GCNT3

Summary

GCNT3 (glucosaminyl (N-acetyl) transferase 3, mucin type, HGNC:4205) is a protein-coding gene on chromosome 15q22.2, encoding Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 3 (O95395). Glycosyltransferase that can synthesize all known mucin beta 6 N-acetylglucosaminides.

This gene encodes a member of the N-acetylglucosaminyltransferase family. The encoded protein is a beta-6-N-acetylglucosamine-transferase that catalyzes the formation of core 2 and core 4 O-glycans on mucin-type glycoproteins.

Source: NCBI Gene 9245 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 85 total
• MANE Select transcript: NM_004751

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4205
Approved symbol	GCNT3
Name	glucosaminyl (N-acetyl) transferase 3, mucin type
Location	15q22.2
Locus type	gene with protein product
Status	Approved
Aliases	C2GnT-M, C2/4GnT, C2GnT2
Ensembl gene	ENSG00000140297
Ensembl biotype	protein_coding
OMIM	606836
Entrez	9245

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 13 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000396065, ENST00000558721, ENST00000559189, ENST00000559200, ENST00000559626, ENST00000560111, ENST00000560210, ENST00000560580, ENST00000560585, ENST00000560874, ENST00000881403, ENST00000953236, ENST00000953237, ENST00000953238, ENST00000953239, ENST00000953240, ENST00000953241, ENST00000953242

RefSeq mRNA: 2 — MANE Select: NM_004751 NM_001426662, NM_004751

CCDS: CCDS10172

Canonical transcript exons

ENST00000396065 — 3 exons

Exon	Start	End
ENSE00001251834	59616692	59616881
ENSE00001523748	59618179	59622723
ENSE00003846492	59611783	59611981

Expression profiles

Bgee: expression breadth ubiquitous, 204 present calls, max score 99.26.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.7757 / max 304.2039, expressed in 178 samples.

FANTOM5 promoters (22 alternative TSS)

Promoter ID	TPM avg	Samples expressed
146986	0.5877	58
146991	0.1951	51
146990	0.1528	53
146993	0.0942	22
146995	0.0734	17
147005	0.0709	17
147002	0.0617	23
146998	0.0595	23
146988	0.0552	28
146996	0.0548	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
palpebral conjunctiva	UBERON:0001812	99.26	gold quality
mucosa of transverse colon	UBERON:0004991	99.18	gold quality
colonic mucosa	UBERON:0000317	98.99	gold quality
mucosa of sigmoid colon	UBERON:0004993	98.98	gold quality
rectum	UBERON:0001052	98.39	gold quality
ileal mucosa	UBERON:0000331	97.56	gold quality
gall bladder	UBERON:0002110	96.40	gold quality
duodenum	UBERON:0002114	95.08	gold quality
jejunal mucosa	UBERON:0000399	94.97	gold quality
pancreatic ductal cell	CL:0002079	94.82	gold quality
epithelial cell of pancreas	CL:0000083	94.40	gold quality
secondary oocyte	CL:0000655	94.23	gold quality
sperm	CL:0000019	93.07	gold quality
islet of Langerhans	UBERON:0000006	92.82	gold quality
lower esophagus mucosa	UBERON:0035834	91.77	gold quality
minor salivary gland	UBERON:0001830	91.59	gold quality
esophagus squamous epithelium	UBERON:0006920	90.22	gold quality
oral cavity	UBERON:0000167	90.11	gold quality
saliva-secreting gland	UBERON:0001044	89.75	gold quality
male germ cell	CL:0000015	89.35	gold quality
epithelium of esophagus	UBERON:0001976	89.20	gold quality
transverse colon	UBERON:0001157	88.43	gold quality
amniotic fluid	UBERON:0000173	88.37	gold quality
mouth mucosa	UBERON:0003729	87.06	gold quality
oocyte	CL:0000023	86.95	gold quality
parotid gland	UBERON:0001831	86.84	gold quality
small intestine Peyer’s patch	UBERON:0003454	85.91	gold quality
small intestine	UBERON:0002108	85.80	gold quality
vermiform appendix	UBERON:0001154	84.90	gold quality
trachea	UBERON:0003126	84.70	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	24.10
E-MTAB-5061	yes	13.68
E-GEOD-81608	yes	9.35
E-ENAD-27	yes	5.16
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting GCNT3, 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-12121	99.99	66.64	255
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-4708-3P	99.51	67.99	870
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-10524-5P	99.05	66.08	963
HSA-MIR-9898	99.00	67.89	500
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-619-3P	98.38	65.58	693
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-490-3P	97.79	65.54	606
HSA-MIR-921	97.09	66.45	562
HSA-MIR-454-5P	96.51	68.35	263
HSA-MIR-6782-5P	96.45	64.42	612
HSA-MIR-4633-3P	93.85	63.56	534
HSA-MIR-6500-5P	93.85	63.64	522

