HS3ST3A1

gene
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Also known as 3OST3A130ST3A1

Summary

HS3ST3A1 (heparan sulfate-glucosamine 3-sulfotransferase 3A1, HGNC:5196) is a protein-coding gene on chromosome 17p12, encoding Heparan sulfate glucosamine 3-O-sulfotransferase 3A1 (Q9Y663). Sulfotransferase that utilizes 3’-phospho-5’-adenylyl sulfate (PAPS) to catalyze the transfer of a sulfo group to an N-unsubstituted glucosamine linked to a 2-O-sulfo iduronic acid unit on heparan sulfate.

Heparan sulfate biosynthetic enzymes are key components in generating a myriad of distinct heparan sulfate fine structures that carry out multiple biologic activities. The enzyme encoded by this gene is a member of the heparan sulfate biosynthetic enzyme family. It is a type II integral membrane protein and possesses heparan sulfate glucosaminyl 3-O-sulfotransferase activity. The sulfotransferase domain of this enzyme is highly similar to the same domain of heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3B1, and these two enzymes sulfate an identical disaccharide. This gene is widely expressed, with the most abundant expression in liver and placenta.

Source: NCBI Gene 9955 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 76 total
  • MANE Select transcript: NM_006042

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:5196
Approved symbolHS3ST3A1
Nameheparan sulfate-glucosamine 3-sulfotransferase 3A1
Location17p12
Locus typegene with protein product
StatusApproved
Aliases3OST3A1, 30ST3A1
Ensembl geneENSG00000153976
Ensembl biotypeprotein_coding
OMIM604057
Entrez9955

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000284110, ENST00000578576

RefSeq mRNA: 1 — MANE Select: NM_006042 NM_006042

CCDS: CCDS11165

Canonical transcript exons

ENST00000284110 — 2 exons

ExonStartEnd
ENSE000010133721349403213496818
ENSE000012205291360053113601929

Expression profiles

Bgee: expression breadth ubiquitous, 176 present calls, max score 93.63.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.5176 / max 127.3264, expressed in 1066 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1646525.13911062
1646500.1898111
1646510.1887106

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cartilage tissueUBERON:000241893.63gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047392.31gold quality
tibiaUBERON:000097989.25gold quality
gingival epitheliumUBERON:000194988.42gold quality
gingivaUBERON:000182887.94gold quality
oral cavityUBERON:000016785.72gold quality
esophagus squamous epitheliumUBERON:000692083.78gold quality
epithelium of esophagusUBERON:000197682.80gold quality
renal glomerulusUBERON:000007482.41gold quality
metanephric glomerulusUBERON:000473681.53gold quality
seminal vesicleUBERON:000099880.98gold quality
squamous epitheliumUBERON:000691480.17gold quality
stromal cell of endometriumCL:000225579.77gold quality
germinal epithelium of ovaryUBERON:000130477.32silver quality
choroid plexus epitheliumUBERON:000391176.06gold quality
left ovaryUBERON:000211975.92gold quality
ovaryUBERON:000099273.18gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099172.90gold quality
tongue squamous epitheliumUBERON:000691972.84silver quality
spleenUBERON:000210671.62gold quality
esophagus mucosaUBERON:000246971.48gold quality
right ovaryUBERON:000211871.29gold quality
sural nerveUBERON:001548870.56gold quality
metanephrosUBERON:000008170.15gold quality
kidney epitheliumUBERON:000481969.48gold quality
ectocervixUBERON:001224968.59gold quality
periodontal ligamentUBERON:000826668.57silver quality
endocervixUBERON:000045868.51gold quality
esophagusUBERON:000104367.27gold quality
tonsilUBERON:000237267.23gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-8271yes6.66
E-CURD-10no122.80
E-ANND-3no3.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

