CHST13

Summary

CHST13 (carbohydrate sulfotransferase 13, HGNC:21755) is a protein-coding gene on chromosome 3q21.3, encoding Carbohydrate sulfotransferase 13 (Q8NET6). Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin.

The protein encoded by this gene belongs to the sulfotransferase 2 family. It is localized to the golgi membrane, and catalyzes the transfer of sulfate to the C4 hydroxyl of beta-1,4-linked N-acetylgalactosamine (GalNAc) flanked by glucuronic acid residue in chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices.

Source: NCBI Gene 166012 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_152889

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21755
Approved symbol	CHST13
Name	carbohydrate sulfotransferase 13
Location	3q21.3
Locus type	gene with protein product
Status	Approved
Aliases	C4ST3
Ensembl gene	ENSG00000180767
Ensembl biotype	protein_coding
OMIM	610124
Entrez	166012

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000319340

RefSeq mRNA: 1 — MANE Select: NM_152889 NM_152889

CCDS: CCDS3039

Canonical transcript exons

ENST00000319340 — 3 exons

Exon	Start	End
ENSE00001220399	126536271	126536353
ENSE00001220408	126541733	126543291
ENSE00002071482	126524155	126524429

Expression profiles

Bgee: expression breadth ubiquitous, 125 present calls, max score 97.19.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2739 / max 120.4397, expressed in 324 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
38350	0.8212	267
38354	0.1905	105
38351	0.1306	63
38359	0.0728	6
38358	0.0387	3
38355	0.0078	3
38357	0.0075	2
38356	0.0048	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	97.19	gold quality
right lobe of liver	UBERON:0001114	91.72	gold quality
liver	UBERON:0002107	86.89	gold quality
granulocyte	CL:0000094	80.24	gold quality
monocyte	CL:0000576	79.62	gold quality
leukocyte	CL:0000738	79.31	gold quality
left testis	UBERON:0004533	79.09	gold quality
right testis	UBERON:0004534	77.96	gold quality
tibia	UBERON:0000979	76.80	gold quality
testis	UBERON:0000473	76.29	gold quality
blood	UBERON:0000178	74.31	gold quality
mucosa of transverse colon	UBERON:0004991	70.08	gold quality
adult organism	UBERON:0007023	69.96	gold quality
ileal mucosa	UBERON:0000331	69.52	silver quality
secondary oocyte	CL:0000655	67.81	silver quality
spleen	UBERON:0002106	64.41	gold quality
pancreatic ductal cell	CL:0002079	64.21	silver quality
adult mammalian kidney	UBERON:0000082	63.28	gold quality
sperm	CL:0000019	62.01	gold quality
bone marrow	UBERON:0002371	58.74	silver quality
tibialis anterior	UBERON:0001385	57.66	silver quality
oocyte	CL:0000023	57.54	silver quality
kidney	UBERON:0002113	57.23	gold quality
myocardium	UBERON:0002349	57.19	gold quality
bone marrow cell	CL:0002092	56.96	gold quality
duodenum	UBERON:0002114	56.84	gold quality
skin of hip	UBERON:0001554	56.37	gold quality
right uterine tube	UBERON:0001302	55.55	gold quality
epithelial cell of pancreas	CL:0000083	55.16	gold quality
kidney epithelium	UBERON:0004819	54.97	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting CHST13, 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-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-6731-5P	99.28	67.42	2375
HSA-MIR-8085	99.28	67.56	2362
HSA-MIR-548AS-3P	99.12	69.12	2294
HSA-MIR-4635	98.74	67.63	1339
HSA-MIR-6859-3P	97.26	64.69	428
HSA-MIR-3194-5P	96.80	64.90	1027
HSA-MIR-6857-3P	96.70	65.43	915
HSA-MIR-1915-5P	95.25	65.78	571
HSA-MIR-5588-3P	94.96	65.59	500
HSA-MIR-4649-5P	93.02	63.85	141
HSA-MIR-6729-5P	93.02	62.76	138
HSA-MIR-10392-3P	88.79	61.83	122

