NDST3

gene
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Also known as HSST3

Summary

NDST3 (N-deacetylase and N-sulfotransferase 3, HGNC:7682) is a protein-coding gene on chromosome 4q26, encoding Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 (O95803). Essential bifunctional enzyme that catalyzes both the N-deacetylation and the N-sulfation of glucosamine (GlcNAc) of the glycosaminoglycan in heparan sulfate.

This gene encodes a member of the heparan sulfate/heparin GlcNAc N-deacetylase/ N-sulfotransferase family. The encoded enzyme is a type II transmembrane protein that resides in the Golgi apparatus. This monomeric bifunctional enzyme catalyzes the N-deacetylation and N-sulfation of N-acetylglucosamine residues in heparan sulfate and heparin, which are the initial chemical modifications required for the biosynthesis of the functional oligosaccharide sequences that define the specific ligand binding activities of heparan sulfate and heparin.

Source: NCBI Gene 9348 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 84 total
  • MANE Select transcript: NM_004784

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:7682
Approved symbolNDST3
NameN-deacetylase and N-sulfotransferase 3
Location4q26
Locus typegene with protein product
StatusApproved
AliasesHSST3
Ensembl geneENSG00000164100
Ensembl biotypeprotein_coding
OMIM603950
Entrez9348

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000296499, ENST00000394488, ENST00000852871

RefSeq mRNA: 1 — MANE Select: NM_004784 NM_004784

CCDS: CCDS3708

Canonical transcript exons

ENST00000296499 — 14 exons

ExonStartEnd
ENSE00000996907118143556118143684
ENSE00000996908118138054118138239
ENSE00001161093118114806118114960
ENSE00001201937118105018118105105
ENSE00001201940118034486118034592
ENSE00001201949118053756118054891
ENSE00001634973118255593118258634
ENSE00001675525118237046118237220
ENSE00001709182118253499118253601
ENSE00001801529118240524118240694
ENSE00002457853118233012118233135
ENSE00002485035118226886118226982
ENSE00002502960118242040118242149
ENSE00002513338118224491118224673

Expression profiles

Bgee: expression breadth ubiquitous, 116 present calls, max score 93.36.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4069 / max 87.1802, expressed in 370 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
494170.4730170
494190.229481
494150.216094
494160.212282
494180.139257
494140.098848
494130.038217

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233693.36gold quality
cerebellar cortexUBERON:000212975.29gold quality
cerebellar hemisphereUBERON:000224575.24gold quality
cortical plateUBERON:000534374.87gold quality
cerebellumUBERON:000203774.82gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047374.20gold quality
right hemisphere of cerebellumUBERON:001489074.02gold quality
prefrontal cortexUBERON:000045172.52gold quality
ganglionic eminenceUBERON:000402372.42gold quality
nucleus accumbensUBERON:000188272.33gold quality
Brodmann (1909) area 9UBERON:001354071.62gold quality
dorsolateral prefrontal cortexUBERON:000983471.36gold quality
right frontal lobeUBERON:000281070.39gold quality
frontal cortexUBERON:000187070.32gold quality
cerebellar vermisUBERON:000472070.01gold quality
neocortexUBERON:000195069.75gold quality
caudate nucleusUBERON:000187369.31gold quality
anterior cingulate cortexUBERON:000983568.90gold quality
cingulate cortexUBERON:000302768.84gold quality
putamenUBERON:000187468.59gold quality
cerebral cortexUBERON:000095667.71gold quality
telencephalonUBERON:000189367.34gold quality
Brodmann (1909) area 46UBERON:000648366.48silver quality
Brodmann (1909) area 23UBERON:001355466.16gold quality
forebrainUBERON:000189065.44gold quality
brainUBERON:000095565.40gold quality
superior frontal gyrusUBERON:000266164.30gold quality
primary visual cortexUBERON:000243664.19gold quality
ventricular zoneUBERON:000305363.79gold quality
tibial nerveUBERON:000132363.29gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-35yes102.01
E-ANND-3yes4.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

