GAL3ST2

Summary

GAL3ST2 (galactose-3-O-sulfotransferase 2, HGNC:24869) is a protein-coding gene on chromosome 2q37.3, encoding Galactose-3-O-sulfotransferase 2 (Q9H3Q3). Catalyzes the transfer of a sulfate group from 3’-phosphoadenylyl sulfate (PAPS) to the C-3 hydroxyl group of terminal non-reducing beta-galactosyl residues.

This gene encodes a member of the galactose-3-O-sulfotransferase protein family. The product of this gene catalyzes sulfonation by transferring a sulfate group to the hydroxyl at C-3 of nonreducing beta-galactosyl residues, and it can act on both type 1 and type 2 (Galbeta 1-3/1-4GlcNAc-R) oligosaccharides with similar efficiencies, and on core 1 glycans. This enzyme has been implicated in tumor metastasis processes. This gene is different from the GAL3ST3 gene located on chromosome 11, which has also been referred to as GAL3ST2 and encodes a related enzyme with distinct tissue distribution and substrate specificities, compared to galactose-3-O-sulfotransferase 2.

Source: NCBI Gene 64090 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 98 total — 1 likely-pathogenic
• MANE Select transcript: NM_022134

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24869
Approved symbol	GAL3ST2
Name	galactose-3-O-sulfotransferase 2
Location	2q37.3
Locus type	gene with protein product
Status	Approved
Aliases	GP3ST
Ensembl gene	ENSG00000154252
Ensembl biotype	protein_coding
OMIM	608237
Entrez	64090

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000192314

RefSeq mRNA: 1 — MANE Select: NM_022134 NM_022134

CCDS: CCDS33427

Canonical transcript exons

ENST00000192314 — 4 exons

Exon	Start	End
ENSE00001869923	241803345	241804287
ENSE00002240869	241776822	241776984
ENSE00002291798	241801781	241802036
ENSE00002310105	241799065	241799154

Expression profiles

Bgee: expression breadth broad, 87 present calls, max score 76.46.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1190 / max 57.1215, expressed in 22 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
26565	0.1190	22

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
olfactory segment of nasal mucosa	UBERON:0005386	76.46	gold quality
mucosa of transverse colon	UBERON:0004991	73.50	gold quality
transverse colon	UBERON:0001157	69.70	gold quality
rectum	UBERON:0001052	69.47	gold quality
colonic epithelium	UBERON:0000397	62.55	silver quality
stromal cell of endometrium	CL:0002255	56.78	gold quality
colon	UBERON:0001155	56.46	gold quality
right uterine tube	UBERON:0001302	52.83	gold quality
superior frontal gyrus	UBERON:0002661	52.69	gold quality
right lobe of liver	UBERON:0001114	52.47	gold quality
vermiform appendix	UBERON:0001154	50.77	gold quality
fallopian tube	UBERON:0003889	50.68	gold quality
gall bladder	UBERON:0002110	50.61	gold quality
intestine	UBERON:0000160	50.30	gold quality
omental fat pad	UBERON:0010414	49.94	gold quality
liver	UBERON:0002107	49.81	gold quality
nucleus accumbens	UBERON:0001882	49.15	gold quality
anterior cingulate cortex	UBERON:0009835	48.93	gold quality
prefrontal cortex	UBERON:0000451	48.27	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	47.92	gold quality
cortex of kidney	UBERON:0001225	47.89	gold quality
hypothalamus	UBERON:0001898	47.82	gold quality
Brodmann (1909) area 9	UBERON:0013540	47.41	gold quality
cerebral cortex	UBERON:0000956	47.36	gold quality
primary visual cortex	UBERON:0002436	47.32	silver quality
frontal cortex	UBERON:0001870	47.23	gold quality
adult mammalian kidney	UBERON:0000082	47.05	gold quality
left uterine tube	UBERON:0001303	46.69	gold quality
mucosa of stomach	UBERON:0001199	46.62	gold quality
temporal lobe	UBERON:0001871	46.38	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting GAL3ST2, 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-4487	99.96	64.58	1252
HSA-MIR-3173-5P	97.35	65.82	1282
HSA-MIR-6799-3P	97.35	65.60	1302
HSA-MIR-4707-5P	90.95	65.69	110
HSA-MIR-6763-3P	90.80	64.32	80

Literature-anchored findings (GeneRIF, showing 4)

