ST6GALNAC1

Summary

ST6GALNAC1 (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1, HGNC:23614) is a protein-coding gene on chromosome 17q25.1, encoding Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 (Q9NSC7). Protein sialyltransferase specifically expressed in goblet cells that plays a key role in intestinal host-commensal homeostasis.

Glycosylation of proteins affects cell-cell interaction, interactions with the matrix, and the functions of intracellular molecules. ST6GALNAC1 transfers a sialic acid, N-acetylneuraminic acid (NeuAc), in an alpha-2,6 linkage to O-linked GalNAc residues. The cancer-associated sialyl-Tn (sTn) antigen is formed by ST6GALNAC1-catalyzed sialylation of GalNAc residues on mucins (Ikehara et al., 1999 [PubMed 10536037]; Sewell et al., 2006 [PubMed 16319059]).

Source: NCBI Gene 55808 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 93 total
• MANE Select transcript: NM_018414

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23614
Approved symbol	ST6GALNAC1
Name	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1
Location	17q25.1
Locus type	gene with protein product
Status	Approved
Aliases	ST6GalNAcI
Ensembl gene	ENSG00000070526
Ensembl biotype	protein_coding
OMIM	610138
Entrez	55808

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 5 protein_coding, 4 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000156626, ENST00000359088, ENST00000585633, ENST00000588375, ENST00000589004, ENST00000589813, ENST00000589992, ENST00000590784, ENST00000590878, ENST00000590915, ENST00000592042, ENST00000877390, ENST00000949404

RefSeq mRNA: 2 — MANE Select: NM_018414 NM_001289107, NM_018414

CCDS: CCDS11748

Canonical transcript exons

ENST00000156626 — 9 exons

Exon	Start	End
ENSE00002876728	76643508	76643757
ENSE00003479723	76626651	76626789
ENSE00003499764	76624763	76625527
ENSE00003520035	76629012	76629711
ENSE00003523452	76626006	76626095
ENSE00003530524	76626289	76626392
ENSE00003630666	76625819	76625918
ENSE00003636433	76627415	76627583
ENSE00003650884	76627067	76627238

Expression profiles

Bgee: expression breadth ubiquitous, 199 present calls, max score 99.30.

FANTOM5 (CAGE): breadth broad, TPM avg 5.1766 / max 220.1558, expressed in 430 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
168262	3.8099	398
168264	0.9556	181
168263	0.2220	78
168265	0.1891	36

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of sigmoid colon	UBERON:0004993	99.30	gold quality
ileal mucosa	UBERON:0000331	99.19	gold quality
colonic mucosa	UBERON:0000317	99.05	gold quality
rectum	UBERON:0001052	98.77	gold quality
nasal cavity epithelium	UBERON:0005384	98.55	gold quality
bronchial epithelial cell	CL:0002328	98.02	gold quality
mucosa of transverse colon	UBERON:0004991	97.94	gold quality
bronchus	UBERON:0002185	97.89	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.33	gold quality
jejunal mucosa	UBERON:0000399	97.04	gold quality
trachea	UBERON:0003126	96.04	gold quality
esophagus squamous epithelium	UBERON:0006920	95.72	gold quality
nasal cavity mucosa	UBERON:0001826	94.74	gold quality
duodenum	UBERON:0002114	94.34	gold quality
lower esophagus mucosa	UBERON:0035834	93.82	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.77	gold quality
transverse colon	UBERON:0001157	92.96	gold quality
pylorus	UBERON:0001166	92.23	gold quality
epithelium of nasopharynx	UBERON:0001951	91.54	gold quality
small intestine Peyer’s patch	UBERON:0003454	90.58	gold quality
esophagus mucosa	UBERON:0002469	90.47	gold quality
body of stomach	UBERON:0001161	90.35	gold quality
small intestine	UBERON:0002108	90.29	gold quality
stomach	UBERON:0000945	89.92	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.85	gold quality
colonic epithelium	UBERON:0000397	88.46	gold quality
cardia of stomach	UBERON:0001162	88.32	gold quality
sural nerve	UBERON:0015488	88.23	gold quality
oral cavity	UBERON:0000167	87.89	gold quality
epithelial cell of pancreas	CL:0000083	87.88	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	40.67
E-MTAB-8410	yes	15.28
E-ANND-3	yes	12.32
E-MTAB-9388	yes	8.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting ST6GALNAC1, 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-4776-3P	100.00	68.73	1340
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-6073	99.60	70.36	793
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-6081	99.48	66.07	1446
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-4777-5P	99.33	67.53	1148
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-20B-3P	99.29	67.05	784
HSA-MIR-520E-5P	99.27	68.90	1513
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-6715B-3P	98.80	68.07	1204
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-548S	98.50	67.17	1213
HSA-MIR-1199-5P	98.44	66.51	829
HSA-MIR-6751-3P	98.44	66.35	835
HSA-MIR-6837-3P	98.42	66.71	1149
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-5007-5P	97.95	64.71	614
HSA-MIR-4305	97.94	68.63	533
HSA-MIR-1914-5P	97.83	66.21	807
HSA-MIR-4724-3P	97.57	67.31	785