207 targeting NDST3, 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-3924100.0072.092394
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3163100.0077.238605
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-3613-3P100.0076.367965
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-656-3P100.0072.152788
HSA-MIR-5692A100.0074.406850
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-607799.9968.042299
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-428299.9975.366408
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-477599.9875.006394
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-1213699.9872.815713
HSA-MIR-569699.9872.364487
HSA-MIR-548N99.9871.944170

Literature-anchored findings (GeneRIF, showing 7)

  • A case-control study evaluating the entire genome for genes associated with the risk of schizophrenia and bipolar disorder demnstrated polymorphisms of NDST3 in case patients. (PMID:24253340)
  • study provides evidence that the minor allele of rs11098403, an SNP near NDST3, is significantly associated with a reduced risk of schizophrenia in a Han Chinese population, further confirming the data obtained from Caucasians (PMID:25139529)
  • A genome-wide association study provided suggestive evidence that the NDST3 variation predisposed patients to schizophrenia and bipolar disorder. (PMID:26731438)
  • Study does not support that the NDST3 gene plays a major role in schizophrenia, bipolar disorder, and major depressive disorder in the Han Chinese population. (PMID:29140583)
  • Hsa_circ_0001017 inhibits proliferation and metastasis via regulating the let-7g-3p/NDST3 axis in glioma. (PMID:34284545)
  • NDST3 deacetylates alpha-tubulin and suppresses V-ATPase assembly and lysosomal acidification. (PMID:34435379)
  • Genetic Variance in Heparan Sulfation Is Associated With Salt Sensitivity. (PMID:39247955)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriosi:dkey-121b10.7ENSDARG00000059948
danio_reriohs3st3b1aENSDARG00000099149
mus_musculusNdst3ENSMUSG00000027977
rattus_norvegicusNdst3ENSRNOG00000015781
drosophila_melanogastersflFBGN0020251
caenorhabditis_elegansWBGENE00002028

Paralogs (10): HS3ST1 (ENSG00000002587), NDST1 (ENSG00000070614), HS3ST2 (ENSG00000122254), HS3ST3B1 (ENSG00000125430), NDST4 (ENSG00000138653), HS3ST3A1 (ENSG00000153976), HS3ST6 (ENSG00000162040), NDST2 (ENSG00000166507), HS3ST4 (ENSG00000182601), HS3ST5 (ENSG00000249853)

Protein

Protein identifiers

Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3O95803 (reviewed: O95803)

Alternative names: Glucosaminyl N-deacetylase/N-sulfotransferase 3, N-heparan sulfate sulfotransferase 3

All UniProt accessions (1): O95803

UniProt curated annotations — full annotation on UniProt →

Function. Essential bifunctional enzyme that catalyzes both the N-deacetylation and the N-sulfation of glucosamine (GlcNAc) of the glycosaminoglycan in heparan sulfate. Modifies the GlcNAc-GlcA disaccharide repeating sugar backbone to make N-sulfated heparosan, a prerequisite substrate for later modifications in heparin biosynthesis. Has high deacetylase activity but low sulfotransferase activity.

Subunit / interactions. Monomer.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Expressed in brain, kidney, liver, fetal and adult lung, adult pancreas, placenta, fetal spleen and fetal thymus. Not detected in adult/ fetal heart and skeletal muscle.

Pathway. Glycan metabolism; heparan sulfate biosynthesis. Glycan metabolism; heparin biosynthesis.

Miscellaneous. The presence of 4 different heparan sulfate N-deacetylase/N-sulfotransferase enzymes in mammals, as well as differences in their enzyme activity suggest that some initiate heparan sulfate modification/sulfation reactions, whereas other later on fill in or extend already modified heparan sulfate sequences.

Similarity. Belongs to the sulfotransferase 1 family. NDST subfamily.

