GAL3ST1

gene
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Also known as CST

Summary

GAL3ST1 (galactose-3-O-sulfotransferase 1, HGNC:24240) is a protein-coding gene on chromosome 22q12.2, encoding Galactosylceramide sulfotransferase (Q99999). Catalyzes the transfer of a sulfate group to position 3 of non-reducing beta-galactosyl residues in glycerolipids and sphingolipids, therefore participates in the biosynthesis of sulfoglycolipids.

Sulfonation, an important step in the metabolism of many drugs, xenobiotics, hormones, and neurotransmitters, is catalyzed by sulfotransferases. This gene encodes galactosylceramide sulfotransferase, which catalyzes the sulfation of membrane glycolipids including the final step in the synthesis of sulfatide, a major lipid component of the myelin sheath. This gene exhibits elevated expression in ovarian epithelial carcinoma and the encoded enzyme exhibits elevated activity in renal cell carcinoma. Mutations in this gene may be associated with reduced insulin resistance. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 9514 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 55 total
  • MANE Select transcript: NM_001318104

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24240
Approved symbolGAL3ST1
Namegalactose-3-O-sulfotransferase 1
Location22q12.2
Locus typegene with protein product
StatusApproved
AliasesCST
Ensembl geneENSG00000128242
Ensembl biotypeprotein_coding
OMIM602300
Entrez9514

Gene structure

Transcript identifiers

Ensembl transcripts: 49 — 49 protein_coding

ENST00000338911, ENST00000401975, ENST00000402321, ENST00000402369, ENST00000406361, ENST00000406955, ENST00000411821, ENST00000416358, ENST00000423299, ENST00000423371, ENST00000426220, ENST00000427899, ENST00000428682, ENST00000431313, ENST00000437282, ENST00000441967, ENST00000443136, ENST00000445645, ENST00000447224, ENST00000448604, ENST00000452827, ENST00000453479, ENST00000903682, ENST00000903683, ENST00000903684, ENST00000903685, ENST00000903686, ENST00000903687, ENST00000903688, ENST00000903689, ENST00000903690, ENST00000903691, ENST00000903692, ENST00000903693, ENST00000903694, ENST00000903695, ENST00000903696, ENST00000903697, ENST00000903698, ENST00000903699, ENST00000911496, ENST00000911497, ENST00000970795, ENST00000970797, ENST00000970799, ENST00000970803, ENST00000970806, ENST00000970808, ENST00000970811

RefSeq mRNA: 15 — MANE Select: NM_001318104 NM_001318103, NM_001318104, NM_001318105, NM_001318106, NM_001318107, NM_001318108, NM_001318109, NM_001318110, NM_001318111, NM_001318112, NM_001318113, NM_001318114, NM_001318115, NM_001318116, NM_004861

CCDS: CCDS13879

Canonical transcript exons

ENST00000406361 — 4 exons

ExonStartEnd
ENSE000015482863055463530556093
ENSE000015559183055726230557401
ENSE000015604773055827930558388
ENSE000015646263057446630574665

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 94.09.

FANTOM5 (CAGE): breadth broad, TPM avg 1.6226 / max 1254.8180, expressed in 281 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter IDTPM avgSamples expressed
1936440.634439
1936420.357977
1936520.207999
1936530.159695
1936500.063440
1936480.053511
1936510.050126
1936490.029719
1936470.01735
1936450.01511