Literature-anchored findings (GeneRIF, showing 13)

• The stable transfection of MDA-MB-231 with an expression vector encoding ST6GalNAc I induces the expression of STn antigen at the cell surface. (PMID:12820722)
• ST6GalNAc-I sialyltransferase localizes throughout the Golgi and has a role in synthesis of the tumor-associated sialyl-Tn O-glycan in human breast cancer (PMID:16319059)
• Expression of ppGalNAc-T6 is significantly higher in breast cancer compared to ’normal’/benign breast tissue samples. ST6GalNAc-I expression in breast cancer is associated with better prognosis. (PMID:19287074)
• Golgi N-glycosyltransferases beta-1,2-N-acetylglucosaminyltransferase I, beta-1,2-N-acetylglucosaminyltransferase II, 1,4-galactosyltransferase I, and alpha-2,6-sialyltransferase I form both homo- and heterodimeric enzyme complexes in live cells (PMID:20378551)
• It was confirmed that MUC1 carries sialyl Tn also in human advanced gastric cancer tissues (PMID:22228572)
• 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)
• ST6GalNAc I regulates the gene expression of IGF-1 through STAT5b activation and plays role in gastric cancer invasion and metastasis. (PMID:25532910)
• upregulated Siat7A expression, which was paralleled by the increased Klf4 in the ischemic myocardium, contributed to cardiomyocyte apoptosis following myocardial infarction (PMID:25860962)
• Our results indicated that ST6GALNAC1 was downregulated in sporadic esophageal squamous cell carcinoma via hyper-methylation and loss of heterozygosity , and it may be a candidate responsible gene for esophageal squamous cell carcinoma (PMID:28035351)
• Sialyltransferase7A promotes angiotensin II-induced cardiomyocyte hypertrophy via HIF-1alpha-TAK1 signalling pathway. (PMID:30854566)
• Cross-talk between Colon Cells and Macrophages Increases ST6GALNAC1 and MUC1-sTn Expression in Ulcerative Colitis and Colitis-Associated Colon Cancer. (PMID:31831633)
• ST6GalNAc-I promotes lung cancer metastasis by altering MUC5AC sialylation. (PMID:33792183)
• Mucus sialylation determines intestinal host-commensal homeostasis. (PMID:35303419)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	st6galnac1.1	ENSDARG00000043814
danio_rerio	st6galnac1.2	ENSDARG00000043816
mus_musculus	St6galnac1	ENSMUSG00000009588
rattus_norvegicus	St6galnac1	ENSRNOG00000000251

Paralogs (14): ST3GAL1 (ENSG00000008513), ST3GAL6 (ENSG00000064225), ST6GALNAC2 (ENSG00000070731), ST6GAL1 (ENSG00000073849), ST3GAL4 (ENSG00000110080), ST3GAL5 (ENSG00000115525), ST6GALNAC5 (ENSG00000117069), C20orf173 (ENSG00000125975), ST3GAL3 (ENSG00000126091), ST6GALNAC4 (ENSG00000136840), ST6GAL2 (ENSG00000144057), ST3GAL2 (ENSG00000157350), ST6GALNAC6 (ENSG00000160408), ST6GALNAC3 (ENSG00000184005)

Protein

Protein identifiers

Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 — Q9NSC7 (reviewed: Q9NSC7)

Alternative names: GalNAc alpha-2,6-sialyltransferase I, ST6GalNAc I, Sialyltransferase 7A

All UniProt accessions (6): Q9NSC7, G3XAD9, K7EJA8, K7EJC9, K7ELU9, K7EMB6

UniProt curated annotations — full annotation on UniProt →

Function. Protein sialyltransferase specifically expressed in goblet cells that plays a key role in intestinal host-commensal homeostasis. Conjugates sialic acid with an alpha-2-6 linkage to N-acetylgalactosamine (GalNAc) glycan chains linked to serine or threonine in glycoproteins. Catalyzes the formation of the sialyl-Tn (S-Tn) antigen, an antigen found in intestinal goblet cells, as well as ulcerative colitis (UC) and various cancers. Protein sialylation in globlet cells is essential for mucus integrity and is required to protect the intestinal mucus against excessive bacterial proteolytic degradation.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Expression is restricted to the gastrointestinal tract. Highly expressed in goblet cells. Also expressed in various tumor cells.