147 targeting HS3ST3A1, 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-656-3P100.0072.152788
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-4262100.0073.263931
HSA-MIR-366299.9973.825684
HSA-MIR-186-5P99.9970.833707
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-314899.9775.066478
HSA-MIR-365899.9673.874379
HSA-MIR-302E99.9670.742669
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-LET-7C-3P99.9573.422862
HSA-MIR-548J-3P99.9472.614881

Literature-anchored findings (GeneRIF, showing 4)

  • Genetic variants of HS3ST3A1 and HS3ST3B1 are associated with Plasmodium falciparum parasitaemia. (PMID:22475533)
  • decreased in pre-eclamptic placental tissue (PMID:26410339)
  • Our findings define 3-OST3A as a novel regulator of breast cancer pathogenicity, displaying tumor-suppressive or oncogenic activities in a cell- and tumor-dependent context, and demonstrate the clinical value of the HS-O-sulfotransferase 3-OST3A as a prognostic marker in HER2+ patients. (PMID:27041583)
  • Detection of MUC1 and HS3ST2 promoter methylation status appears to be useful molecular markers for assessing the progressive state of the disease and could be helpful in discriminating breast cancer molecular subtypes. These results validate the methylation-based microarray analysis, thus trust their output in the future. (PMID:28618938)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriohs3st1l2ENSDARG00000035578
danio_reriosi:dkey-121b10.7ENSDARG00000059948
danio_reriohs3st3b1aENSDARG00000099149
mus_musculusHs3st3a1ENSMUSG00000047759
rattus_norvegicusHs3st3a1ENSRNOG00000024591
drosophila_melanogastersflFBGN0020251
caenorhabditis_elegansWBGENE00002028

Paralogs (10): HS3ST1 (ENSG00000002587), NDST1 (ENSG00000070614), HS3ST2 (ENSG00000122254), HS3ST3B1 (ENSG00000125430), NDST4 (ENSG00000138653), HS3ST6 (ENSG00000162040), NDST3 (ENSG00000164100), NDST2 (ENSG00000166507), HS3ST4 (ENSG00000182601), HS3ST5 (ENSG00000249853)

Protein

Protein identifiers

Heparan sulfate glucosamine 3-O-sulfotransferase 3A1Q9Y663 (reviewed: Q9Y663)

Alternative names: Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1

All UniProt accessions (2): Q9Y663, J3KSX5

UniProt curated annotations — full annotation on UniProt →

Function. Sulfotransferase that utilizes 3’-phospho-5’-adenylyl sulfate (PAPS) to catalyze the transfer of a sulfo group to an N-unsubstituted glucosamine linked to a 2-O-sulfo iduronic acid unit on heparan sulfate. Catalyzes the O-sulfation of glucosamine in IdoUA2S-GlcNS and also in IdoUA2S-GlcNH2. The substrate-specific O-sulfation generates an enzyme-modified heparan sulfate which acts as a binding receptor to Herpes simplex virus-1 (HSV-1) and permits its entry. Unlike HS3ST1/3-OST-1, does not convert non-anticoagulant heparan sulfate to anticoagulant heparan sulfate.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Ubiquitous. Most abundant in heart and placenta, followed by liver and kidney.

Similarity. Belongs to the sulfotransferase 1 family.

RefSeq proteins (1): NP_006033* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000863Sulfotransferase_domDomain
IPR027417P-loop_NTPaseHomologous_superfamily
IPR037359NST/OSTFamily

Pfam: PF00685

Enzyme classification (BRENDA):

  • EC 2.8.2.30 — [heparan sulfate]-glucosamine 3-sulfotransferase 3 (BRENDA: 5 organisms, 27 substrates, 0 inhibitors, 1 Km, 0 kcat entries)

Catalyzed reactions (Rhea), 1 shown:

  • alpha-D-glucosaminyl-heparan sulfate + 3’-phosphoadenylyl sulfate = 3-sulfo-alpha-D-glucosaminyl-heparan sulfate + adenosine 3’,5’-bisphosphate + H(+) (RHEA:15461)

