ST3GAL6

Summary

ST3GAL6 (ST3 beta-galactoside alpha-2,3-sialyltransferase 6, HGNC:18080) is a protein-coding gene on chromosome 3q12.1, encoding Type 2 lactosamine alpha-2,3-sialyltransferase (Q9Y274). Transfers the sialyl residue from CMP-N-acetyl-beta-neuraminate to the terminal galactose residue on sugar chains of glycoproteins and glycolipids.

The protein encoded by this gene is a member of the sialyltransferase family. Members of this family are enzymes that transfer sialic acid from the activated cytidine 5’-monophospho-N-acetylneuraminic acid to terminal positions on sialylated glycolipids (gangliosides) or to the N- or O-linked sugar chains of glycoproteins. This protein has high specificity for neolactotetraosylceramide and neolactohexaosylceramide as glycolipid substrates and may contribute to the formation of selectin ligands and sialyl Lewis X, a carbohydrate important for cell-to-cell recognition and a blood group antigen.

Source: NCBI Gene 10402 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 43 total
• MANE Select transcript: NM_001323368

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18080
Approved symbol	ST3GAL6
Name	ST3 beta-galactoside alpha-2,3-sialyltransferase 6
Location	3q12.1
Locus type	gene with protein product
Status	Approved
Aliases	ST3GALVI
Ensembl gene	ENSG00000064225
Ensembl biotype	protein_coding
OMIM	607156
Entrez	10402

Gene structure

Transcript identifiers

Ensembl transcripts: 69 — 53 protein_coding, 10 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 2 retained_intron

ENST00000265261, ENST00000394162, ENST00000460774, ENST00000462152, ENST00000465004, ENST00000466482, ENST00000468553, ENST00000469105, ENST00000474595, ENST00000476833, ENST00000477574, ENST00000477899, ENST00000480133, ENST00000483910, ENST00000485145, ENST00000485391, ENST00000486249, ENST00000486334, ENST00000489112, ENST00000490684, ENST00000491912, ENST00000492254, ENST00000493953, ENST00000495376, ENST00000495502, ENST00000497008, ENST00000613264, ENST00000881500, ENST00000881501, ENST00000881502, ENST00000881503, ENST00000881504, ENST00000881505, ENST00000881506, ENST00000881507, ENST00000881508, ENST00000881509, ENST00000881510, ENST00000881511, ENST00000881512, ENST00000881513, ENST00000881514, ENST00000881515, ENST00000881516, ENST00000881517, ENST00000881518, ENST00000881519, ENST00000881520, ENST00000881521, ENST00000881522, ENST00000881523, ENST00000881524, ENST00000881525, ENST00000881526, ENST00000881527, ENST00000881528, ENST00000946763, ENST00000946764, ENST00000946765, ENST00000946766, ENST00000946767, ENST00000946768, ENST00000946769, ENST00000946770, ENST00000946771, ENST00000946772, ENST00000946773, ENST00000946774, ENST00000946775

RefSeq mRNA: 18 — MANE Select: NM_001323368 NM_001271142, NM_001271145, NM_001271146, NM_001271147, NM_001271148, NM_001323352, NM_001323353, NM_001323358, NM_001323359, NM_001323360, NM_001323362, NM_001323363, NM_001323364, NM_001323365, NM_001323366, NM_001323367, NM_001323368, NM_006100

CCDS: CCDS2933

Canonical transcript exons

ENST00000483910 — 10 exons

Exon	Start	End
ENSE00001863685	98793675	98795852
ENSE00001922606	98763340	98763439
ENSE00003464130	98791841	98791993
ENSE00003536885	98788326	98788463
ENSE00003585478	98772813	98772916
ENSE00003611479	98770879	98770956
ENSE00003633992	98788036	98788222
ENSE00003644735	98784945	98785040
ENSE00003665142	98768430	98768529
ENSE00003688252	98773920	98773983