• Gal3ST-2 is involved in tumor metastasis process by regulation of adhesion ability to selectins and expression of integrin alphaV but not beta3 (PMID:15921657)
• The substrate specificity and cofactor requirements of human, porcine, and murine GAL3ST are reported (PMID:15926885)
• GAL3ST2 is present in breast cancer cell lines and is more strongly expressed in more metastatic tumors. (PMID:25532485)
• D2HGDH-GAL3ST2 is more frequently seen in prostate cancer samples, and seems to be enriched in African Americans. (PMID:27322736)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	gal3st2	ENSDARG00000079502
mus_musculus	Gal3st2c	ENSMUSG00000073608
mus_musculus	Gal3st2b	ENSMUSG00000093805
mus_musculus	Gal3st2	ENSMUSG00000094651
rattus_norvegicus	Gal3st2c	ENSRNOG00000070509

Paralogs (3): GAL3ST1 (ENSG00000128242), GAL3ST3 (ENSG00000175229), GAL3ST4 (ENSG00000197093)

Protein

Protein identifiers

Galactose-3-O-sulfotransferase 2 — Q9H3Q3 (reviewed: Q9H3Q3)

Alternative names: Beta-galactose-3-O-sulfotransferase 2, Gal-beta-1, 3-GalNAc 3’-sulfotransferase 2, Glycoprotein beta-Gal 3’-sulfotransferase 2

All UniProt accessions (1): Q9H3Q3

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the transfer of a sulfate group from 3’-phosphoadenylyl sulfate (PAPS) to the C-3 hydroxyl group of terminal non-reducing beta-galactosyl residues. Acts both on type 1 (Gal-beta-1,3-GlcNAc-R) and type 2 (Gal-beta-1,4-GlcNAc-R) chains with similar efficiency. Displays species-dependent substrate specificity. Participates in galactose sulfation and shows substrate preference for structures such as lactose, lacto-N-tetraose (Lc4), lacto-N-neotetraose (nLc4), the Gal-beta-1,4-GlcNAc-beta unit in mucin core-2, and the cancer antigen Globo H precursor Gal-beta-1,3-GlcNAc-beta-1,3-Gal-R.

Subcellular location. Golgi apparatus. Golgi stack membrane.

Tissue specificity. Ubiquitous. Detected in heart, stomach, colon, liver and spleen, in epithelial cells lining the lower to middle layer of the crypts in colonic mucosa, hepatocytes surrounding the central vein of the liver, extravillous cytotrophoblasts in the basal plate of the septum of the placenta, renal tubules of the kidney, and neuronal cells of the cerebral cortex.

Activity regulation. Strongly inhibited by Cu(2+) and Zn(2+). Activated by Mn(2+) up to a concentration of 10 mM, and the activity gradually decreased with further increase in Mn2(2+) concentration.

Pathway. Protein modification; carbohydrate sulfation.

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

RefSeq proteins (1): NP_071417* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009729	Gal-3-0_sulfotransfrase	Family
IPR027417	P-loop_NTPase	Homologous_superfamily

Pfam: PF06990

UniProt features (11 total): glycosylation site 6, topological domain 2, chain 1, sequence variant 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H3Q3-F1	93.04	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.

Glycosylation sites (6): 79, 132, 179, 287, 330, 360

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 37 (showing top): GOBP_GLYCOLIPID_BIOSYNTHETIC_PROCESS, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, GOBP_LIPOSACCHARIDE_METABOLIC_PROCESS, GOBP_MEMBRANE_LIPID_METABOLIC_PROCESS, GOBP_MEMBRANE_LIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, GOCC_GOLGI_CISTERNA_MEMBRANE, GOCC_ORGANELLE_SUBCOMPARTMENT, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_SULPHUR_CONTAINING_GROUPS

GO Biological Process (2): glycoprotein biosynthetic process (GO:0009101), glycolipid biosynthetic process (GO:0009247)

GO Molecular Function (5): galactosylceramide sulfotransferase activity (GO:0001733), galactose 3-O-sulfotransferase activity (GO:0050694), protein binding (GO:0005515), sulfotransferase activity (GO:0008146), transferase activity (GO:0016740)

GO Cellular Component (3): membrane (GO:0016020), Golgi cisterna membrane (GO:0032580), Golgi apparatus (GO:0005794)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
carbohydrate derivative biosynthetic process	2
macromolecule biosynthetic process	1
glycoprotein metabolic process	1
glycolipid metabolic process	1
lipid biosynthetic process	1
galactose 3-O-sulfotransferase activity	1
sulfotransferase activity	1
binding	1
transferase activity, transferring sulphur-containing groups	1
catalytic activity	1
cellular anatomical structure	1
organelle membrane	1
Golgi cisterna	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

