CHST7

gene
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Also known as C6ST-2C6ST2

Summary

CHST7 (carbohydrate sulfotransferase 7, HGNC:13817) is a protein-coding gene on chromosome Xp11.3, encoding Carbohydrate sulfotransferase 7 (Q9NS84). Sulfotransferase that utilizes 3’-phospho-5’-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues.

This gene is a member of the Gal/GalNAc/GlcNAc (galactose/N-acetylgalactosamine/N-acetylglucosamine) 6-O-sulfotransferase (GST) family. Members of this family encode enzymes that catalyze the specific addition of sulfate groups to distinct hydroxyl and amino groups of carbohydrates. The encoded protein catalyzes the sulfation of 6-hydroxyl group of GalNAc in chondroitin.

Source: NCBI Gene 56548 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 64 total — 3 pathogenic, 1 likely-pathogenic
  • MANE Select transcript: NM_019886

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13817
Approved symbolCHST7
Namecarbohydrate sulfotransferase 7
LocationXp11.3
Locus typegene with protein product
StatusApproved
AliasesC6ST-2, C6ST2
Ensembl geneENSG00000147119
Ensembl biotypeprotein_coding
OMIM300375
Entrez56548

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000276055, ENST00000868793, ENST00000868794, ENST00000925570

RefSeq mRNA: 1 — MANE Select: NM_019886 NM_019886

CCDS: CCDS14268

Canonical transcript exons

ENST00000276055 — 2 exons

ExonStartEnd
ENSE000009788104657376546575423
ENSE000010432064659776046598496

Expression profiles

Bgee: expression breadth ubiquitous, 186 present calls, max score 91.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.8768 / max 201.3321, expressed in 1590 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1961275.79801447
1961261.3463800
1961280.9486463
1961250.5839339
1961290.200094

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
deciduaUBERON:000245091.25gold quality
left ovaryUBERON:000211988.82gold quality
right ovaryUBERON:000211887.40gold quality
right atrium auricular regionUBERON:000663183.99gold quality
stromal cell of endometriumCL:000225583.69gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.06gold quality
heart left ventricleUBERON:000208482.82gold quality
endocervixUBERON:000045882.51gold quality
cardiac ventricleUBERON:000208282.38gold quality
cardiac atriumUBERON:000208181.79gold quality
ovaryUBERON:000099281.55gold quality
heartUBERON:000094880.56gold quality
left coronary arteryUBERON:000162680.00gold quality
subcutaneous adipose tissueUBERON:000219078.29gold quality
monocyteCL:000057678.15gold quality
mucosa of stomachUBERON:000119978.14gold quality
coronary arteryUBERON:000162178.08gold quality
leukocyteCL:000073877.94gold quality
spleenUBERON:000210677.78gold quality
mononuclear cellCL:000084277.70gold quality
omental fat padUBERON:001041477.51gold quality
apex of heartUBERON:000209877.46gold quality
peritoneumUBERON:000235877.41gold quality
granulocyteCL:000009477.06gold quality
adipose tissue of abdominal regionUBERON:000780877.04gold quality
bloodUBERON:000017876.60gold quality
right lobe of liverUBERON:000111476.03gold quality
heart right ventricleUBERON:000208075.29gold quality
adipose tissueUBERON:000101374.97gold quality
ectocervixUBERON:001224974.92gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.85
E-GEOD-99795no9.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting CHST7, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-656-3P100.0072.152788
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-32-5P99.9875.211964
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-569699.9872.364487
HSA-MIR-590-3P99.9674.346478
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548Y99.9471.283514
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482

Literature-anchored findings (GeneRIF, showing 2)

  • CHST7 methylation in white blood cells is positively associated with CRC risk, especially in females, and may potentially serve as a blood-based predictive biomarker for CRC risk. (PMID:30815821)
  • CHST7 Methylation Status Related to the Proliferation and Differentiation of Pituitary Adenomas. (PMID:35954244)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriochst7ENSDARG00000044341
mus_musculusChst7ENSMUSG00000037347
rattus_norvegicusChst7ENSRNOG00000077798
drosophila_melanogasterCG9550FBGN0031826
drosophila_melanogasterCG31637FBGN0051637

Paralogs (6): CHST3 (ENSG00000122863), CHST5 (ENSG00000135702), CHST4 (ENSG00000140835), CHST2 (ENSG00000175040), CHST1 (ENSG00000175264), CHST6 (ENSG00000183196)

Protein

Protein identifiers

Carbohydrate sulfotransferase 7Q9NS84 (reviewed: Q9NS84)

Alternative names: Chondroitin 6-sulfotransferase 2, Galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 5, N-acetylglucosamine 6-O-sulfotransferase 4