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
C1 segment of cervical spinal cordUBERON:000646994.09gold quality
spinal cordUBERON:000224091.58gold quality
tibial nerveUBERON:000132387.81gold quality
metanephros cortexUBERON:001053387.21gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099184.89gold quality
putamenUBERON:000187482.41gold quality
duodenumUBERON:000211482.24gold quality
nucleus accumbensUBERON:000188282.05gold quality
amygdalaUBERON:000187682.04gold quality
caudate nucleusUBERON:000187381.27gold quality
substantia nigraUBERON:000203881.14gold quality
sural nerveUBERON:001548881.08gold quality
jejunal mucosaUBERON:000039980.56gold quality
Ammon’s hornUBERON:000195479.96gold quality
adult mammalian kidneyUBERON:000008279.85gold quality
mucosa of transverse colonUBERON:000499179.66gold quality
midbrainUBERON:000189179.58gold quality
Brodmann (1909) area 9UBERON:001354078.90gold quality
prefrontal cortexUBERON:000045178.83gold quality
hypothalamusUBERON:000189878.56gold quality
cingulate cortexUBERON:000302778.46gold quality
anterior cingulate cortexUBERON:000983578.43gold quality
corpus callosumUBERON:000233678.28gold quality
right frontal lobeUBERON:000281078.26gold quality
inferior olivary complexUBERON:000212777.52gold quality
small intestine Peyer’s patchUBERON:000345477.50gold quality
middle frontal gyrusUBERON:000270277.45gold quality
small intestineUBERON:000210877.44gold quality
right uterine tubeUBERON:000130277.13gold quality
body of stomachUBERON:000116176.97gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-CURD-10yes40.49
E-ANND-3no2.21

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCFL

miRNA regulators (miRDB)

22 targeting GAL3ST1, 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-6825-5P99.9669.813431
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-182799.6368.573265
HSA-MIR-9851-3P99.6369.681110
HSA-MIR-1249-5P99.6166.552049
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-444199.4966.563216
HSA-MIR-3127-3P98.9467.341055
HSA-MIR-6756-3P98.9466.791104
HSA-MIR-629-5P98.7868.721032
HSA-MIR-193B-5P97.9165.88837
HSA-MIR-393697.6464.47732
HSA-MIR-582-3P96.6967.381019
HSA-MIR-4774-5P95.9268.27827
HSA-MIR-6889-5P90.2664.13291
HSA-MIR-6777-5P88.7662.64222

Literature-anchored findings (GeneRIF, showing 3)

  • results suggest that heterozygosity at SNP rs2267161 in the gene encoding the CST enzyme confers increased risk of type 2 diabetes; females with the CC allele showed lower insulin resistance (PMID:19587831)
  • These results suggest that GAL3ST1 is a HIF-responsive gene that may contribute to clear cell renal cell carcinoma (ccRCC) development via promoting cancer cell evasion of immune surveillance. (PMID:31427440)
  • The prognostic value of galactosylceramide-sulfotransferase (Gal3ST1) in human renal cell carcinoma. (PMID:34035403)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriogal3st1aENSDARG00000062711
danio_reriogal3st1bENSDARG00000078245
mus_musculusGal3st1ENSMUSG00000049721
rattus_norvegicusGal3st1ENSRNOG00000042041

Paralogs (3): GAL3ST2 (ENSG00000154252), GAL3ST3 (ENSG00000175229), GAL3ST4 (ENSG00000197093)

Protein

Protein identifiers

Galactosylceramide sulfotransferaseQ99999 (reviewed: Q99999)

Alternative names: 3’-phosphoadenosine-5’-phosphosulfate:GalCer sulfotransferase, 3’-phosphoadenylylsulfate:galactosylceramide 3’-sulfotransferase, Cerebroside sulfotransferase

All UniProt accessions (17): Q99999, C9J2M1, C9J2X7, C9J3S3, C9J4I2, C9J6M2, C9J993, C9JE31, C9JGL4, C9JIS3, C9JKD7, C9JLB5, C9JN55, C9JTV3, C9JU54, C9JYD7, C9K037

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the transfer of a sulfate group to position 3 of non-reducing beta-galactosyl residues in glycerolipids and sphingolipids, therefore participates in the biosynthesis of sulfoglycolipids. Catalyzes the synthesis of galactosylceramide sulfate (sulfatide), a major lipid component of the myelin sheath and of monogalactosylalkylacylglycerol sulfate (seminolipid), present in spermatocytes. Seems to prefer beta-glycosides at the non-reducing termini of sugar chains attached to a lipid moiety. Also acts on lactosylceramide, galactosyl 1-alkyl-2-sn-glycerol and galactosyl diacylglycerol (in vitro).

