CHSY3

Summary

CHSY3 (chondroitin sulfate synthase 3, HGNC:24293) is a protein-coding gene on chromosome 5q23.3, encoding Chondroitin sulfate synthase 3 (Q70JA7). Has both beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity.

CSS3 is a glycosyltransferase that has both glucuronyltransferase and N-acetylgalactosaminyltransferase activities (Yada et al., 2003 [PubMed 12907687]).

Source: NCBI Gene 337876 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 138 total
• MANE Select transcript: NM_175856

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24293
Approved symbol	CHSY3
Name	chondroitin sulfate synthase 3
Location	5q23.3
Locus type	gene with protein product
Status	Approved
Aliases	CSS3, CHSY-2
Ensembl gene	ENSG00000198108
Ensembl biotype	protein_coding
OMIM	609963
Entrez	337876

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000305031, ENST00000507545

RefSeq mRNA: 1 — MANE Select: NM_175856 NM_175856

CCDS: CCDS34223

Canonical transcript exons

ENST00000305031 — 3 exons

Exon	Start	End
ENSE00001321614	130184229	130186634
ENSE00001368738	129904465	129905631
ENSE00001389773	129908077	129908360

Expression profiles

Bgee: expression breadth ubiquitous, 193 present calls, max score 88.82.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0816 / max 31.2975, expressed in 875 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58384	1.2990	678
58383	0.6443	369
58385	0.1384	66

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	88.82	gold quality
endothelial cell	CL:0000115	87.63	gold quality
tibia	UBERON:0000979	86.83	gold quality
middle temporal gyrus	UBERON:0002771	83.65	gold quality
popliteal artery	UBERON:0002250	81.86	gold quality
tibial artery	UBERON:0007610	81.82	gold quality
aorta	UBERON:0000947	80.89	gold quality
stromal cell of endometrium	CL:0002255	80.10	gold quality
ascending aorta	UBERON:0001496	79.92	gold quality
thoracic aorta	UBERON:0001515	79.79	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.64	gold quality
Brodmann (1909) area 23	UBERON:0013554	78.93	gold quality
cartilage tissue	UBERON:0002418	78.51	gold quality
descending thoracic aorta	UBERON:0002345	75.71	gold quality
cortical plate	UBERON:0005343	75.60	gold quality
subcutaneous adipose tissue	UBERON:0002190	74.16	gold quality
epithelial cell of pancreas	CL:0000083	73.60	silver quality
visceral pleura	UBERON:0002401	73.36	gold quality
superior frontal gyrus	UBERON:0002661	73.13	gold quality
tendon	UBERON:0000043	73.07	gold quality
left coronary artery	UBERON:0001626	72.26	gold quality
right coronary artery	UBERON:0001625	72.15	gold quality
prefrontal cortex	UBERON:0000451	71.88	gold quality
coronary artery	UBERON:0001621	71.53	gold quality
gall bladder	UBERON:0002110	71.47	gold quality
entorhinal cortex	UBERON:0002728	71.30	gold quality
kidney epithelium	UBERON:0004819	71.26	gold quality
endometrium	UBERON:0001295	71.01	gold quality
smooth muscle tissue	UBERON:0001135	70.54	gold quality
postcentral gyrus	UBERON:0002581	70.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	65.61
E-ANND-3	no	2.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

136 targeting CHSY3, 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-3163	100.00	77.23	8605
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-548N	99.98	71.94	4170
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-568	99.98	69.86	2084
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787

Literature-anchored findings (GeneRIF, showing 7)

• The full-length open reading frame consists of 882 amino acids and encodes a typical type II membrane protein. This enzyme contains a beta 3-glycosyltransferase motif and a beta 4-glycosyltransferase motif similar to that found in CSS1. (PMID:12907687)
• results suggest that chondroitin polymerization is achieved by multiple combinations of chondroitin synthase-1, chondroitin synthase-2, and chondroitin-polymerizing factor (PMID:17253960)
• The present study focused on the expression of chondroitin-synthesizing enzymes in colorectal cancer. (PMID:21468578)
• Chondroitin synthase-3 regulates nucleus pulposus degeneration through actin-induced YAP signaling. (PMID:33089528)
• Reduction of pl-CSA through ChSy-2 knockout inhibits tumorigenesis and metastasis of choriocarcinoma in JEG3 cells. (PMID:33390789)
• CHSY3 promotes proliferation and migration in gastric cancer and is associated with immune infiltration. (PMID:37461041)
• The prognostic implications and tumor-promoting functions of CHSY3 in gastric cancer. (PMID:38812506)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	chsy3	ENSDARG00000069472
mus_musculus	Chsy3	ENSMUSG00000058152
rattus_norvegicus	Chsy3	ENSRNOG00000050152
drosophila_melanogaster	Chsy	FBGN0030662
caenorhabditis_elegans	sqv-5	WBGENE00005023