Literature-anchored findings (GeneRIF, showing 16)

• EGF suppressed C2GnT activity in a time- and dose-dependent fashion, and also suppressed core 4 beta1,6 N-acetylglucosaminyltransferase (C4GnT) activity (PMID:12600830)
• Frequently downregulated in colorectal cancer and suppresses colon cancer cell growth. (PMID:16418723)
• Results describe the identification of the cis-regulatory elements of human C2GnT-M gene. (PMID:17303715)
• C2GnT2 KO mice have decreased mucosal barrier function in the digestive tract, reduced levels of circulating IgGs and fecal IgA, and increased susceptibility to experimental colitis (PMID:20816165)
• 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)
• Golgi fragmentation is accompanied by the increased association of NMIIA with C2GnT-M and its degradation by proteasomes. (PMID:23396488)
• low GCNT3 expression is a promising prognostic biomarker for colon cancer that could be used to identify early-stage colon cancer patients at high risk of relapse. (PMID:25466507)
• In HeLa cells transiently expressing C2GnT-M-GFP, knockdown of KRT1 does not affect Golgi morphology but leaves C2GnT-M outside of the Golgi, resulting in the formation of sialyl-T antigen. (PMID:25605727)
• This study provides the concepts toward the design of carbohydrate-dependent inhibition of EPEC and EHEC O157:H7 adhesion to human intestinal epithelial cells. (PMID:25701318)
• In this Molecular Pathways article, we briefly discuss the potential role of mucin synthesis in cancers, ways to improve drug delivery and disrupt mucin mesh to overcome chemoresistance by targeting mucin synthesis, and the unique opportunity to target the GCNT3 pathway for the prevention and treatment of cancers. (PMID:28039261)
• High GCNT3 expression is associated with metastatic melanomas. (PMID:28923134)
• GCNT3 was regarded as an oncogene in non-small cell lung cancer, and a target of miR-302b-3p, which regulated cell proliferation, migration and invasion in a GCNT3-dependent manner and E-cadherin, N-cadherin, vimentin, cyclin D1 and p-Erk appeared to be downstream molecules of the miR-302b-3p/GCNT3 pathway. (PMID:30355927)
• Global analysis of human glycosyltransferases reveals novel targets for pancreatic cancer pathogenesis. (PMID:32203219)
• LINC00511 enhances LUAD malignancy by upregulating GCNT3 via miR-195-5p. (PMID:35399076)
• Functional analysis of GCNT3 for cell migration and EMT of castration-resistant prostate cancer cells. (PMID:35867813)
• GCNT3 regulated MUC13 to promote the development of hepatocellular carcinoma through the GSK3beta/beta-catenin pathway. (PMID:38369410)

Cross-species orthologs

22 orthologs

Organism	Symbol	Gene ID
danio_rerio	gcnt3	ENSDARG00000060471
mus_musculus	Gcnt3	ENSMUSG00000032226
rattus_norvegicus	Gcnt3	ENSRNOG00000059540
drosophila_melanogaster	oxt	FBGN0015360
drosophila_melanogaster	CG9164	FBGN0030634
caenorhabditis_elegans	gly-15	WBGENE00001640
caenorhabditis_elegans	gly-16	WBGENE00001641
caenorhabditis_elegans	gly-17	WBGENE00001642
caenorhabditis_elegans	gly-18	WBGENE00001643
caenorhabditis_elegans	gly-19	WBGENE00001644
caenorhabditis_elegans		WBGENE00005024
caenorhabditis_elegans		WBGENE00009148
caenorhabditis_elegans	F30A10.4	WBGENE00009263
caenorhabditis_elegans		WBGENE00011090
caenorhabditis_elegans	T09E11.6	WBGENE00011655
caenorhabditis_elegans	T09E11.9	WBGENE00011658
caenorhabditis_elegans	T27F6.1	WBGENE00012102
caenorhabditis_elegans		WBGENE00012135
caenorhabditis_elegans		WBGENE00013119
caenorhabditis_elegans	ZK1225.2	WBGENE00014236
caenorhabditis_elegans		WBGENE00019270
caenorhabditis_elegans		WBGENE00019919