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Expressed in kidney proximal tubule, gastric mucosa and adenocarcinoma. Highly expressed in renal cell carcinoma cell lines.

Pathway. Lipid metabolism; sphingolipid metabolism.

Similarity. Belongs to the galactose-3-O-sulfotransferase family.

RefSeq proteins (15): NP_001305032, NP_001305033, NP_001305034, NP_001305035, NP_001305036, NP_001305037, NP_001305038, NP_001305039, NP_001305040, NP_001305041, NP_001305042, NP_001305043, NP_001305044, NP_001305045, NP_004852 (=MANE)

Domains & families (InterPro)

IDNameType
IPR009729Gal-3-0_sulfotransfraseFamily
IPR027417P-loop_NTPaseHomologous_superfamily

Pfam: PF06990

Enzyme classification (BRENDA):

  • EC 2.8.2.11 — galactosylceramide sulfotransferase (BRENDA: 7 organisms, 30 substrates, 20 inhibitors, 10 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

5 substrates with measured Km, best-characterized 5. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
3’-PHOSPHOADENYLYLSULFATE0.0009–0.0745
CEREBROSIDE0.026–0.06032
GALACTOCEREBROSIDE0.0021
GALACTOSYLCERAMIDE0.0271
PSYCHOSINE0.1031

Catalyzed reactions (Rhea), 5 shown:

  • a beta-D-galactosyl-(1<->1’)-N-acylsphing-4-enine + 3’-phosphoadenylyl sulfate = an N-acyl-1-beta-D-(3-O-sulfo)-galactosyl-sphing-4-enine + adenosine 3’,5’-bisphosphate + H(+) (RHEA:20613)
  • a beta-D-Gal-(1->4)-beta-D-Glc-(1<->1)-Cer(d18:1(4E)) + 3’-phosphoadenylyl sulfate = beta-D-3-sulfogalactosyl-(1->4)-beta-D-glucosyl-(1<->1’)-N-acylsphing-4-enine + adenosine 3’,5’-bisphosphate + H(+) (RHEA:41736)
  • a 1-O-alkyl-2-acyl-3-O-(beta-D-galactosyl)-sn-glycerol + 3’-phosphoadenylyl sulfate = a 1-O-alkyl-2-acyl-3-(beta-D-3-sulfogalactosyl)-sn-glycerol + adenosine 3’,5’-bisphosphate + H(+) (RHEA:41744)
  • a 1,2-diacyl-3-O-(beta-D-galactosyl)-sn-glycerol + 3’-phosphoadenylyl sulfate = 1,2-diacyl-3-(3-O-sulfo-beta-D-galactosyl)-sn-glycerol + adenosine 3’,5’-bisphosphate + H(+) (RHEA:41748)
  • a beta-D-Gal-(1<->1’)-ceramide + 3’-phosphoadenylyl sulfate = 1-(3-O-sulfo-beta-D-galactosyl)-ceramide + adenosine 3’,5’-bisphosphate + H(+) (RHEA:43304)

UniProt features (10 total): sequence conflict 3, topological domain 2, glycosylation site 2, chain 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q99999-F188.960.74

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 (2): 66, 312

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9840309Glycosphingolipid biosynthesis

MSigDB gene sets: 122 (showing top): GOBP_GLYCOLIPID_BIOSYNTHETIC_PROCESS, GOBP_PROTEIN_N_LINKED_GLYCOSYLATION, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_MALE_GAMETE_GENERATION, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CERAMIDE_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GOBP_SPHINGOLIPID_METABOLIC_PROCESS, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_AMIDE_METABOLIC_PROCESS, GOBP_ENSHEATHMENT_OF_NEURONS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_AMIDE_BIOSYNTHETIC_PROCESS