Paralogs (7): CHPF2 (ENSG00000033100), CHPF (ENSG00000123989), CHSY1 (ENSG00000131873), B4GALNT3 (ENSG00000139044), CSGALNACT1 (ENSG00000147408), CSGALNACT2 (ENSG00000169826), B4GALNT4 (ENSG00000182272)

Protein

Protein identifiers

Chondroitin sulfate synthase 3 — Q70JA7 (reviewed: Q70JA7)

Alternative names: Carbohydrate synthase 2, Chondroitin glucuronyltransferase 3, Chondroitin synthase 2, Glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase II, N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase 3, N-acetylgalactosaminyltransferase 3

All UniProt accessions (1): Q70JA7

UniProt curated annotations — full annotation on UniProt →

Function. Has both beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity. Transfers glucuronic acid (GlcUA) from UDP-GlcUA and N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of the elongating chondroitin polymer. Specific activity is much reduced compared to CHSY1.

Subcellular location. Golgi apparatus. Golgi stack membrane.

Tissue specificity. Detected at low levels in brain, cerebral cortex, uterus and small intestine.

Cofactor. Divalent metal cations. Highest activities are measured with Co(2+), Mn(2+) and Cd(2+).

Similarity. Belongs to the chondroitin N-acetylgalactosaminyltransferase family.

RefSeq proteins (1): NP_787052* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008428	Chond_GalNAc	Family
IPR029044	Nucleotide-diphossugar_trans	Homologous_superfamily
IPR051227	CS_glycosyltransferase	Family

Pfam: PF05679

Enzyme classification (BRENDA):

• EC 2.4.1.175 — glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase (BRENDA: 8 organisms, 92 substrates, 7 inhibitors, 8 Km, 1 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
UDP-N-ACETYL-BETA-D-GALACTOSAMINE	0.0059–0.05	3
UDP-GALNAC	0.221–9.275	2
CHONDROITIN SULFATE CS-11	0.36	1
UDP-N-ACETYL-ALPHA-D-GLUCOSAMINE	0.0059	1

Catalyzed reactions (Rhea), 4 shown:

• 3-O-(beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-(beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + UDP + H(+) (RHEA:20800)
• 3-O-(beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + UDP-alpha-D-glucuronate = 3-O-(beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + UDP + H(+) (RHEA:23428)
• 3-O-{beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + UDP-alpha-D-glucuronate = 3-O-{beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + UDP + H(+) (RHEA:54996)
• 3-O-{beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-{beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + UDP + H(+) (RHEA:55000)

UniProt features (23 total): sequence conflict 8, glycosylation site 4, topological domain 2, sequence variant 2, compositionally biased region 2, binding site 2, chain 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
9Q8Z	ELECTRON MICROSCOPY	3
9O4G	ELECTRON MICROSCOPY	3.42

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q70JA7-F1	77.97	0.49

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 (2): 720; 834

Glycosylation sites (4): 279, 710, 878, 155

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-2022870	CS-GAG biosynthesis

MSigDB gene sets: 107 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, TGAGATT_MIR216, ACTTTAT_MIR1425P, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_METABOLIC_PROCESS, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, REACTOME_METABOLISM_OF_CARBOHYDRATES_AND_CARBOHYDRATE_DERIVATIVES, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, ATGTACA_MIR493, GOCC_GOLGI_CISTERNA_MEMBRANE

GO Biological Process (1): chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)

GO Molecular Function (5): metal ion binding (GO:0046872), glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238), N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510), acetylgalactosaminyltransferase activity (GO:0008376), transferase activity (GO:0016740)

GO Cellular Component (4): Golgi membrane (GO:0000139), Golgi cisterna membrane (GO:0032580), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Chondroitin sulfate/dermatan sulfate metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
proteoglycan biosynthetic process	1
chondroitin sulfate proteoglycan metabolic process	1
protein O-linked glycosylation via xylose	1
cation binding	1
acetylgalactosaminyltransferase activity	1
glucuronosyltransferase activity	1
UDP-glycosyltransferase activity	1
hexosyltransferase activity	1
catalytic activity	1
Golgi apparatus	1
bounding membrane of organelle	1
organelle membrane	1
Golgi cisterna	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