Paralogs (8): XYLT2 (ENSG00000015532), WSCD2 (ENSG00000075035), XYLT1 (ENSG00000103489), GCNT2 (ENSG00000111846), GCNT7 (ENSG00000124091), GCNT4 (ENSG00000176928), WSCD1 (ENSG00000179314), GCNT1 (ENSG00000187210)

Protein

Protein identifiers

Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 3 — O95395 (reviewed: O95395)

Alternative names: C2GnT-mucin type, Core 2/core 4 beta-1,6-N-acetylglucosaminyltransferase

All UniProt accessions (4): O95395, H0YM40, H0YMW7, H0YNA3

UniProt curated annotations — full annotation on UniProt →

Function. Glycosyltransferase that can synthesize all known mucin beta 6 N-acetylglucosaminides. Mediates core 2 and core 4 O-glycan branching, 2 important steps in mucin-type biosynthesis. Also has I-branching enzyme activity by converting linear into branched poly-N-acetyllactosaminoglycans, leading to introduce the blood group I antigen during embryonic development.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Primarily expressed in mucus-secreting tissues. Expressed in colon, kidney, small intestine, trachea, and stomach, where mucin is produced.

Post-translational modifications. N-glycosylated.

Induction. By all-trans retinoic acid (ATRA), TNF and IL13/interleukin-13. Strongly down-regulated in colorectal cancer.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 14 family.

RefSeq proteins (2): NP_001413591, NP_004742* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003406	Glyco_trans_14	Family

Pfam: PF02485

Enzyme classification (BRENDA):

• EC 2.4.1.102 — beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase (BRENDA: 13 organisms, 110 substrates, 35 inhibitors, 50 Km, 0 kcat entries)
• EC 2.4.1.150 — N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase (BRENDA: 14 organisms, 65 substrates, 15 inhibitors, 5 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

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

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

Catalyzed reactions (Rhea), 5 shown:

• a beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-beta-D-GlcNAc derivative + UDP-N-acetyl-alpha-D-glucosamine = a beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->3)-[beta-D-GlcNAc-(1->6)]-beta-D-Gal-(1->4)-N-acetyl-beta-D-GlcNAc derivative + UDP + H(+) (RHEA:54820)
• 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP + H(+) (RHEA:56188)
• a 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-[N-acetyl-beta-D-glucosaminyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP + H(+) (RHEA:56192)
• a 3-O-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-seryl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + UDP + H(+) (RHEA:56212)
• a 3-O-[beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl]-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = a 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + UDP + H(+) (RHEA:56216)

UniProt features (9 total): disulfide bond 4, topological domain 2, chain 1, transmembrane region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95395-F1	94.00	0.86

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 (4): 70–227, 161–382, 182–209, 391–423

Glycosylation sites (1): 289

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 127 (showing top): GOBP_DIGESTION, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, MYOD_01, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, LIAO_METASTASIS, GOBP_DIGESTIVE_SYSTEM_PROCESS, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, CHO_NR4A1_TARGETS, RYTTCCTG_ETS2_B, GOBP_KIDNEY_MORPHOGENESIS, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION_VIA_N_ACETYL_GALACTOSAMINE, IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR, GOBP_TISSUE_MORPHOGENESIS

GO Biological Process (8): carbohydrate metabolic process (GO:0005975), protein O-linked glycosylation (GO:0006493), protein O-linked glycosylation via N-acetylgalactosamine (GO:0016266), tissue morphogenesis (GO:0048729), intestinal absorption (GO:0050892), kidney morphogenesis (GO:0060993), obsolete protein glycosylation (GO:0006486), glycoprotein biosynthetic process (GO:0009101)