All UniProt accessions (1): Q9NS84

UniProt curated annotations — full annotation on UniProt →

Function. Sulfotransferase that utilizes 3’-phospho-5’-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues. Preferentially acts on mannose-linked GlcNAc. Also able to catalyze the transfer of sulfate to position 6 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Also acts on core 2 mucin-type oligosaccharide and N-acetyllactosamine oligomer with a lower efficiency. Has weak or no activity toward keratan sulfate and oligosaccharides containing the Galbeta1-4GlcNAc. Catalyzes 6-O-sulfation of beta-benzyl GlcNAc but not alpha- or beta-benzyl GalNAc.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Widely expressed. Highly expressed in heart, spleen, liver and ovary. Expressed at lower level in brain, placenta, thyroid, spinal cord and peripheral blood leukocytes. Not expressed in adult skin.

Similarity. Belongs to the sulfotransferase 1 family. Gal/GlcNAc/GalNAc subfamily.

RefSeq proteins (1): NP_063939* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000863Sulfotransferase_domDomain
IPR016469Carbohydrate_sulfotransferaseFamily
IPR027417P-loop_NTPaseHomologous_superfamily
IPR051135Gal/GlcNAc/GalNAc_STFamily

Pfam: PF00685

Enzyme classification (BRENDA):

  • EC 2.8.2.17 — chondroitin 6-sulfotransferase (BRENDA: 7 organisms, 62 substrates, 14 inhibitors, 31 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

14 substrates with measured Km, best-characterized 14. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
3’-PHOSPHOADENYLYL SULFATE0.0003–0.00426
CHONDROITIN0.0008–0.156
3’-PHOSPHOADENYLYLSULFATE0.0001–0.03335
CHONDROITIN 4-SULFATE0.0005–0.0382
KERATAN SULFATE0.0029–0.0052
DECASACCHARIDE0.91
DESULFATED CHONDROITIN SULFATE1.81
DODECASACCHARIDE0.481
GLCUABETA(1->3)GALNAC(4S)BETA(1->4)GLCUABETA(1->0.051
HEXASACCHARIDE51
N-ACETYLGALACTOSAMINE 4-SULFATE0.361
NATIVE CHONDROITIN0.061
OCTASACCHARIDE2.51
UDP-N-ACETYLGALACTOSAMINE 4-SULFATE0.0271

Catalyzed reactions (Rhea), 1 shown:

  • chondroitin beta-D-glucuronate + n 3’-phosphoadenylyl sulfate = chondroitin 6’-sulfate + n adenosine 3’,5’-bisphosphate + n H(+) (RHEA:11108)

UniProt features (16 total): glycosylation site 3, compositionally biased region 3, topological domain 2, binding site 2, region of interest 2, chain 1, modified residue 1, sequence conflict 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NS84-F180.600.57

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): 278–286; 110–116

Post-translational modifications (1): 462

Glycosylation sites (3): 88, 186, 407

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2022870CS-GAG biosynthesis

MSigDB gene sets: 195 (showing top): XU_GH1_AUTOCRINE_TARGETS_UP, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_BIOSYNTHETIC_PROCESS, CEBP_Q2, CATTTCA_MIR203, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, BILD_E2F3_ONCOGENIC_SIGNATURE, CAIRO_HEPATOBLASTOMA_DN, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_AMINO_SUGAR_METABOLIC_PROCESS, MORF_ETV3, POU3F2_02, MULLIGHAN_NPM1_SIGNATURE_3_DN, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_METABOLIC_PROCESS

GO Biological Process (5): polysaccharide metabolic process (GO:0005976), N-acetylglucosamine metabolic process (GO:0006044), sulfur compound metabolic process (GO:0006790), chondroitin sulfate proteoglycan biosynthetic process (GO:0050650), carbohydrate metabolic process (GO:0005975)

GO Molecular Function (4): N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517), chondroitin 6-sulfotransferase activity (GO:0008459), sulfotransferase activity (GO:0008146), 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:

CategoryPathways
Chondroitin sulfate/dermatan sulfate metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
carbohydrate metabolic process1
macromolecule metabolic process1
amino sugar metabolic process1
metabolic process1
proteoglycan biosynthetic process1
chondroitin sulfate proteoglycan metabolic process1
protein O-linked glycosylation via xylose1
primary metabolic process1
sulfotransferase activity1
chondroitin sulfotransferase activity1
transferase activity, transferring sulphur-containing groups1
catalytic activity1
Golgi apparatus1
bounding membrane of organelle1
cellular anatomical structure1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