UniProt features (71 total): mutagenesis site 23, helix 16, binding site 10, strand 10, compositionally biased region 3, topological domain 2, glycosylation site 2, chain 1, transmembrane region 1, disulfide bond 1, region of interest 1, turn 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
6XKGX-RAY DIFFRACTION1.55
1T8TX-RAY DIFFRACTION1.85
1T8UX-RAY DIFFRACTION1.95
6XL8X-RAY DIFFRACTION2.34

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y663-F182.140.68

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 (10): 184–190; 215–218; 243; 251; 255–259; 283–284; 367–370; 368–372; 162–166; 166

Disulfide bonds (1): 351–363

Glycosylation sites (2): 273, 344

Mutagenesis-validated functional residues (23):

PositionPhenotype
16199.6% loss of enzymatic activity.
16299.6% loss of enzymatic activity; no hsv1 entry activity.
16699.8% loss of enzymatic activity.
17017% loss of enzymatic activity.
17344.1% loss of enzymatic activity.
182no effect on enzymatic activity.
18499.9% loss of enzymatic activity.
186abolishes enzymatic activity.
18999.1% loss of enzymatic activity.
19032% loss of enzymatic activity.
19499.5% loss of enzymatic activity.
21599.9% loss of enzymatic activity.
21823.3% loss of enzymatic activity.
22447.6% loss of enzymatic activity.
25599.6% loss of enzymatic activity.
25948.3% loss of enzymatic activity.
28865% loss of enzymatic activity.
29333.6% loss of enzymatic activity.
362no effect on enzymatic activity.
36543% loss of enzymatic activity.
36699.8% loss of enzymatic activity.
36899.9% loss of enzymatic activity.
37099.2% loss of enzymatic activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2022928HS-GAG biosynthesis

MSigDB gene sets: 180 (showing top): ATF_B, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, RNGTGGGC_UNKNOWN, chr17p12, GOBP_EPITHELIUM_DEVELOPMENT, WALLACE_PROSTATE_CANCER_RACE_UP, GOBP_KIDNEY_EPITHELIUM_DEVELOPMENT, USF_C, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_AMINOGLYCAN_BIOSYNTHETIC_PROCESS, CDP_01, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_NEPHRON_EPITHELIUM_DEVELOPMENT, ATF1_Q6, GOBP_HEPARAN_SULFATE_PROTEOGLYCAN_METABOLIC_PROCESS

GO Biological Process (3): branching involved in ureteric bud morphogenesis (GO:0001658), glycosaminoglycan biosynthetic process (GO:0006024), heparan sulfate proteoglycan biosynthetic process (GO:0015012)

GO Molecular Function (3): sulfotransferase activity (GO:0008146), [heparan sulfate]-glucosamine 3-sulfotransferase activity (GO:0008467), 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
Heparan sulfate/heparin (HS-GAG) metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
branching morphogenesis of an epithelial tube1
ureteric bud morphogenesis1
aminoglycan biosynthetic process1
glycosaminoglycan metabolic process1
proteoglycan biosynthetic process1
heparan sulfate proteoglycan metabolic process1
protein O-linked glycosylation via xylose1
transferase activity, transferring sulphur-containing groups1
heparan sulfate sulfotransferase activity1
catalytic activity1
Golgi apparatus1
bounding membrane of organelle1
cellular anatomical structure1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

372 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HS3ST3A1SULT1C4O75897838
HS3ST3A1SULT1B1O43704834
HS3ST3A1SULT1C3Q6IMI6833
HS3ST3A1HS2ST1Q7LGA3644
HS3ST3A1HS6ST2Q96MM7557
HS3ST3A1HS6ST1O60243547
HS3ST3A1HS6ST3Q8IZP7518
HS3ST3A1GLCEO94923506
HS3ST3A1USTQ9Y2C2501
HS3ST3A1K7EP71K7EP71486
HS3ST3A1XYLT1Q86Y38476
HS3ST3A1CHST12Q9NRB3436
HS3ST3A1CSGALNACT2Q8N6G5429
HS3ST3A1EXT1Q16394428
HS3ST3A1CDRT15Q96T59417