GO Biological Process (10): protein N-linked glycosylation (GO:0006487), sphingolipid metabolic process (GO:0006665), galactosylceramide metabolic process (GO:0006681), galactosylceramide biosynthetic process (GO:0006682), glycosphingolipid biosynthetic process (GO:0006688), spermatogenesis (GO:0007283), myelination (GO:0042552), glycerolipid metabolic process (GO:0046486), lipid metabolic process (GO:0006629), glycolipid biosynthetic process (GO:0009247)

GO Molecular Function (3): galactosylceramide sulfotransferase activity (GO:0001733), sulfotransferase activity (GO:0008146), transferase activity (GO:0016740)

GO Cellular Component (4): Golgi membrane (GO:0000139), plasma membrane (GO:0005886), membrane (GO:0016020), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Glycosphingolipid metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
lipid metabolic process2
glycoprotein biosynthetic process1
glycosylceramide metabolic process1
galactolipid metabolic process1
galactosylceramide metabolic process1
glycosphingolipid biosynthetic process1
galactolipid biosynthetic process1
ceramide biosynthetic process1
glycosphingolipid metabolic process1
glycolipid biosynthetic process1
sphingolipid biosynthetic process1
developmental process involved in reproduction1
male gamete generation1
axon ensheathment1
primary metabolic process1
glycolipid metabolic process1
lipid biosynthetic process1
carbohydrate derivative biosynthetic process1
galactose 3-O-sulfotransferase activity1
transferase activity, transferring sulphur-containing groups1
catalytic activity1
Golgi apparatus1
bounding membrane of organelle1
membrane1
cell periphery1
cellular anatomical structure1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

416 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GAL3ST1UGT8Q16880647
GAL3ST1ARSAP15289581
GAL3ST1FUT3P21217554
GAL3ST1OR13C8Q8NGS7446
GAL3ST1TMEM54Q969K7405
GAL3ST1GALCP54803401
GAL3ST1B4GALT6Q9UBX8395
GAL3ST1UGCGQ16739380
GAL3ST1CHST10O43529371
GAL3ST1CHST12Q9NRB3367
GAL3ST1DZIP1LQ8IYY4366
GAL3ST1SULT1B1O43704348
GAL3ST1SPNP16150343
GAL3ST1TMEM92Q6UXU6337
GAL3ST1PRSS50Q9UI38331

IntAct

11 interactions, top by confidence:

ABTypeScore
GAL3ST1NDUFA3psi-mi:“MI:0914”(association)0.530
SDCBPGAL3ST1psi-mi:“MI:0407”(direct interaction)0.440
CHST8CLSTN1psi-mi:“MI:0914”(association)0.350
SHTN1psi-mi:“MI:0914”(association)0.350
TMEM223psi-mi:“MI:0914”(association)0.350
TNFRSF10Apsi-mi:“MI:0914”(association)0.350
CHST8CALUpsi-mi:“MI:0914”(association)0.350

BioGRID (25): GAL3ST1 (Affinity Capture-MS), NDUFA3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG1 (Affinity Capture-MS), PSG4 (Affinity Capture-MS), PIGU (Affinity Capture-MS), GAL3ST1 (Affinity Capture-MS), PSG4 (Affinity Capture-MS), PIGW (Affinity Capture-MS), NDUFA3 (Affinity Capture-MS), LRIG3 (Affinity Capture-MS), LRIG1 (Affinity Capture-MS), CANX (Affinity Capture-MS), GAL3ST1 (Affinity Capture-MS), GAL3ST1 (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: A6QNK1, P61315, Q0VCH4, Q5E9W5, Q6XQG9, Q6XQH0, Q96A11, Q96RP7, Q99999, Q9H3Q3, Q9JHE4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance51
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