556 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CHST7KRABD4Q5JUW0950
CHST7ZNF674Q2M3X9842
CHST7SLC9A7Q96T83838
CHST7CHST13Q8NET6811
CHST7CHST12Q9NRB3811
CHST7CHST15Q7LFX5764
CHST7CSGALNACT2Q8N6G5700
CHST7CHST14Q8NCH0698
CHST7CSGALNACT1Q8TDX6666
CHST7CHST11Q9NPF2666
CHST7LACTBL1A8MY62561
CHST7CHPFQ8IZ52532
CHST7CHSY1Q86X52531
CHST7GLCEO94923515
CHST7B3GAT3O94766476

IntAct

19 interactions, top by confidence:

ABTypeScore
NIPAL1ESYT2psi-mi:“MI:0914”(association)0.640
PEX19FAM20Bpsi-mi:“MI:0914”(association)0.530
DCAF4IGLL5psi-mi:“MI:0914”(association)0.350
TTMPTMEM223psi-mi:“MI:0914”(association)0.350
TTYH1TMEM223psi-mi:“MI:0914”(association)0.350
CLEC12BGXYLT2psi-mi:“MI:0914”(association)0.350
CDH23GTPBP10psi-mi:“MI:0914”(association)0.350
TMEM74KLRG2psi-mi:“MI:0914”(association)0.350
CHST7POTEFpsi-mi:“MI:0914”(association)0.350
CCL3KRBA1psi-mi:“MI:0914”(association)0.350
SCGB2A2RTL8Cpsi-mi:“MI:0914”(association)0.350
CEACAM8PRRT4psi-mi:“MI:0914”(association)0.350
C1orf54AGRNpsi-mi:“MI:0914”(association)0.350
C1QTNF7AGRNpsi-mi:“MI:0914”(association)0.350
HFEPODXLpsi-mi:“MI:0914”(association)0.350
LCN6COCHpsi-mi:“MI:0914”(association)0.350
XPR1GOLIM4psi-mi:“MI:0914”(association)0.350

BioGRID (32): CHST7 (Affinity Capture-MS), CHST7 (Affinity Capture-MS), CHST7 (Affinity Capture-MS), CHST7 (Affinity Capture-RNA), CHST7 (Reconstituted Complex), CHST7 (Affinity Capture-MS), CHST7 (Affinity Capture-MS), POTEF (Affinity Capture-MS), GOSR1 (Affinity Capture-MS), CHST7 (Affinity Capture-MS), CHST7 (Affinity Capture-MS), CHST7 (Affinity Capture-MS), GOSR2 (Affinity Capture-MS), CHST7 (Affinity Capture-MS), CST4 (Affinity Capture-MS)

ESM2 similar proteins: A2A9Q0, A5PKD8, A9JSM3, D4A2Q0, E7ERA6, F1SAM7, F2Z333, P0CG25, Q07303, Q0IIA6, Q1RMK9, Q24JP5, Q2MJR0, Q2WF71, Q3MIP1, Q3UV16, Q3ZCQ3, Q504Y2, Q5EBM0, Q5GH56, Q5GH64, Q5GH72, Q5RJI4, Q5SZI1, Q641Q3, Q6IEE6, Q6IQX7, Q6P6N5, Q6UKI2, Q6ZMC9, Q6ZVW7, Q86UD0, Q8IUW3, Q8IZ52, Q8K064, Q8N4K4, Q8NAC3, Q8NBR0, Q8NCL9, Q8NFR9

Diamond homologs: O43916, O88199, O93403, Q0VBN2, Q5RJQ0, Q6DBY9, Q6XQG8, Q7LGC8, Q80WV3, Q8IZU8, Q8NCG5, Q92179, Q9EP78, Q9EQC0, Q9GZS9, Q9GZX3, Q9NS84, Q9QUP4, Q9QZL2, Q9R1I1, Q9Y4C5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic3
Likely pathogenic1
Uncertain significance45
Likely benign4
Benign3

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
1175843GRCh37/hg19 Xp11.3-11.23(chrX:44879855-46541970)x1Pathogenic
2685063GRCh37/hg19 Xp11.4-11.23(chrX:42046069-46491183)x0Pathogenic
830980NC_000023.10:g.(?45605561)(46952346_?)delPathogenic
183366NC_000023.10:g.(?43479884)(46741003_?)delLikely pathogenic

SpliceAI

238 predictions. Top by Δscore:

VariantEffectΔscore
X:46575422:GG:Gdonor_gain0.9900
X:46575422:GGGTA:Gdonor_loss0.9900
X:46575423:GG:Gdonor_gain0.9900
X:46575424:GT:Gdonor_loss0.9900
X:46575425:T:Adonor_loss0.9900
X:46597754:TTCTA:Tacceptor_loss0.9900
X:46597756:CTA:Cacceptor_loss0.9900
X:46597757:TA:Tacceptor_loss0.9900
X:46597759:GGTCA:Gacceptor_gain0.9900
X:46575424:G:GGdonor_gain0.9800
X:46595489:A:Tdonor_gain0.9800
X:46575348:G:Tdonor_gain0.9700
X:46597758:A:AGacceptor_gain0.9700
X:46597759:G:GGacceptor_gain0.9700
X:46575390:T:TAdonor_gain0.9600
X:46575391:A:AAdonor_gain0.9600
X:46595444:GGC:Gdonor_gain0.9600
X:46597759:GGTC:Gacceptor_gain0.9600
X:46595437:TCA:Tdonor_gain0.9400
X:46592240:A:AGacceptor_gain0.9300
X:46595042:G:GGdonor_gain0.9200
X:46575388:C:Gdonor_gain0.9100
X:46575413:C:Tdonor_gain0.9000
X:46575431:G:GAdonor_gain0.9000
X:46575430:T:TAdonor_gain0.8600
X:46597758:AGGT:Aacceptor_gain0.8600
X:46591471:TTC:Tdonor_gain0.8400
X:46595443:T:TAdonor_gain0.8400
X:46597759:GGT:Gacceptor_gain0.8400
X:46576088:T:TAdonor_gain0.8100

AlphaMissense

3073 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:46574326:A:TE132V1.000
X:46574773:G:TR281M1.000
X:46574977:G:AC349Y1.000
X:46575190:T:GF420C1.000
X:46575233:G:CW434C1.000
X:46575233:G:TW434C1.000
X:46574259:T:AW110R0.999
X:46574259:T:CW110R0.999
X:46574261:G:CW110C0.999
X:46574261:G:TW110C0.999
X:46574262:C:AR111S0.999
X:46574266:C:TT112I0.999
X:46574278:T:CF116S0.999
X:46574278:T:GF116C0.999
X:46574327:G:CE132D0.999
X:46574327:G:TE132D0.999
X:46574329:C:AP133H0.999
X:46574336:G:CW135C0.999
X:46574336:G:TW135C0.999
X:46574343:T:AW138R0.999
X:46574343:T:CW138R0.999
X:46574345:G:CW138C0.999
X:46574345:G:TW138C0.999
X:46574525:C:AN198K0.999
X:46574525:C:GN198K0.999
X:46574536:G:AC202Y0.999
X:46574652:T:AC241S0.999
X:46574653:G:CC241S0.999
X:46574680:A:TK250M0.999
X:46574681:G:CK250N0.999

dbSNP variants (sampled 300 via entrez): RS1000004642 (X:46582467 T>C), RS1000323288 (X:46574795 C>G), RS1000483927 (X:46585100 A>G), RS1000738310 (X:46590395 A>G), RS1001000422 (X:46596213 G>T), RS1001256104 (X:46591877 C>T), RS1001368558 (X:46576811 C>T), RS1001377482 (X:46588403 G>A), RS1001606376 (X:46598712 C>A), RS1002411568 (X:46590406 G>A), RS1002775031 (X:46579091 C>G), RS1002946033 (X:46589016 T>C), RS1002977366 (X:46589439 A>G), RS1003140372 (X:46575349 A>G), RS1003278435 (X:46586094 G>A)

Disease associations

OMIM: gene MIM:300375 | disease phenotypes: MIM:300867

GenCC curated gene-disease

Mondo (1): Kabuki syndrome 2 (MONDO:0010465)

Orphanet (1): Kabuki syndrome (Orphanet:2322)

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

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

ChemicalActions (top 5)PubMed papers
Tretinoindecreases expression, increases expression3
Particulate Matterincreases abundance, affects cotreatment, decreases expression3
Estradioldecreases expression, affects cotreatment, increases expression2
Progesteroneincreases expression, affects cotreatment2
Tobacco Smoke Pollutiondecreases expression, increases methylation2
aristolochic acid Iincreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
2-hydroxychavicolincreases expression1
pentabromodiphenyl etherincreases expression1
CGP 52608increases reaction, affects binding1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
apple polyphenol extractincreases expression1
Temozolomidedecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzeneincreases expression1
Benzo(a)pyreneaffects methylation1
Calcitriolincreases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Ethyl Methanesulfonateincreases expression1
Fluorouracilaffects response to substance1
Formaldehydeincreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Lipopolysaccharidesincreases expression, affects response to substance1
Parathionincreases expression, affects cotreatment1
Polycyclic Aromatic Hydrocarbonsaffects cotreatment, decreases expression, increases abundance1
Urethaneincreases expression1
Valproic Aciddecreases expression, increases methylation1
Okadaic Acidincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Kabuki syndrome 2