Post-translational modifications. Glycosylated; autosialylated.

Disease relevance. Inflammatory bowel disease. A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. Disease susceptibility is associated with variants affecting the gene represented in this entry.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 29 family.

RefSeq proteins (2): NP_001276036, NP_060884* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001675	Glyco_trans_29	Family
IPR038578	GT29-like_sf	Homologous_superfamily

Pfam: PF00777

Enzyme classification (BRENDA):

• EC 2.4.99.3 — alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase (BRENDA: 0 organisms, 0 substrates, 0 inhibitors, 0 Km, 0 kcat entries)

Catalyzed reactions (Rhea), 6 shown:

• a beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl derivative + CMP-N-acetyl-beta-neuraminate = a beta-D-galactosyl-(1->3)-[N-acetyl-alpha-neuraminyl-(2->6)]-N-acetyl-alpha-D-galactosaminyl derivative + CMP + H(+) (RHEA:11136)
• a 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + CMP-N-acetyl-beta-neuraminate = a 3-O-[N-acetyl-alpha-neuraminosyl-(2->6)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + CMP + H(+) (RHEA:81643)
• a 3-O-[N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + CMP-N-acetyl-beta-neuraminate = a 3-O-[N-acetyl-alpha-neuraminosyl-(2->6)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + CMP + H(+) (RHEA:81647)
• a 3-O-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + CMP-N-acetyl-beta-neuraminate = a 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-alpha-neuraminosyl-(2->6)]-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + CMP + H(+) (RHEA:81651)
• a 3-O-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + CMP-N-acetyl-beta-neuraminate = a 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-alpha-neuraminosyl-(2->6)]-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + CMP + H(+) (RHEA:81655)
• a 3-O-[N-acetyl-alpha-neuraminyl-(2->3)-beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + CMP-N-acetyl-beta-neuraminate = a 3-O-{alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-[alpha-Neu5Ac-(2->6)]-alpha-D-GalNAc}-L-threonyl-[protein] + CMP + H(+) (RHEA:81659)

UniProt features (23 total): sequence variant 6, glycosylation site 5, compositionally biased region 4, topological domain 2, disulfide bond 2, region of interest 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NSC7-F1	73.44	0.56

Functional residue map

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

Disulfide bonds (2): 279–362, 365–533

Glycosylation sites (5): 300, 311, 331, 375, 460

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

ID	Pathway
R-HSA-4085001	Sialic acid metabolism
R-HSA-392499	Metabolism of proteins
R-HSA-446193	Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
R-HSA-446203	Asparagine N-linked glycosylation
R-HSA-446219	Synthesis of substrates in N-glycan biosythesis
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 141 (showing top): GOBP_OLIGOSACCHARIDE_METABOLIC_PROCESS, GOBP_MODULATION_OF_PROCESS_OF_ANOTHER_ORGANISM, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, CADWELL_ATG16L1_TARGETS_DN, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_OLIGOSACCHARIDE_BIOSYNTHETIC_PROCESS, GOBP_MULTICELLULAR_ORGANISMAL_LEVEL_HOMEOSTASIS, MODULE_95, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, GAVIN_FOXP3_TARGETS_CLUSTER_P2, GOBP_HOMEOSTATIC_PROCESS, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOBP_HOMEOSTASIS_OF_NUMBER_OF_CELLS

GO Biological Process (5): glycoprotein biosynthetic process (GO:0009101), oligosaccharide biosynthetic process (GO:0009312), host-mediated modulation of intestinal microbiota composition (GO:0048874), obsolete protein glycosylation (GO:0006486), host-mediated perturbation of symbiont process (GO:0051851)

GO Molecular Function (5): alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665), sialyltransferase activity (GO:0008373), protein binding (GO:0005515), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

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

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
Synthesis of substrates in N-glycan biosythesis	1
Asparagine N-linked glycosylation	1
Post-translational protein modification	1
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
macromolecule biosynthetic process	1
glycoprotein metabolic process	1
carbohydrate derivative biosynthetic process	1
oligosaccharide metabolic process	1
carbohydrate biosynthetic process	1
homeostasis of number of cells	1
host-mediated perturbation of symbiont process	1
modulation of process of another organism	1
sialyltransferase activity	1
glycosyltransferase activity	1
binding	1
catalytic activity	1
transferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