318 predictions. Top by Δscore:

VariantEffectΔscore
22:30557260:A:ACdonor_gain1.0000
22:30557261:C:CCdonor_gain1.0000
22:30557397:GACAC:Gacceptor_gain1.0000
22:30557398:ACAC:Aacceptor_gain1.0000
22:30557399:CAC:Cacceptor_gain1.0000
22:30557399:CACC:Cacceptor_gain1.0000
22:30557400:AC:Aacceptor_gain1.0000
22:30557400:ACCT:Aacceptor_loss1.0000
22:30557401:CC:Cacceptor_gain1.0000
22:30557401:CCTG:Cacceptor_loss1.0000
22:30557402:C:CCacceptor_gain1.0000
22:30557402:CTG:Cacceptor_loss1.0000
22:30557412:A:Tacceptor_gain1.0000
22:30556094:CTG:Cacceptor_gain0.9900
22:30556097:C:CCacceptor_gain0.9900
22:30557256:ACTCA:Adonor_loss0.9900
22:30557259:CACG:Cdonor_loss0.9900
22:30557260:A:AGdonor_loss0.9900
22:30557261:C:Adonor_loss0.9900
22:30557261:CG:Cdonor_gain0.9900
22:30557261:CGTGG:Cdonor_gain0.9900
22:30557405:C:CTacceptor_gain0.9900
22:30557411:C:CTacceptor_gain0.9900
22:30556092:TCCTG:Tacceptor_gain0.9800
22:30556093:CCTGC:Cacceptor_gain0.9800
22:30557261:CGT:Cdonor_gain0.9800
22:30557261:CGTG:Cdonor_gain0.9800
22:30557414:C:CTacceptor_gain0.9800
22:30556104:C:CTacceptor_gain0.9700
22:30557402:C:Tacceptor_gain0.9600

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000105900 (22:30571642 T>C), RS1000224422 (22:30554523 A>T), RS1000478022 (22:30559535 G>A), RS1000784610 (22:30565094 C>A,G,T), RS1000817145 (22:30563551 G>A), RS1000828838 (22:30564063 T>C), RS1000832119 (22:30564779 T>C), RS1001079010 (22:30558849 A>G), RS1001223818 (22:30570650 G>A), RS1001315896 (22:30571935 C>A), RS1001380550 (22:30565823 G>A), RS1001463047 (22:30559417 T>A), RS1001691102 (22:30560544 C>T), RS1001712575 (22:30560788 G>T), RS1001852458 (22:30559854 T>C)

Disease associations

OMIM: gene MIM:602300 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST010703_155Brain morphology (MOSTest)3.000000e-09
GCST012231_18A body shape index3.000000e-08
GCST90001389_3Creutzfeldt-Jakob disease (sporadic)2.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement
EFO:0007789BMI-adjusted waist circumference
EFO:1000656sporadic Creutzfeld Jacob disease

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Acetaminophendecreases expression, increases expression2
Tetrachlorodibenzodioxinincreases expression2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
sotorasibaffects cotreatment, decreases expression1
perfluorotetradecanoic acidincreases expression1
dicrotophosdecreases expression1
propionaldehydedecreases expression1
bisphenol Aaffects cotreatment, decreases methylation1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteincreases expression1
butyraldehydedecreases expression1
perfluorooctanoic acidincreases expression1
methyl salicylateaffects expression1
perfluorobutyric acidincreases expression1
abrinedecreases expression1
trametinibaffects cotreatment, decreases expression1
NVP-BKM120affects cotreatment, decreases expression1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinonedecreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Gemcitabinedecreases expression1
Acroleinaffects expression1
Amphotericin Bdecreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Chloroquineaffects reaction, increases lipidation1
Cisplatindecreases expression1
Dinitrochlorobenzeneaffects expression1
Hydrogen Peroxideaffects expression1
Oxygenincreases expression1
Quercetinincreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.