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 95.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.1892 / max 371.8933, expressed in 1325 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
37543	5.3581	444
37538	2.2865	862
37536	2.0948	768
37537	1.2904	571
37542	1.1394	256
37546	0.9531	377
37539	0.7773	466
37541	0.2738	151
37547	0.0159	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	95.62	gold quality
buccal mucosa cell	CL:0002336	95.37	gold quality
right lobe of liver	UBERON:0001114	94.64	gold quality
monocyte	CL:0000576	94.60	gold quality
renal glomerulus	UBERON:0000074	94.31	gold quality
right uterine tube	UBERON:0001302	93.80	gold quality
metanephric glomerulus	UBERON:0004736	93.76	gold quality
calcaneal tendon	UBERON:0003701	93.60	gold quality
mononuclear cell	CL:0000842	93.56	gold quality
germinal epithelium of ovary	UBERON:0001304	93.49	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.38	gold quality
leukocyte	CL:0000738	93.03	gold quality
heart left ventricle	UBERON:0002084	92.66	gold quality
liver	UBERON:0002107	92.65	gold quality
cardiac ventricle	UBERON:0002082	92.53	gold quality
apex of heart	UBERON:0002098	92.17	gold quality
tibia	UBERON:0000979	92.14	gold quality
skin of abdomen	UBERON:0001416	91.09	gold quality
skin of leg	UBERON:0001511	91.08	gold quality
heart right ventricle	UBERON:0002080	90.58	gold quality
tendon	UBERON:0000043	90.54	gold quality
metanephros	UBERON:0000081	90.36	gold quality
heart	UBERON:0000948	90.29	gold quality
right atrium auricular region	UBERON:0006631	89.29	gold quality
zone of skin	UBERON:0000014	89.10	gold quality
left ventricle myocardium	UBERON:0006566	89.06	gold quality
metanephros cortex	UBERON:0010533	88.94	gold quality
cardiac atrium	UBERON:0002081	88.67	gold quality
cortex of kidney	UBERON:0001225	88.59	gold quality
tibial nerve	UBERON:0001323	87.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-119	yes	32.23
E-HCAD-10	yes	20.56
E-ANND-3	yes	12.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting ST3GAL6, 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-5193	100.00	67.26	1744
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-1208	99.70	68.28	1533

Literature-anchored findings (GeneRIF, showing 6)

• Epigenetic changes in a group of glycosyltransferases including B4GALNT2 and ST3GAL6 represent a malignant phenotype of gastric cancer caused by silencing of the activity of these enzymes (PMID:18485915)
• Expression of ST3Gal IV in several gastrointestinal cell lines is correlated with the expression of sialyl Lewis x at the cell surface. (PMID:19781661)
• the occurrence of CD75s- and iso-CD75s-gangliosides in tumor tissues is largely independent of the transcriptional expression of ST6GAL1 and ST3GAL6 (PMID:21147760)
• The sialyltransferase ST3GAL6 influences homing and survival in multiple myeloma. (PMID:25061176)
• a cross-restoration of each of the three genes in ST3GAL6 KO cells showed that overexpression of ST3GAL6 sufficiently rescued the total alpha2,3-sialylation levels, cell morphology, and alpha2,3-sialylation of EGFR, whereas the alpha2,3-sialylation levels of beta1 were greatly enhanced by an overexpression of ST3GAL4 (PMID:31914669)
• lncRNA ST3GAL6AS1 promotes invasion by inhibiting hnRNPA2B1mediated ST3GAL6 expression in multiple myeloma. (PMID:33649796)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	St3gal6	ENSMUSG00000022747
rattus_norvegicus	St3gal6	ENSRNOG00000001653

Paralogs (14): ST3GAL1 (ENSG00000008513), ST6GALNAC1 (ENSG00000070526), 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

Type 2 lactosamine alpha-2,3-sialyltransferase — Q9Y274 (reviewed: Q9Y274)

Alternative names: CMP-NeuAc:beta-galactoside alpha-2,3-sialyltransferase VI, ST3Gal VI, Sialyltransferase 10

All UniProt accessions (10): Q9Y274, A0A087WXB8, C9IZL6, C9J0E2, C9J480, C9J9Y4, C9JMW7, C9JWI9, C9JWJ3, F2Z2F4

UniProt curated annotations — full annotation on UniProt →

Function. Transfers the sialyl residue from CMP-N-acetyl-beta-neuraminate to the terminal galactose residue on sugar chains of glycoproteins and glycolipids. Its alpha-2,3-sialyltransferase activity is specific toward type II glycan chains (Galbeta1-4GlcNAc) on glycoproteins and glycolipids such as neolactosides nLc4Cer and nLc6Cer, whose sialyl-products serve as precursors for the Lewis X antigen. Critically involved in the synthesis of functional selectin ligands needed for neutrophil recruitment during inflammation and lymphocyte homing to the lymph nodes.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Ubiquitous.

