q7K755, Q80VA0, Q86SF2, Q86SR1, Q8BVG5, Q8C7U7, Q8CF93, Q8I136, Q8IA42, Q8IUC8, Q8MRC9, Q8MV48

Diamond homologs: A8Y236, H0ZAB5, O08832, O08912, O45293, O45947, O61394, O61397, O88422, P34678, P70419, Q07537, Q10471, Q10472, Q10473, Q14435, Q29121, Q49A17, Q5EA41, Q5RFJ6, Q6DJR8, Q6IS24, Q6P6V1, Q6P9A2, Q6P9S7, Q6PB93, Q6UE39, Q6WV16, Q6WV17, Q6WV19, Q6WV20, Q7K755, Q7TT15, Q7Z4T8, Q7Z7M9, Q80VA0, Q86SF2, Q86SR1, Q8BGT9, Q8BVG5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 103 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
R-HSA-425366	6	16.5×	5e-04
SLC-mediated transmembrane transport	8	7.2×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1519 predictions. Top by Δscore:

Variant	Effect	Δscore
18:35654798:GATG:G	donor_gain	1.0000
18:35654799:ATGGT:A	donor_loss	1.0000
18:35654801:GGTG:G	donor_loss	1.0000
18:35654802:G:GA	donor_loss	1.0000
18:35654802:G:GG	donor_gain	1.0000
18:35654803:T:A	donor_loss	1.0000
18:35663801:GG:G	donor_gain	1.0000
18:35663802:GG:G	donor_gain	1.0000
18:35687006:AT:A	acceptor_gain	1.0000
18:35687007:T:G	acceptor_gain	1.0000
18:35687007:T:TA	acceptor_gain	1.0000
18:35689289:GG:G	donor_gain	1.0000
18:35689290:GG:G	donor_gain	1.0000
18:35692180:GGT:G	acceptor_gain	1.0000
18:35692317:AGAGG:A	donor_loss	1.0000
18:35692318:GAG:G	donor_gain	1.0000
18:35692318:GAGGT:G	donor_loss	1.0000
18:35692322:T:G	donor_loss	1.0000
18:35702891:CCATA:C	acceptor_loss	1.0000
18:35702892:CATAG:C	acceptor_loss	1.0000
18:35702893:ATAG:A	acceptor_loss	1.0000
18:35702894:TAGAT:T	acceptor_loss	1.0000
18:35702895:A:AG	acceptor_gain	1.0000
18:35702895:A:G	acceptor_loss	1.0000
18:35702896:G:A	acceptor_loss	1.0000
18:35702896:G:GG	acceptor_gain	1.0000
18:35702896:GATAC:G	acceptor_gain	1.0000
18:35703492:T:TA	acceptor_gain	1.0000
18:35703495:A:AG	acceptor_gain	1.0000
18:35703496:T:G	acceptor_gain	1.0000

AlphaMissense

3715 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:35654711:T:A	W17R	1.000
18:35654711:T:C	W17R	1.000
18:35663664:G:A	G59E	1.000
18:35663672:G:A	G62R	1.000
18:35663672:G:C	G62R	1.000
18:35663672:G:T	G62W	1.000
18:35663673:G:A	G62E	1.000
18:35663673:G:T	G62V	1.000
18:35663682:T:A	V65D	1.000
18:35663723:T:C	F79L	1.000
18:35663725:T:A	F79L	1.000
18:35663725:T:G	F79L	1.000
18:35663738:T:C	F84L	1.000
18:35663739:T:C	F84S	1.000
18:35663740:C:A	F84L	1.000
18:35663740:C:G	F84L	1.000
18:35663743:T:A	N85K	1.000
18:35663743:T:G	N85K	1.000
18:35663753:A:C	S89R	1.000
18:35663755:T:A	S89R	1.000
18:35663755:T:G	S89R	1.000
18:35663775:G:C	R96T	1.000
18:35663775:G:T	R96I	1.000
18:35663776:A:C	R96S	1.000
18:35663776:A:T	R96S	1.000
18:35677592:T:A	C106S	1.000
18:35677592:T:C	C106R	1.000
18:35677593:G:A	C106Y	1.000
18:35677593:G:C	C106S	1.000
18:35677649:C:G	H125D	1.000

dbSNP variants (sampled 300 via entrez): RS1000008438 (18:35630932 A>G), RS1000014358 (18:35682572 T>C), RS1000017140 (18:35699418 C>T), RS1000039314 (18:35602146 G>C,T), RS1000051557 (18:35670771 A>G), RS1000064653 (18:35647593 T>C), RS1000076562 (18:35681805 A>G), RS1000094937 (18:35608643 C>A,G), RS1000104298 (18:35581455 T>C), RS1000125726 (18:35591787 C>T), RS1000127719 (18:35582525 T>C), RS1000131461 (18:35699075 C>A), RS1000140162 (18:35582589 A>AT), RS1000173004 (18:35644686 C>T), RS1000182344 (18:35635176 A>G)

Disease associations

OMIM: gene MIM:602273 | 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
GCST002269_1	Drug-induced torsades de pointes	4.000000e-07
GCST003262_207	Post bronchodilator FEV1	5.000000e-06
GCST009265_10	Superior parietal cortex volume	8.000000e-06
GCST009708_2	Serum sclerostin levels	4.000000e-11
GCST90027899_15	Eosinophilic esophagitis	2.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004314	forced expiratory volume
EFO:0010606	sclerostin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4523282 (SINGLE PROTEIN)

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

ChEMBL bioactivities

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

pChembl	Type	Value	Unit	Molecule
5.61	IC50	2460	nM	CHEMBL6338

PubChem BioAssay actives

1 with measured affinity, of 1 total; 1 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
3,4,8,9-tetrahydroxybenzo[c]chromen-6-one	1588072: Inhibition of catalytic activity of ppGalNAcT1 (unknown origin) using EA2 peptide as substrate incubated for 30 mins by HPLC-based enzyme assay	ic50	2.4600	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	decreases expression	3
potassium chromate(VI)	affects cotreatment, decreases expression, increases expression	2
Benzo(a)pyrene	decreases expression, decreases methylation	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
nicotinate mononucleotide	increases expression	1
bisphenol A	affects cotreatment, increases methylation, decreases methylation	1
deoxynivalenol	decreases expression	1
methylselenic acid	decreases expression	1
kojic acid	decreases expression	1
beta-lapachone	increases expression	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
nicotinic acid adenine dinucleotide	increases expression	1
perfluorooctanoic acid	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
puag-haad	increases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
chromium hexavalent ion	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	decreases expression	1
jinfukang	decreases expression	1
bis-N,N-dimethylamino-2-(N-methylpyrrolyl)methyl cyclopentadienyl titanium (IV)	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Carbamazepine	affects expression	1
Coumestrol	affects cotreatment, decreases expression	1
Cycloheximide	affects cotreatment, decreases expression	1
Estradiol	affects expression	1
Gold	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
CHEMBL4386617	Binding	Inhibition of catalytic activity of ppGalNAcT1 (unknown origin) using EA2 peptide as substrate incubated for 30 mins by HPLC-based enzyme assay	Inhibition of polypeptide N-acetyl-α-galactosaminyltransferases is an underlying mechanism of dietary polyphenols preventing colorectal tumorigenesis. — Bioorg Med Chem

Clinical trials (associated diseases)

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