440 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CHSY3	GALNT3	Q14435	762
CHSY3	FGF23	Q9GZV9	570
CHSY3	B4GALT7	Q9UBV7	453
CHSY3	CHSY1	Q86X52	442
CHSY3	KL	Q9UEF7	436
CHSY3	XYLT1	Q86Y38	426
CHSY3	SLC34A3	Q8N130	419
CHSY3	CHST11	Q9NPF2	415
CHSY3	GRAMD1A	Q96CP6	408
CHSY3	B3GAT3	O94766	400
CHSY3	STXBP6	Q8NFX7	398
CHSY3	RALGAPA1	Q6GYQ0	386
CHSY3	C1orf198	Q9H425	380
CHSY3	PHEX	P78562	370
CHSY3	NPEPL1	Q8NDH3	360

IntAct

47 interactions, top by confidence:

A	B	Type	Score
MGAT4C	GXYLT2	psi-mi:“MI:0914”(association)	0.530
LRFN4	RIMOC1	psi-mi:“MI:0914”(association)	0.530
GDPD5	GOLIM4	psi-mi:“MI:0914”(association)	0.530
ISLR	BCKDK	psi-mi:“MI:0914”(association)	0.530
PLAUR	XRCC3	psi-mi:“MI:0914”(association)	0.530
ADAM21	PLXNA2	psi-mi:“MI:0914”(association)	0.530
MYCBPAP	CHSY3	psi-mi:“MI:0914”(association)	0.530
CHSY3	CHSY1	psi-mi:“MI:0914”(association)	0.530
SV2A	EXTL3	psi-mi:“MI:0914”(association)	0.530
FOXN3	FOXN3	psi-mi:“MI:0914”(association)	0.350
SCGB2A2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
ISLR	DDX11L8	psi-mi:“MI:0914”(association)	0.350
PLAUR	DDX11L8	psi-mi:“MI:0914”(association)	0.350
ADAM21	PLXNB2	psi-mi:“MI:0914”(association)	0.350
SIAE	COCH	psi-mi:“MI:0914”(association)	0.350
CHSY3	STK17B	psi-mi:“MI:0914”(association)	0.350
PDGFRA	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CLEC12B	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CCL3	KRBA1	psi-mi:“MI:0914”(association)	0.350
SCGB2A2	RTL8C	psi-mi:“MI:0914”(association)	0.350
CEACAM8	PRRT4	psi-mi:“MI:0914”(association)	0.350
C1orf54	AGRN	psi-mi:“MI:0914”(association)	0.350
LCN6	COCH	psi-mi:“MI:0914”(association)	0.350
CHSY3	TLR5	psi-mi:“MI:0914”(association)	0.350
MAN1A1	GPC4	psi-mi:“MI:0914”(association)	0.350
CHSY3	LRP5	psi-mi:“MI:0914”(association)	0.350
C1orf54	QSOX1	psi-mi:“MI:0914”(association)	0.350

BioGRID (60): CHSY3 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), CHSY1 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), GOLPH3 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), CHSY3 (Affinity Capture-MS), RMND1 (Affinity Capture-MS), CCPG1 (Affinity Capture-MS)

ESM2 similar proteins: A2BGL3, D4PHA7, F4I6V0, O43916, O88199, Q0IIY2, Q13219, Q16WU7, Q28CF8, Q2TBF2, Q505J3, Q5DTK1, Q5E9N5, Q5NDE3, Q5NDE4, Q5NDE5, Q5NDE6, Q5NDE7, Q5NDE8, Q5NDF0, Q5NDF1, Q5RJQ0, Q5XHM7, Q64610, Q658N2, Q66PG1, Q66PG2, Q66PG3, Q68CR1, Q6DBY9, Q6L8S8, Q70JA7, Q7LFX5, Q7LGC8, Q80TS8, Q80XH4, Q811B1, Q8BW41, Q8C1F4, Q8CHI9

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	127
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2078 predictions. Top by Δscore:

Variant	Effect	Δscore
5:129908074:TAGG:T	acceptor_loss	1.0000
5:129908075:A:AG	acceptor_gain	1.0000
5:129908075:AG:A	acceptor_gain	1.0000
5:129908075:AGGT:A	acceptor_gain	1.0000
5:129908076:G:GT	acceptor_gain	1.0000
5:129908076:GG:G	acceptor_gain	1.0000
5:129908076:GGT:G	acceptor_gain	1.0000
5:129908076:GGTG:G	acceptor_gain	1.0000
5:129908356:ACGAG:A	donor_loss	1.0000
5:129908361:G:GC	donor_loss	1.0000
5:129908362:T:A	donor_loss	1.0000
5:130115995:G:GT	donor_gain	1.0000
5:130184221:C:G	acceptor_gain	1.0000
5:130184223:TTTCA:T	acceptor_loss	1.0000
5:130184224:TTCA:T	acceptor_loss	1.0000
5:130184225:TCA:T	acceptor_loss	1.0000
5:130184226:CAG:C	acceptor_loss	1.0000
5:130184227:A:AG	acceptor_gain	1.0000
5:130184227:AGATG:A	acceptor_loss	1.0000
5:130184228:G:GG	acceptor_gain	1.0000
5:130184228:GA:G	acceptor_gain	1.0000
5:130184228:GAT:G	acceptor_gain	1.0000
5:130184228:GATGC:G	acceptor_gain	1.0000
5:129905627:CAAAG:C	donor_loss	0.9900
5:129905628:AAAG:A	donor_loss	0.9900
5:129905629:AAG:A	donor_loss	0.9900
5:129905630:AG:A	donor_loss	0.9900
5:129905631:GG:G	donor_loss	0.9900
5:129905632:GTGA:G	donor_loss	0.9900
5:129905633:T:A	donor_loss	0.9900

AlphaMissense

5822 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:129905355:G:T	G176W	1.000
5:129905412:T:A	W195R	1.000
5:129905412:T:C	W195R	1.000
5:129905595:T:A	W256R	1.000
5:129905595:T:C	W256R	1.000
5:129905611:A:T	D261V	1.000
5:129905613:G:C	D262H	1.000
5:129905613:G:T	D262Y	1.000
5:129905614:A:T	D262V	1.000
5:129905616:G:C	D263H	1.000
5:129905617:A:T	D263V	1.000
5:129908134:G:A	G287E	1.000
5:129908196:T:C	F308L	1.000
5:129908198:C:A	F308L	1.000
5:129908198:C:G	F308L	1.000
5:129908199:T:A	C309S	1.000
5:129908199:T:C	C309R	1.000
5:129908200:G:A	C309Y	1.000
5:129908200:G:C	C309S	1.000
5:129908201:T:G	C309W	1.000
5:129908226:A:C	S318R	1.000
5:129908227:G:T	S318I	1.000
5:129908228:C:A	S318R	1.000
5:129908228:C:G	S318R	1.000
5:129908268:T:C	C332R	1.000
5:129908296:A:T	E341V	1.000
5:129908298:G:C	D342H	1.000
5:129908299:A:C	D342A	1.000
5:129908299:A:G	D342G	1.000
5:129908299:A:T	D342V	1.000

dbSNP variants (sampled 300 via entrez): RS1000000041 (5:130132535 C>T), RS1000017732 (5:130096326 C>G,T), RS1000029362 (5:129923938 T>C), RS1000030013 (5:129952595 T>C), RS1000036900 (5:130174826 A>T), RS1000052941 (5:130173579 A>G), RS1000062083 (5:129971282 A>G), RS1000066783 (5:130107893 A>C), RS1000076792 (5:130173367 G>A), RS1000089146 (5:130086251 C>G), RS1000105135 (5:130090077 C>T), RS1000111285 (5:129993996 T>A), RS1000138 (5:130042056 A>C,G), RS1000139 (5:130041876 G>C), RS1000140 (5:130041354 G>A,C)

Disease associations

OMIM: gene MIM:609963 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST009391_2128	Metabolite levels	2.000000e-06
GCST009724_48	Vertical cup-disc ratio (multi-trait analysis)	8.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010383	phosphatidylcholine 36:5 measurement
EFO:0006939	cup-to-disc ratio measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	8
bisphenol A	decreases expression, decreases methylation	3
Acetaminophen	decreases expression, increases expression	2
Benzo(a)pyrene	affects methylation, increases methylation, increases mutagenesis	2
Progesterone	affects cotreatment, increases expression	2
aristolochic acid I	decreases expression	1
trichostatin A	increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
3,4,5,4’-tetramethoxystilbene	affects expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases methylation	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Lipopolysaccharides	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Okadaic Acid	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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