Similarity. Belongs to the glycosyltransferase 29 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y274-1	1	yes
Q9Y274-2	2

RefSeq proteins (18): NP_001258071, NP_001258074, NP_001258075, NP_001258076, NP_001258077, NP_001310281, NP_001310282, NP_001310287, NP_001310288, NP_001310289, NP_001310291, NP_001310292, NP_001310293, NP_001310294, NP_001310295, NP_001310296, NP_001310297, NP_006091 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001675	Glyco_trans_29	Family
IPR012163	Sialyl_trans	Family
IPR038578	GT29-like_sf	Homologous_superfamily
IPR051142	Glycosyltransferase_29	Family

Pfam: PF00777

Catalyzed reactions (Rhea), 3 shown:

• a neolactoside nLc4Cer(d18:1(4E)) + CMP-N-acetyl-beta-neuraminate = a neolactoside IV(3)-alpha-NeuAc-nLc4Cer(d18:1(4E)) + CMP + H(+) (RHEA:18913)
• a beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + CMP-N-acetyl-beta-neuraminate = an N-acetyl-alpha-neuraminyl-(2->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + CMP + H(+) (RHEA:52316)
• a neolactoside nLc6Cer(d18:1(4E)) + CMP-N-acetyl-beta-neuraminate = a neolactoside VI(3)-alpha-NeuNAc-nLc6Cer(d18:1(4E)) + CMP + H(+) (RHEA:80751)

UniProt features (14 total): glycosylation site 6, topological domain 2, splice variant 2, chain 1, sequence variant 1, sequence conflict 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y274-F1	91.36	0.78

Functional residue map

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

Glycosylation sites (6): 129, 181, 282, 295, 308, 327

Function

Pathways and Gene Ontology

Reactome pathways

17 pathways

ID	Pathway
R-HSA-1912420	Pre-NOTCH Processing in Golgi
R-HSA-2022854	Keratan sulfate biosynthesis
R-HSA-4085001	Sialic acid metabolism
R-HSA-9037629	Lewis blood group biosynthesis
R-HSA-1430728	Metabolism
R-HSA-157118	Signaling by NOTCH
R-HSA-162582	Signal Transduction
R-HSA-1630316	Glycosaminoglycan metabolism
R-HSA-1638074	Keratan sulfate/keratin metabolism
R-HSA-1912422	Pre-NOTCH Expression and Processing
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
R-HSA-71387	Metabolism of carbohydrates and carbohydrate derivatives
R-HSA-9033658	Blood group systems biosynthesis

MSigDB gene sets: 270 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_OLIGOSACCHARIDE_METABOLIC_PROCESS, REACTOME_SIGNALING_BY_NOTCH, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_RESPONSE_TO_PEPTIDE, GOBP_GLYCOLIPID_BIOSYNTHETIC_PROCESS, YANG_BREAST_CANCER_ESR1_LASER_DN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOLDRATH_ANTIGEN_RESPONSE, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, RAMALHO_STEMNESS_DN, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS

GO Biological Process (6): glycoprotein biosynthetic process (GO:0009101), glycolipid biosynthetic process (GO:0009247), oligosaccharide biosynthetic process (GO:0009312), keratan sulfate proteoglycan biosynthetic process (GO:0018146), cellular response to interleukin-6 (GO:0071354), obsolete protein glycosylation (GO:0006486)

GO Molecular Function (5): beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836), N-acetyllactosaminide alpha-2,3-sialyltransferase activity (GO:0008118), sialyltransferase activity (GO:0008373), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (4): Golgi membrane (GO:0000139), membrane (GO:0016020), extracellular exosome (GO:0070062), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-13 pathways:

Category	Pathways
Metabolism of carbohydrates and carbohydrate derivatives	2
Pre-NOTCH Expression and Processing	1
Keratan sulfate/keratin metabolism	1
Synthesis of substrates in N-glycan biosythesis	1
Blood group systems biosynthesis	1
Signal Transduction	1
Glycosaminoglycan metabolism	1
Signaling by NOTCH	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
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
carbohydrate derivative biosynthetic process	2
sialyltransferase activity	2
macromolecule biosynthetic process	1
glycoprotein metabolic process	1
glycolipid metabolic process	1
lipid biosynthetic process	1
oligosaccharide metabolic process	1
carbohydrate biosynthetic process	1
proteoglycan biosynthetic process	1
keratan sulfate proteoglycan metabolic process	1
response to interleukin-6	1
cellular response to cytokine stimulus	1
glycosyltransferase activity	1
catalytic activity	1
transferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cellular anatomical structure	1
extracellular vesicle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