IntAct

1 interactions, top by confidence:

ABTypeScore
PIPSLC1orf226psi-mi:“MI:0914”(association)0.350

BioGRID (3): HS3ST3A1 (Affinity Capture-RNA), HS3ST3A1 (Affinity Capture-MS), HS3ST3A1 (Two-hybrid)

ESM2 similar proteins: A1A4K5, A2BGL3, D4PHA7, O43916, O88199, O95461, Q0IIY2, Q2TBF2, Q3TCT4, Q505J3, Q5DTK1, Q5NDE3, Q5NDE9, Q5NDF0, Q5NDF1, Q5NDF2, Q5QQ49, Q5QQ56, Q5QQ57, Q5REF6, Q5RJQ0, Q658N2, Q66PG1, Q66PG2, Q66PG3, Q66PG4, Q6L8S8, Q6L9W6, Q70JA7, Q7LFX5, Q7LGC8, Q80TS8, Q80XH4, Q811B1, Q86Y38, Q8BW41, Q8CHI9, Q8NAT1, Q8R4K8, Q91XQ5

Diamond homologs: O14792, O35310, O95803, O97583, Q5GFD5, Q673U1, Q80W66, Q8BKN6, Q8BSL4, Q8IZT8, Q96QI5, Q9EQW8, Q9ESG5, Q9H3R1, Q9QZS6, Q9Y278, Q9Y661, Q9Y662, Q9Y663, P52849, Q60V90, Q966W3, Q9EQH7, Q9V3L1, P52848, P52850, Q02353, Q3UHN9, Q5U4X8, Q6GQK9, Q55GK8, Q91XQ5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance75
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1193 predictions. Top by Δscore:

VariantEffectΔscore
17:13496814:GGTCC:Gacceptor_gain1.0000
17:13496815:GTCC:Gacceptor_gain1.0000
17:13496816:TCC:Tacceptor_gain1.0000
17:13496817:CC:Cacceptor_gain1.0000
17:13496817:CCC:Cacceptor_gain1.0000
17:13496818:CC:Cacceptor_gain1.0000
17:13496818:CCTGA:Cacceptor_loss1.0000
17:13496819:C:CCacceptor_gain1.0000
17:13496819:C:Tacceptor_gain1.0000
17:13496820:T:Cacceptor_loss1.0000
17:13496815:GTCCC:Gacceptor_gain0.9900
17:13496816:TCCCT:Tacceptor_gain0.9900
17:13496817:CCCTG:Cacceptor_gain0.9900
17:13496827:C:CTacceptor_gain0.9900
17:13546816:T:Cacceptor_gain0.9900
17:13600557:G:Cdonor_gain0.9900
17:13600529:A:ACdonor_gain0.9800
17:13600530:C:CCdonor_gain0.9800
17:13581031:T:Cacceptor_gain0.9700
17:13600525:GCTCA:Gdonor_loss0.9700
17:13600526:CTCA:Cdonor_loss0.9700
17:13600527:TCA:Tdonor_loss0.9700
17:13600529:A:AGdonor_loss0.9700
17:13600530:CC:Cdonor_loss0.9700
17:13496829:C:CTacceptor_gain0.9600
17:13496830:A:Tacceptor_gain0.9600
17:13497465:T:Adonor_gain0.9500
17:13496818:CCT:Cacceptor_gain0.9400
17:13533294:T:Cdonor_gain0.9400
17:13546816:T:TCacceptor_gain0.9400