702 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ST6GALNAC1	EEF1A2	P54266	930
ST6GALNAC1	C1GALT1	Q9NS00	817
ST6GALNAC1	SLC25A18	Q9H1K4	795
ST6GALNAC1	GC	P02774	746
ST6GALNAC1	C1GALT1C1	Q96EU7	743
ST6GALNAC1	GCNT1	Q02742	655
ST6GALNAC1	SCIN	Q9Y6U3	636
ST6GALNAC1	PPOX	P50336	631
ST6GALNAC1	ST6GALNAC5	Q9BVH7	627
ST6GALNAC1	ST6GALNAC6	Q969X2	611
ST6GALNAC1	B3GNT6	Q6ZMB0	596
ST6GALNAC1	ST6GALNAC3	Q8NDV1	591
ST6GALNAC1	AHSG	P02765	588
ST6GALNAC1	GCNT3	O95395	584
ST6GALNAC1	SLC35A1	P78382	563

IntAct

9 interactions, top by confidence:

A	B	Type	Score
ST6GALNAC1	EEF1A2	psi-mi:“MI:0915”(physical association)	0.560
ST6GALNAC1	EEF1A2	psi-mi:“MI:0914”(association)	0.560
ST6GALNAC1	CFTR	psi-mi:“MI:0915”(physical association)	0.510
CFTR	ST6GALNAC1	psi-mi:“MI:0915”(physical association)	0.510
	ST6GALNAC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (8): EEF1A2 (Affinity Capture-MS), EEF1A2 (Affinity Capture-MS), VAT1L (Affinity Capture-MS), ST6GALNAC1 (PCA), ST6GALNAC1 (Cross-Linking-MS (XL-MS)), ST6GALNAC1 (Cross-Linking-MS (XL-MS)), ST6GALNAC1 (Affinity Capture-MS), ST6GALNAC1 (Two-hybrid)

ESM2 similar proteins: A2A699, A2BD09, A4IIT5, A5D7T4, A6QLD2, A8MVW0, O35764, O43278, O70624, O95502, O95897, P35054, P51693, Q03157, Q2PT31, Q3UPI1, Q3UZZ4, Q3V1G4, Q568Y7, Q594P2, Q5QQ37, Q66H86, Q68BL7, Q68BL8, Q6AYE5, Q6P7B4, Q6UWH4, Q6UWY5, Q6ZMI3, Q701R2, Q701R3, Q701R4, Q766D5, Q76KP1, Q80WL1, Q863A3, Q866N2, Q86VZ4, Q8BHP7, Q8BM13

Diamond homologs: O15466, O43173, P61132, P61642, P61644, P61646, P61647, P61648, P70126, P70277, P97325, Q02734, Q11203, Q64687, Q64689, Q6DNG6, Q6ZXA0, Q6ZXC8, Q6ZXD2, Q8K4T1, Q92183, Q92184, Q92185, Q9NSC7, Q9QZ39, Q9UJ37, A2ZI41, Q2QXM3, O35696, P61643, P61645, Q07977, Q11200, Q64690, Q64692, Q6KB59, Q6ZXC9, Q92186, Q92187, Q02745

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	73
Likely benign	8
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2017 predictions. Top by Δscore:

Variant	Effect	Δscore
17:76626785:TCAAT:T	acceptor_gain	1.0000
17:76626786:CAAT:C	acceptor_gain	1.0000
17:76626786:CAATC:C	acceptor_gain	1.0000
17:76626787:AAT:A	acceptor_gain	1.0000
17:76626789:TCTGT:T	acceptor_loss	1.0000
17:76626790:C:CC	acceptor_gain	1.0000
17:76626790:C:CG	acceptor_loss	1.0000
17:76626791:T:C	acceptor_loss	1.0000
17:76626792:G:C	acceptor_gain	1.0000
17:76626795:C:CT	acceptor_gain	1.0000
17:76626796:A:T	acceptor_gain	1.0000
17:76627061:GCTTA:G	donor_loss	1.0000
17:76627062:CTTAC:C	donor_loss	1.0000
17:76627063:TTA:T	donor_loss	1.0000
17:76627064:TACCG:T	donor_loss	1.0000
17:76627065:A:AC	donor_gain	1.0000
17:76627066:C:CT	donor_gain	1.0000
17:76627066:CCGG:C	donor_gain	1.0000
17:76627234:CACCA:C	acceptor_gain	1.0000
17:76627235:ACCA:A	acceptor_gain	1.0000
17:76627236:CCA:C	acceptor_gain	1.0000
17:76627236:CCAC:C	acceptor_gain	1.0000
17:76627237:CA:C	acceptor_gain	1.0000
17:76627237:CAC:C	acceptor_gain	1.0000
17:76627239:C:CC	acceptor_gain	1.0000
17:76627239:C:T	acceptor_loss	1.0000
17:76627240:T:C	acceptor_loss	1.0000
17:76627410:CTCA:C	donor_loss	1.0000
17:76627411:TCA:T	donor_loss	1.0000
17:76627412:CACAG:C	donor_loss	1.0000