718 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ST3GAL6	FUT7	Q11130	626
ST3GAL6	CHST4	Q8NCG5	605
ST3GAL6	GCNT1	Q02742	587
ST3GAL6	B3GNT3	Q9Y2A9	567
ST3GAL6	ST8SIA1	Q92185	546
ST3GAL6	ST8SIA6	P61647	544
ST3GAL6	FUT3	P21217	536
ST3GAL6	B4GALT5	O43286	535
ST3GAL6	MGAT5	Q09328	515
ST3GAL6	B4GALT4	O60513	508
ST3GAL6	FUT6	P51993	480
ST3GAL6	FUT1	P19526	480
ST3GAL6	NEU4	Q8WWR8	478
ST3GAL6	GCNT2	Q8N0V5	477
ST3GAL6	B4GALT1	P15291	475

IntAct

26 interactions, top by confidence:

A	B	Type	Score
CLGN	NPC1	psi-mi:“MI:0914”(association)	0.530
CHRNA3	TMEM223	psi-mi:“MI:0914”(association)	0.350
SLAMF1	RTCA	psi-mi:“MI:0914”(association)	0.350
PTCH1	PLXNB2	psi-mi:“MI:0914”(association)	0.350
PON2	ENTPD6	psi-mi:“MI:0914”(association)	0.350
NCEH1	C1QL1	psi-mi:“MI:0914”(association)	0.350
HLA-DRA	TMEM223	psi-mi:“MI:0914”(association)	0.350
CHRNA4	TMEM223	psi-mi:“MI:0914”(association)	0.350
PDGFRA	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CLEC2D	TMEM120B	psi-mi:“MI:0914”(association)	0.350
CHRNB2	TMEM131L	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
SCGB2A2	RTL8C	psi-mi:“MI:0914”(association)	0.350
C1orf54	AGRN	psi-mi:“MI:0914”(association)	0.350
INS	LAMA5	psi-mi:“MI:0914”(association)	0.350
SPX	ERI3	psi-mi:“MI:0914”(association)	0.350
MSMB	ADAM11	psi-mi:“MI:0914”(association)	0.350
TAFA2	ERN1	psi-mi:“MI:0914”(association)	0.350
PTCH1	TMEM131L	psi-mi:“MI:0914”(association)	0.350
ITM2C		psi-mi:“MI:0914”(association)	0.350
PDGFRA	QSOX1	psi-mi:“MI:0914”(association)	0.350

BioGRID (31): ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Negative Genetic), ST3GAL6 (Affinity Capture-RNA), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS), ST3GAL6 (Affinity Capture-MS)

ESM2 similar proteins: A7XDQ9, B9S2H4, B9SLR1, O22807, O22943, O65431, O81007, P0C2H4, P61132, P61943, P97325, Q02734, Q09341, Q0VBN2, Q0WV13, Q11203, Q18416, Q18473, Q19417, Q20593, Q20806, Q21802, Q23469, Q4G148, Q501D6, Q564G7, Q6YRM6, Q701R0, Q701R1, Q84WU0, Q8BLI4, Q8GWT1, Q8IZU8, Q8L7F9, Q8RY00, Q93834, Q966A0, Q9ASW1, Q9C8W3, Q9C9Q5

Diamond homologs: A2WX64, A2XVC2, A2ZI41, A5D7T4, O35696, O43173, P13721, P15907, P61130, P61131, P61643, P61644, P61645, P61943, P70277, Q02745, Q07977, Q08E15, Q11200, Q11201, Q11204, Q11205, Q11206, Q16842, Q2QXM3, Q2R2B1, Q5K027, Q5QQ37, Q5RE85, Q64685, Q64689, Q64690, Q6H8M7, Q6KB54, Q6KB58, Q6KB59, Q6ZH45, Q6ZXC9, Q701R0, Q701R1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3241 predictions. Top by Δscore:

Variant	Effect	Δscore
3:98770873:TCATA:T	acceptor_loss	1.0000
3:98770874:CATA:C	acceptor_loss	1.0000
3:98770875:ATAG:A	acceptor_gain	1.0000
3:98770876:TA:T	acceptor_loss	1.0000
3:98770877:A:AG	acceptor_gain	1.0000
3:98770877:AG:A	acceptor_gain	1.0000
3:98770877:AGGGT:A	acceptor_gain	1.0000
3:98770878:G:GG	acceptor_gain	1.0000
3:98770878:GG:G	acceptor_gain	1.0000
3:98770878:GGGTG:G	acceptor_gain	1.0000
3:98772807:TTCCA:T	acceptor_loss	1.0000
3:98772809:CCA:C	acceptor_loss	1.0000
3:98772810:CAG:C	acceptor_loss	1.0000
3:98772812:G:GC	acceptor_loss	1.0000
3:98773918:A:AG	acceptor_gain	1.0000
3:98773919:G:GG	acceptor_gain	1.0000
3:98773984:G:GG	donor_gain	1.0000
3:98791839:A:AG	acceptor_gain	1.0000
3:98791840:G:GG	acceptor_gain	1.0000
3:98791840:GAA:G	acceptor_gain	1.0000
3:98791840:GAAA:G	acceptor_gain	1.0000
3:98791840:GAAAC:G	acceptor_gain	1.0000
3:98793669:CTTTA:C	acceptor_loss	1.0000
3:98793670:TTTAG:T	acceptor_loss	1.0000
3:98793671:TTA:T	acceptor_loss	1.0000
3:98793673:A:AG	acceptor_gain	1.0000
3:98793674:G:A	acceptor_loss	1.0000
3:98793674:G:GA	acceptor_gain	1.0000
3:98793674:GAAC:G	acceptor_gain	1.0000
3:98799675:AGG:A	donor_gain	1.0000