AlphaMissense

2617 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:13496237:A:GF394S1.000
17:13496304:G:CH372D1.000
17:13496309:C:AR370M1.000
17:13496309:C:GR370T1.000
17:13496312:C:TG369D1.000
17:13496313:C:AG369C1.000
17:13496313:C:GG369R1.000
17:13496314:C:AK368N1.000
17:13496314:C:GK368N1.000
17:13496315:T:AK368M1.000
17:13496327:A:TL364Q1.000
17:13496329:G:CC363W1.000
17:13496330:C:AC363F1.000
17:13496330:C:GC363S1.000
17:13496330:C:TC363Y1.000
17:13496331:A:GC363R1.000
17:13496331:A:TC363S1.000
17:13496365:G:CC351W1.000
17:13496366:C:AC351F1.000
17:13496366:C:GC351S1.000
17:13496366:C:TC351Y1.000
17:13496367:A:GC351R1.000
17:13496367:A:TC351S1.000
17:13496371:G:CF349L1.000
17:13496371:G:TF349L1.000
17:13496372:A:CF349C1.000
17:13496372:A:GF349S1.000
17:13496373:A:CF349V1.000
17:13496373:A:GF349L1.000
17:13496377:C:AK347N1.000

dbSNP variants (sampled 300 via entrez): RS1000005817 (17:13561522 G>T), RS1000005956 (17:13542292 G>T), RS1000014652 (17:13506558 T>C), RS1000052801 (17:13511116 C>A), RS1000058307 (17:13561263 T>A,C,G), RS1000063977 (17:13598905 A>T), RS1000064602 (17:13520018 A>C), RS1000105337 (17:13585118 T>C), RS1000122367 (17:13580587 G>A,C,T), RS1000123483 (17:13548238 G>A), RS1000123707 (17:13555771 G>A), RS1000135907 (17:13550154 CATTTT>C), RS1000136465 (17:13585792 G>A), RS1000193676 (17:13593099 A>G), RS1000199492 (17:13549360 G>A,T)

Disease associations

OMIM: gene MIM:604057 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST000107_11Tonometry4.000000e-06
GCST003075_27Cognitive decline rate in late mild cognitive impairment8.000000e-08
GCST003075_58Cognitive decline rate in late mild cognitive impairment2.000000e-07
GCST003628_8Clozapine-induced agranulocytosis/granulocytopenia in treatment-resistant schizophrenia5.000000e-06
GCST004283_9Midgestational circulating levels of PCBs8.000000e-06
GCST004750_11Squamous cell lung carcinoma4.000000e-06
GCST007831_3Anti-thyroglobulin (TgAb) levels in Hashimoto’s thyroiditis1.000000e-06
GCST007851_4Anti-thyroid peroxidase (TPOAb) and anti-thyroglobulin (TgAb) levels in Hashimoto’s thyroiditis4.000000e-06
GCST010147_1White matter hyperintensity volume3.000000e-08

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0007710cognitive decline measurement
EFO:0007042polychlorinated biphenyls measurement
EFO:0007964gestational serum measurement
EFO:0005665white matter hyperintensity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, increases expression, increases methylation6
trichostatin Aaffects cotreatment, decreases expression3
sodium arseniteincreases expression, decreases expression, affects cotreatment, increases abundance2
mercuric bromidedecreases expression, affects cotreatment2
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation2
bisphenol Adecreases methylation1
lead acetateincreases expression1
mono-(2-ethylhexyl)phthalateincreases expression1
zinc chromatedecreases expression, increases abundance1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
cupric chlorideincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
chromium hexavalent iondecreases expression, increases abundance1
pentabromodiphenyl etherincreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Sunitinibdecreases expression1
Zoledronic Acidincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Calcitriolincreases expression1
Cisplatindecreases expression1
Estradiolincreases expression1
Leadaffects methylation1
Lipopolysaccharidesincreases expression, affects response to substance1
Manganeseincreases expression, affects cotreatment, increases abundance1
Nickelincreases expression1
Seleniumdecreases 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.