AlphaMissense

3925 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:76625407:A:G	W576R	0.996
17:76625407:A:T	W576R	0.996
17:76626749:C:A	G405W	0.996
17:76625417:C:A	E572D	0.995
17:76625417:C:G	E572D	0.995
17:76625865:G:A	T520I	0.994
17:76626748:C:A	G405V	0.994
17:76627070:A:G	F390S	0.994
17:76625418:T:A	E572V	0.993
17:76625434:G:C	H567D	0.993
17:76625826:C:T	C533Y	0.993
17:76626347:A:G	W453R	0.993
17:76626347:A:T	W453R	0.993
17:76626748:C:T	G405E	0.993
17:76625405:C:A	W576C	0.992
17:76625405:C:G	W576C	0.992
17:76625432:A:C	H567Q	0.992
17:76625432:A:T	H567Q	0.992
17:76625486:A:C	F549L	0.992
17:76625486:A:T	F549L	0.992
17:76625488:A:G	F549L	0.992
17:76625510:G:C	F541L	0.992
17:76625510:G:T	F541L	0.992
17:76625511:A:G	F541S	0.992
17:76625512:A:G	F541L	0.992
17:76625520:G:T	A538D	0.992
17:76625826:C:G	C533S	0.992
17:76625827:A:T	C533S	0.992
17:76625825:A:C	C533W	0.991
17:76625514:C:T	G540D	0.990

dbSNP variants (sampled 300 via entrez): RS1000030302 (17:76638808 T>C), RS1000278937 (17:76622450 G>A,T), RS1000319731 (17:76638708 A>G), RS1000447257 (17:76617000 G>A), RS1000519010 (17:76618156 A>T), RS1000541746 (17:76621533 T>C), RS1000547912 (17:76632910 T>C), RS1000570030 (17:76617911 G>A,T), RS1000712469 (17:76622238 C>T), RS1000838646 (17:76628466 C>G), RS1001032810 (17:76626781 C>T), RS1001450822 (17:76627913 C>T), RS1001517257 (17:76634429 T>C), RS1001586587 (17:76627672 G>A,T), RS1001619516 (17:76633498 G>A)

Disease associations

OMIM: gene MIM:610138 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	affects expression, decreases expression	3
Air Pollutants	affects cotreatment, increases abundance, increases expression, decreases expression	2
Benzo(a)pyrene	affects methylation, increases methylation	2
Estradiol	affects cotreatment, increases expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Aflatoxin B1	increases methylation	2
alpha-pinene	increases abundance, affects cotreatment, increases expression	1
propionaldehyde	decreases expression	1
sodium arsenite	increases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
ormosil	affects binding, decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
enzalutamide	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Zoledronic Acid	increases expression	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Calcitriol	increases expression, affects cotreatment	1
Lead	increases expression	1
Ozone	affects cotreatment, increases expression, increases abundance	1
Polyethylene Glycols	affects binding, decreases expression	1
Progesterone	affects cotreatment, increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Dihydrotestosterone	increases expression	1
Testosterone	affects cotreatment, increases expression	1
Tretinoin	increases expression	1
Triclosan	decreases expression	1
Cadmium Chloride	increases expression	1

Cellosaurus cell lines

5 cell lines: 4 cancer cell line, 1 spontaneously immortalized cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E3IV	MDA-STn a	Cancer cell line	Female
CVCL_E3IW	MDA-STn b	Cancer cell line	Female
CVCL_E3IY	CHO-K1 MUC1-IgG ST6GALNAC1	Spontaneously immortalized cell line	Female
CVCL_HG16	T47D-StN	Cancer cell line	Female
CVCL_HG17	T47D-ST3-STn	Cancer cell line	Female

Clinical trials (associated diseases)

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