AlphaMissense

2192 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:98788095:G:C	R164P	0.999
3:98788387:G:C	R227P	0.999
3:98784961:T:A	C118S	0.998
3:98784961:T:C	C118R	0.998
3:98784962:G:C	C118S	0.998
3:98784971:T:A	V121D	0.998
3:98785040:G:C	R144T	0.998
3:98788036:A:C	R144S	0.998
3:98788036:A:T	R144S	0.998
3:98788076:G:T	G158W	0.998
3:98791895:T:C	C271R	0.998
3:98791896:G:A	C271Y	0.998
3:98791897:T:G	C271W	0.998
3:98791919:T:C	F279L	0.998
3:98791921:T:A	F279L	0.998
3:98791921:T:G	F279L	0.998
3:98784963:T:G	C118W	0.997
3:98784978:T:A	N123K	0.997
3:98784978:T:G	N123K	0.997
3:98788042:T:A	N146K	0.997
3:98788042:T:G	N146K	0.997
3:98788077:G:A	G158E	0.997
3:98788077:G:T	G158V	0.997
3:98791895:T:A	C271S	0.997
3:98791896:G:C	C271S	0.997
3:98785037:T:A	I143K	0.996
3:98785039:A:G	R144G	0.996
3:98788112:T:C	S170P	0.996
3:98788190:T:A	W196R	0.996
3:98788190:T:C	W196R	0.996

dbSNP variants (sampled 300 via entrez): RS1000049376 (3:98730772 C>T), RS1000067078 (3:98784633 G>A,C), RS1000103923 (3:98731867 C>T), RS1000117681 (3:98732317 G>A), RS1000127715 (3:98736427 C>T), RS1000133714 (3:98785898 G>A), RS1000144029 (3:98788474 A>C,G), RS1000169846 (3:98733150 C>G,T), RS1000177613 (3:98781246 C>A,T), RS1000179394 (3:98744555 C>T), RS1000180354 (3:98736662 A>G), RS1000252239 (3:98792207 T>C), RS1000301480 (3:98750963 C>T), RS1000304006 (3:98732109 A>G), RS1000354275 (3:98742372 C>A)

Disease associations

OMIM: gene MIM:607156 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST008870_39	Keratinocyte cancer (MTAG)	2.000000e-08
GCST008871_2	Basal cell carcinoma	9.000000e-09
GCST010002_434	Refractive error	5.000000e-25
GCST90000654_10	Central corneal thickness	5.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010176	keratinocyte carcinoma
EFO:0005213	central corneal thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	5
sodium arsenite	affects methylation, increases expression	4
Air Pollutants	decreases expression, increases abundance, increases expression	3
Tretinoin	increases expression	3
trichostatin A	affects cotreatment, increases expression	2
Silicon Dioxide	decreases expression, increases expression	2
Smoke	decreases expression, decreases reaction, increases abundance, increases expression	2
Cyclosporine	decreases expression	2
Particulate Matter	decreases expression, increases abundance	2
testosterone enanthate	affects expression	1
triphenyl phosphate	affects expression	1
pyrimidin-2-one beta-ribofuranoside	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
9,10-dihydro-9,10-dihydroxybenzo(a)pyrene	increases expression	1
nickel sulfate	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
2-palmitoylglycerol	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
abrine	decreases expression	1
mirdametinib	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
(+)-JQ1 compound	affects cotreatment, decreases expression	1
Decitabine	decreases expression, decreases reaction	1
Sunitinib	decreases expression	1
Fulvestrant	increases methylation	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Atrazine	decreases expression	1
Azacitidine	increases expression	1

Clinical trials (associated diseases)

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