Literature-anchored findings (GeneRIF, showing 4)

• mol cloning and characterization (PMID:12080076)
• These results have demonstrated that CHST11 and CHST13 negatively modulate metastasis and drug resistance of HCC cells probably via oncogenic MAPK signal pathway. (PMID:26993826)
• We show that the CHST3 and CHST13 alleles are significantly more frequent in pulmonary arterial hypertension patients with elevated aminotransferases during therapy with bosentan than those in patients without liver injury. This is the first pharmacogenomics study linking proteoglycan sulfating genes to drug-induced liver dysfunction. (PMID:30118797)
• Abnormal expression of chondroitin sulfate sulfotransferases in the articular cartilage of pediatric patients with Kashin-Beck disease. (PMID:31845005)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	chst13	ENSDARG00000004018
mus_musculus	Chst13	ENSMUSG00000056643
rattus_norvegicus	Chst13	ENSRNOG00000025930

Paralogs (6): CHST10 (ENSG00000115526), CHST8 (ENSG00000124302), CHST12 (ENSG00000136213), CHST9 (ENSG00000154080), CHST14 (ENSG00000169105), CHST11 (ENSG00000171310)

Protein

Protein identifiers

Carbohydrate sulfotransferase 13 — Q8NET6 (reviewed: Q8NET6)

Alternative names: Chondroitin 4-O-sulfotransferase 3, Chondroitin 4-sulfotransferase 3

All UniProt accessions (1): Q8NET6

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Transfers sulfate to the C4 hydroxyl of beta1,4-linked GalNAc that is substituted with a beta-linked glucuronic acid at the C-3 hydroxyl. No activity toward dermatan.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Highly expressed in adult liver. Expressed at lower level in kidney, lymph nodes and fetal kidney.

Similarity. Belongs to the sulfotransferase 2 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NET6-1	1	yes
Q8NET6-2	2

RefSeq proteins (1): NP_690849* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005331	Sulfotransferase	Family
IPR018011	Carb_sulfotrans_8-10	Family

Pfam: PF03567

Enzyme classification (BRENDA):

• EC 2.8.2.5 — chondroitin 4-sulfotransferase (BRENDA: 8 organisms, 31 substrates, 8 inhibitors, 14 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
3’-PHOSPHOADENYLYLSULFATE	0.0003–1.4	6
CHONDROITIN	0.0038–2.7	4
3’-PHOSPHOADENYLYL SULFATE	0.0013–0.036	2

Catalyzed reactions (Rhea), 1 shown:

• chondroitin beta-D-glucuronate + n 3’-phosphoadenylyl sulfate = chondroitin 4’-sulfate + n adenosine 3’,5’-bisphosphate + n H(+) (RHEA:16101)

UniProt features (14 total): sequence variant 3, topological domain 2, splice variant 2, binding site 2, chain 1, transmembrane region 1, short sequence motif 1, modified residue 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NET6-F1	87.44	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.

Ligand- & substrate-binding residues (2): 113–119; 174–182

Post-translational modifications (1): 139

Glycosylation sites (1): 331

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-2022870	CS-GAG biosynthesis

MSigDB gene sets: 70 (showing top): GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, chr3q21, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_METABOLIC_PROCESS, TAL1BETAE47_01, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, REACTOME_METABOLISM_OF_CARBOHYDRATES_AND_CARBOHYDRATE_DERIVATIVES, KEGG_SULFUR_METABOLISM, KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_SULPHUR_CONTAINING_GROUPS, GOBP_GLYCOPROTEIN_BIOSYNTHETIC_PROCESS

GO Biological Process (3): carbohydrate biosynthetic process (GO:0016051), proteoglycan biosynthetic process (GO:0030166), chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)

GO Molecular Function (5): dermatan 4-sulfotransferase activity (GO:0001537), sulfotransferase activity (GO:0008146), chondroitin 4-sulfotransferase activity (GO:0047756), protein binding (GO:0005515), transferase activity (GO:0016740)