GO Molecular Function (7): beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829), N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109), acetylglucosaminyltransferase activity (GO:0008375), acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225), UDP-glycosyltransferase activity (GO:0008194), 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-1 pathways:

Category	Pathways
O-linked glycosylation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
acetylglucosaminyltransferase activity	3
catalytic activity, acting on a glycoprotein	2
primary metabolic process	1
glycoprotein biosynthetic process	1
protein O-linked glycosylation	1
anatomical structure morphogenesis	1
tissue development	1
digestive system process	1
kidney development	1
animal organ morphogenesis	1
macromolecule biosynthetic process	1
glycoprotein metabolic process	1
carbohydrate derivative biosynthetic process	1
UDP-glycosyltransferase activity	1
hexosyltransferase activity	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

704 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GCNT3	C1GALT1	Q9NS00	720
GCNT3	B3GNT6	Q6ZMB0	689
GCNT3	ST3GAL1	Q11201	593
GCNT3	ST6GALNAC1	Q9NSC7	584
GCNT3	C1GALT1C1	Q96EU7	582
GCNT3	B3GNT3	Q9Y2A9	556
GCNT3	ST6GALNAC4	Q9H4F1	554
GCNT3	GALNT3	Q14435	534
GCNT3	B3GALT5	Q9Y2C3	534
GCNT3	A4GNT	Q9UNA3	533
GCNT3	GALNT12	Q8IXK2	514
GCNT3	FUT1	P19526	512
GCNT3	MGAT5	Q09328	499
GCNT3	GALNT4	Q8N4A0	471
GCNT3	GALNT6	Q8NCL4	467

IntAct

12 interactions, top by confidence:

A	B	Type	Score
GCNT3	BCKDK	psi-mi:“MI:0914”(association)	0.530
GCNT3	CASK	psi-mi:“MI:0915”(physical association)	0.370
SNUPN	GCNT3	psi-mi:“MI:0915”(physical association)	0.370
GCNT3	RBM18	psi-mi:“MI:0915”(physical association)	0.370
DHRSX	GCNT3	psi-mi:“MI:0915”(physical association)	0.370
rep	GPR89A	psi-mi:“MI:0914”(association)	0.350
	SHTN1	psi-mi:“MI:0914”(association)	0.350
GLRA3	GCNT3	psi-mi:“MI:0914”(association)	0.350

BioGRID (29): HERC1 (Affinity Capture-MS), RBM14-RBM4 (Affinity Capture-MS), CXCR4 (Affinity Capture-MS), CUL4B (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), BCKDK (Affinity Capture-MS), SORL1 (Affinity Capture-MS), GCNT3 (Affinity Capture-MS), GCNT3 (Affinity Capture-MS), GCNT3 (Proximity Label-MS), APPBP2 (Affinity Capture-MS), BCKDK (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), CUL2 (Affinity Capture-MS), GCNT3 (Affinity Capture-MS)

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	78
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

390 predictions. Top by Δscore:

Variant	Effect	Δscore
15:59611978:AAAGG:A	donor_loss	1.0000
15:59611980:AGGT:A	donor_loss	1.0000
15:59611982:G:C	donor_loss	1.0000
15:59611983:T:A	donor_loss	1.0000
15:59616878:AAAGG:A	donor_loss	0.9900
15:59616879:AAGGT:A	donor_loss	0.9900
15:59616880:AGGTG:A	donor_loss	0.9900
15:59616882:G:A	donor_loss	0.9900
15:59616883:T:A	donor_loss	0.9900
15:59611982:G:GG	donor_gain	0.9800
15:59639155:TATCT:T	acceptor_loss	0.9800
15:59639157:TC:T	acceptor_loss	0.9800
15:59639158:C:CC	acceptor_gain	0.9800
15:59639158:CTA:C	acceptor_loss	0.9800
15:59639159:T:G	acceptor_loss	0.9800
15:59616687:TGCAG:T	acceptor_loss	0.9700
15:59616688:GC:G	acceptor_loss	0.9700
15:59616689:CAGAT:C	acceptor_loss	0.9700
15:59616690:A:AG	acceptor_gain	0.9700
15:59616690:AGA:A	acceptor_loss	0.9700
15:59616691:G:GA	acceptor_loss	0.9700
15:59616691:G:GG	acceptor_gain	0.9700
15:59616691:GAT:G	acceptor_gain	0.9500
15:59612002:T:G	donor_gain	0.9400
15:59616617:G:GC	acceptor_gain	0.9400
15:59618176:AAG:A	acceptor_gain	0.9400
15:59639155:TAT:T	acceptor_gain	0.9300
15:59618178:GGATT:G	acceptor_gain	0.9200
15:59639160:A:C	acceptor_loss	0.9200
15:59616882:G:GG	donor_gain	0.9100