184 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GAL3ST2	NEU4	Q8WWR8	892
GAL3ST2	DTYMK	P23919	840
GAL3ST2	CHST5	Q9GZS9	719
GAL3ST2	NEU2	Q9Y3R4	669
GAL3ST2	FUT3	P21217	668
GAL3ST2	SULT1C3	Q6IMI6	589
GAL3ST2	SULT1C4	O75897	582
GAL3ST2	SULT1B1	O43704	581
GAL3ST2	TFF3	Q07654	414
GAL3ST2	TMEM232	C9JQI7	396
GAL3ST2	MUC2	Q02817	380
GAL3ST2	SPN	P16150	339
GAL3ST2	LRRC25	Q8N386	333
GAL3ST2	CHST1	O43916	327
GAL3ST2	GCNT3	O95395	315

IntAct

6 interactions, top by confidence:

A	B	Type	Score
MTUS2	GAL3ST2	psi-mi:“MI:0915”(physical association)	0.560
GAL3ST2	MTUS2	psi-mi:“MI:0915”(physical association)	0.560
GAL3ST2	STX16	psi-mi:“MI:0914”(association)	0.350
LIPA	CLGN	psi-mi:“MI:0914”(association)	0.350

BioGRID (17): GAL3ST2 (Two-hybrid), GAL3ST2 (Affinity Capture-MS), GAL3ST2 (Affinity Capture-MS), ATP1A3 (Affinity Capture-MS), MANEA (Affinity Capture-MS), STX16 (Affinity Capture-MS), GPR50 (Affinity Capture-MS), CANX (Affinity Capture-MS), GPRC5C (Affinity Capture-MS), STX6 (Affinity Capture-MS), ATP2B2 (Affinity Capture-MS), ATP12A (Affinity Capture-MS), OS9 (Affinity Capture-MS), GALNT12 (Affinity Capture-MS), HLA-C (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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	86
Likely benign	6
Benign	2

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
190940	NM_022134.3(GAL3ST2):c.197C>T (p.Thr66Met)	Likely pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

2560 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:241803391:G:T	R141M	0.996
2:241801844:G:C	K61N	0.995
2:241801844:G:T	K61N	0.995
2:241801835:G:C	K58N	0.994
2:241801835:G:T	K58N	0.994
2:241801851:A:C	S64R	0.992
2:241801853:C:A	S64R	0.992
2:241801853:C:G	S64R	0.992
2:241801843:A:C	K61T	0.991
2:241801843:A:T	K61M	0.991
2:241803391:G:C	R141T	0.991
2:241801852:G:T	S64I	0.990
2:241801855:G:T	S65I	0.987
2:241803477:T:C	F170L	0.987
2:241803479:C:A	F170L	0.987
2:241803479:C:G	F170L	0.987
2:241803552:T:C	F195L	0.987
2:241803554:C:A	F195L	0.987
2:241803554:C:G	F195L	0.987
2:241803805:A:T	D279V	0.987
2:241801834:A:C	K58T	0.986
2:241801854:A:C	S65R	0.986
2:241801856:C:A	S65R	0.986
2:241801856:C:G	S65R	0.986
2:241803392:G:C	R141S	0.986
2:241803392:G:T	R141S	0.986
2:241803420:T:C	F151L	0.986
2:241803422:C:A	F151L	0.986
2:241803422:C:G	F151L	0.986
2:241803542:C:A	N191K	0.986

dbSNP variants (sampled 300 via entrez): RS1000026073 (2:241798307 C>T), RS1000152829 (2:241803511 G>A,C), RS1000301134 (2:241800655 A>C,T), RS1000399859 (2:241781238 G>C), RS1000453955 (2:241795507 T>C,G), RS1000465579 (2:241776001 G>A), RS1000577301 (2:241787961 C>A), RS1000626567 (2:241799821 C>A), RS1000681685 (2:241794237 C>T), RS1000755301 (2:241794572 A>C), RS1000917836 (2:241799287 C>T), RS1001105685 (2:241804478 C>A), RS1001154786 (2:241804357 G>C,T), RS1001174617 (2:241783036 G>A,C), RS1001175801 (2:241794562 C>A,G)

Disease associations

OMIM: gene MIM:608237 | 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)

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
dicrotophos	increases expression	1
bisphenol A	decreases methylation, affects cotreatment	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases methylation	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	decreases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol S	decreases methylation	1
Fulvestrant	affects cotreatment, decreases methylation	1
Arsenic	affects methylation	1
Diethylhexyl Phthalate	increases abundance, increases methylation	1
Folic Acid	decreases expression	1
Lipopolysaccharides	increases expression, affects response to substance	1
Methapyrilene	increases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Triclosan	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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