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

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
carbohydrate metabolic process	1
biosynthetic process	1
proteoglycan metabolic process	1
glycoprotein biosynthetic process	1
proteoglycan biosynthetic process	1
chondroitin sulfate proteoglycan metabolic process	1
protein O-linked glycosylation via xylose	1
dermatan sulfotransferase activity	1
transferase activity, transferring sulphur-containing groups	1
chondroitin sulfotransferase activity	1
binding	1
catalytic activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cellular anatomical structure	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

528 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CHST13	CHST7	Q9NS84	811
CHST13	CHST15	Q7LFX5	780
CHST13	CHST3	Q7LGC8	738
CHST13	CSGALNACT2	Q8N6G5	687
CHST13	CSGALNACT1	Q8TDX6	608
CHST13	CHSY1	Q86X52	604
CHST13	CHPF2	Q9P2E5	598
CHST13	CHPF	Q8IZ52	598
CHST13	HS2ST1	Q7LGA3	540
CHST13	DSEL	Q8IZU8	539
CHST13	DSE	Q9UL01	507
CHST13	DEFB124	Q8NES8	504
CHST13	B3GAT3	O94766	497
CHST13	GLCE	O94923	463
CHST13	B4GALT7	Q9UBV7	460

IntAct

7 interactions, top by confidence:

A	B	Type	Score
TTMP	CHST13	psi-mi:“MI:0915”(physical association)	0.560
	AP3D1	psi-mi:“MI:0914”(association)	0.350
		psi-mi:“MI:0914”(association)	0.350
CHST13	NUCB1	psi-mi:“MI:0914”(association)	0.350
TTMP	CHST13	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): CHST13 (Affinity Capture-MS), CHST13 (Two-hybrid), NUCB1 (Affinity Capture-MS), PCSK1N (Affinity Capture-MS), CHST13 (Affinity Capture-MS)

ESM2 similar proteins: A6QNK1, O14792, O19058, O35310, O43916, O88199, Q10979, Q11127, Q29043, Q5E9W5, Q5RJQ0, Q5XPT3, Q6P7A1, Q6XQG8, Q6XQG9, Q6XQH0, Q712G6, Q7LGC8, Q7T3S3, Q800H9, Q80WV3, Q866C5, Q866C7, Q866D2, Q866D6, Q866D9, Q866E1, Q866E6, Q866E7, Q866E8, Q866F0, Q866F1, Q8HYJ3, Q8HYJ4, Q8HYJ7, Q8N3Y3, Q8NET6, Q92179, Q96RP7, Q99999

Diamond homologs: O43529, O54702, P69478, Q5RBZ6, Q5XHM7, Q5ZIE4, Q6AXM1, Q6GNS1, Q6PGK7, Q76EC5, Q7L1S5, Q7T3S3, Q805E5, Q8BQ86, Q8NET6, Q99LL3, Q9H2A9, Q9JME2, Q9NPF2, Q9NRB3, Q80V53, Q8NCH0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

923 predictions. Top by Δscore:

Variant	Effect	Δscore
3:126524427:CGGG:C	donor_loss	0.9900
3:126524428:GG:G	donor_gain	0.9900
3:126524429:GG:G	donor_gain	0.9900
3:126524429:GGT:G	donor_loss	0.9900
3:126524430:G:GG	donor_gain	0.9900
3:126524430:GT:G	donor_loss	0.9900
3:126524431:T:A	donor_loss	0.9900
3:126524432:GAGT:G	donor_loss	0.9900
3:126525207:ATGT:A	acceptor_gain	0.9900
3:126541721:T:A	acceptor_gain	0.9900
3:126541724:C:A	acceptor_gain	0.9900
3:126541731:AG:A	acceptor_gain	0.9900
3:126541732:GG:G	acceptor_gain	0.9900
3:126541732:GGA:G	acceptor_gain	0.9900
3:126541732:GGACC:G	acceptor_gain	0.9900
3:126525208:T:G	acceptor_gain	0.9800
3:126527907:G:GT	donor_gain	0.9800
3:126538574:G:GT	donor_gain	0.9800
3:126541729:ACAG:A	acceptor_gain	0.9800
3:126541731:A:AG	acceptor_gain	0.9800
3:126541732:G:GT	acceptor_gain	0.9800
3:126541732:GGAC:G	acceptor_gain	0.9800
3:126527924:TCAGG:T	donor_gain	0.9700
3:126532727:G:GC	acceptor_gain	0.9700
3:126524433:AGTG:A	donor_loss	0.9600
3:126525210:T:TA	acceptor_gain	0.9600
3:126527928:G:GT	donor_gain	0.9600
3:126536270:GC:G	acceptor_gain	0.9600
3:126538567:G:GT	donor_gain	0.9600
3:126524425:CCCGG:C	donor_gain	0.9500

AlphaMissense

2154 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:126542293:G:C	W247C	0.999
3:126542293:G:T	W247C	0.999
3:126541881:G:A	C110Y	0.997
3:126541882:C:G	C110W	0.997
3:126541915:G:C	K121N	0.996
3:126541915:G:T	K121N	0.996
3:126542113:G:C	K187N	0.996
3:126542113:G:T	K187N	0.996
3:126542139:T:G	F196C	0.996
3:126542235:T:C	F228S	0.996
3:126542235:T:G	F228C	0.996
3:126542291:T:A	W247R	0.996
3:126542291:T:C	W247R	0.996
3:126542234:T:C	F228L	0.995
3:126542236:C:A	F228L	0.995
3:126542236:C:G	F228L	0.995
3:126542540:T:A	F330I	0.995
3:126541905:C:T	T118I	0.994
3:126541910:T:A	W120R	0.994
3:126541910:T:C	W120R	0.994
3:126542290:C:A	H246Q	0.994
3:126542290:C:G	H246Q	0.994
3:126542313:G:A	C254Y	0.994
3:126542528:G:C	D326H	0.994
3:126541881:G:T	C110F	0.993
3:126542102:T:G	Y184D	0.993
3:126542138:T:C	F196L	0.993
3:126542140:C:A	F196L	0.993
3:126542140:C:G	F196L	0.993
3:126542529:A:T	D326V	0.993

dbSNP variants (sampled 300 via entrez): RS1000072177 (3:126532101 T>G), RS1000190774 (3:126539558 T>TGC), RS1000300113 (3:126532789 A>G), RS1000486227 (3:126532537 A>G), RS1000549130 (3:126537597 C>T), RS1000895517 (3:126525600 C>T), RS1000977417 (3:126537777 A>G), RS1001820778 (3:126542019 G>A), RS1001852940 (3:126532416 G>A), RS1001900321 (3:126524286 C>A), RS1001936454 (3:126542634 G>A,C,T), RS1001951225 (3:126524408 G>A,T), RS1001978114 (3:126536659 G>A), RS1002102180 (3:126526021 C>T), RS1002458919 (3:126543623 C>A)

Disease associations

OMIM: gene MIM:610124 | 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)

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1054097	C3orf22, CHST13		0.00	0

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	4
Tobacco Smoke Pollution	decreases expression, increases methylation	3
Valproic Acid	increases expression, decreases expression, increases methylation, affects cotreatment	3
Aflatoxin B1	affects expression, decreases expression, increases methylation	3
Cyclosporine	decreases expression	2
triphenyl phosphate	affects expression	1
bisphenol A	affects expression	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects cotreatment, decreases expression, affects response to substance	1
tebuconazole	decreases expression	1
K 7174	decreases expression	1
ICG 001	increases expression	1
Acetaminophen	decreases expression	1
Diethylnitrosamine	decreases expression	1
Hydralazine	affects cotreatment, increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Quercetin	decreases expression	1
Smoke	decreases expression	1
Triclosan	decreases expression	1
Urethane	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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