AlphaMissense

2910 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:59619336:G:C	W366C	0.997
15:59619336:G:T	W366C	0.997
15:59618896:T:A	W220R	0.996
15:59618896:T:C	W220R	0.996
15:59619235:T:A	W333R	0.996
15:59619235:T:C	W333R	0.996
15:59619409:T:A	C391S	0.996
15:59619410:G:C	C391S	0.996
15:59618865:C:G	C209W	0.994
15:59619334:T:A	W366R	0.994
15:59619334:T:C	W366R	0.994
15:59619409:T:C	C391R	0.994
15:59619410:G:A	C391Y	0.994
15:59619411:C:G	C391W	0.994
15:59618639:C:A	A134E	0.993
15:59619382:T:A	C382S	0.993
15:59619383:G:C	C382S	0.993
15:59619471:G:C	K411N	0.993
15:59619471:G:T	K411N	0.993
15:59618898:G:C	W220C	0.992
15:59618898:G:T	W220C	0.992
15:59619384:C:G	C382W	0.992
15:59619237:G:C	W333C	0.991
15:59619237:G:T	W333C	0.991
15:59619469:A:G	K411E	0.991
15:59619121:G:T	G295W	0.990
15:59619383:G:A	C382Y	0.990
15:59619410:G:T	C391F	0.990
15:59618712:C:A	N158K	0.989
15:59618712:C:G	N158K	0.989

dbSNP variants (sampled 300 via entrez): RS1000017134 (15:59609895 A>G), RS1000068130 (15:59610028 A>T), RS1000075202 (15:59583600 T>A), RS1000121636 (15:59610156 T>C,G), RS1000144059 (15:59587679 T>A), RS1000175599 (15:59587894 G>A), RS1000255816 (15:59588110 A>G), RS1000368320 (15:59619367 G>A,T), RS1000480018 (15:59564737 C>A,T), RS1000543244 (15:59599982 A>C), RS1000581215 (15:59595725 A>G), RS1000601940 (15:59560528 A>C), RS1000621808 (15:59568546 C>A,T), RS1000641083 (15:59614871 A>G), RS1000653406 (15:59595933 C>T)

Disease associations

OMIM: gene MIM:606836 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006976_117	Macular thickness	2.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, affects methylation, decreases methylation	8
Cyclosporine	increases expression	5
Tetrachlorodibenzodioxin	increases expression	4
Acetaminophen	decreases expression, increases expression	3
Zoledronic Acid	increases expression	2
Arsenic Trioxide	decreases expression, decreases response to substance	2
Azathioprine	increases expression	2
Dimethylnitrosamine	decreases expression, increases expression	2
Estradiol	increases expression	2
Hydrogen Peroxide	affects expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Cadmium Chloride	increases expression	2
3,19-(2-bromobenzylidene)andrographolide	decreases response to substance, increases expression	1
sotorasib	affects cotreatment, decreases expression	1
chloroacetaldehyde	increases expression	1
methyleugenol	increases expression	1
bis(tri-n-butyltin)oxide	increases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	affects expression	1
terbufos	increases methylation	1
tris(2-butoxyethyl) phosphate	affects expression	1
cresidine	increases expression	1
diethyl maleate	increases expression	1
sulforaphane	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
potassium bromate	increases expression	1
9,10-dihydro-9,10-dihydroxybenzo(a)pyrene	increases expression	1
nickel chloride	increases expression	1
ochratoxin A	decreases expression	1

Clinical trials (associated diseases)

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