Isoforms (3)

UniProt IDNamesCanonical?
O95803-11yes
O95803-22
O95803-33

RefSeq proteins (1): NP_004775* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000863Sulfotransferase_domDomain
IPR021930Heparan_SO4_deacetylase_domDomain
IPR027417P-loop_NTPaseHomologous_superfamily
IPR037359NST/OSTFamily
IPR056793HSNSD_NDomain

Pfam: PF00685, PF12062, PF25119

Enzyme classification (BRENDA):

  • EC 2.8.2.8 — [heparan sulfate]-glucosamine N-sulfotransferase (BRENDA: 11 organisms, 86 substrates, 14 inhibitors, 13 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’-PHOSPHOADENYLYLSULFATE0.005–0.1086
N-DEACETYLASE K5-POLYSACCHARIDE0.0009–0.02243
N,O-DESULFOHEPARAN SULFATE TETRASACCHARIDE2.51
N-DESULFOHEPARAN SULFATE1.891
N-DESULFOHEPARIN0.0131

Catalyzed reactions (Rhea), 1 shown:

  • alpha-D-glucosaminyl-heparan sulfate + 3’-phosphoadenylyl sulfate = N-sulfo-alpha-D-glucosaminyl-heparan sulfate + adenosine 3’,5’-bisphosphate + 2 H(+) (RHEA:21980)

UniProt features (24 total): glycosylation site 6, splice variant 5, binding site 3, topological domain 2, region of interest 2, chain 1, disulfide bond 1, transmembrane region 1, sequence variant 1, sequence conflict 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95803-F190.550.76

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 605 (for sulfotransferase activity)

Ligand- & substrate-binding residues (3): 605–609; 703; 824–828

Disulfide bonds (1): 809–819

Glycosylation sites (6): 146, 226, 342, 392, 658, 794

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-2022928HS-GAG biosynthesis
R-HSA-1430728Metabolism
R-HSA-1630316Glycosaminoglycan metabolism
R-HSA-1638091Heparan sulfate/heparin (HS-GAG) metabolism
R-HSA-71387Metabolism of carbohydrates and carbohydrate derivatives

MSigDB gene sets: 141 (showing top): ATACCTC_MIR202, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, BRN2_01, GOBP_HEPARAN_SULFATE_PROTEOGLYCAN_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, AACTTT_UNKNOWN, CREBP1_01, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, REACTOME_METABOLISM_OF_CARBOHYDRATES_AND_CARBOHYDRATE_DERIVATIVES, GOMF_HEPARAN_SULFATE_SULFOTRANSFERASE_ACTIVITY, E4BP4_01, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS, GOMF_CARBOXYLIC_ESTER_HYDROLASE_ACTIVITY, GOMF_DEACETYLASE_ACTIVITY

GO Biological Process (2): heparan sulfate proteoglycan biosynthetic process (GO:0015012), heparin proteoglycan biosynthetic process (GO:0030210)

GO Molecular Function (7): heparan sulfate N-sulfotransferase activity (GO:0015016), deacetylase activity (GO:0019213), heparan sulfate N-deacetylase activity (GO:0102140), catalytic activity (GO:0003824), sulfotransferase activity (GO:0008146), transferase activity (GO:0016740), hydrolase activity (GO:0016787)

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

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Heparan sulfate/heparin (HS-GAG) metabolism1
Metabolism of carbohydrates and carbohydrate derivatives1
Glycosaminoglycan metabolism1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein O-linked glycosylation via xylose2
catalytic activity2
proteoglycan biosynthetic process1
heparan sulfate proteoglycan metabolic process1
heparin proteoglycan metabolic process1
heparan sulfate sulfotransferase activity1
deacylase activity1
deacetylase activity1
carboxylic ester hydrolase activity1
molecular_function1
transferase activity, transferring sulphur-containing groups1
Golgi apparatus1
bounding membrane of organelle1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

570 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NDST3SULT1C3Q6IMI6759
NDST3SULT1C4O75897756
NDST3SULT1B1O43704729
NDST3HS2ST1Q7LGA3711
NDST3GLCEO94923650
NDST3EXTL1Q92935642
NDST3HS6ST1O60243636
NDST3EXTL3O43909591
NDST3HS6ST2Q96MM7571
NDST3HS6ST3Q8IZP7570
NDST3EXT1Q16394568
NDST3EXT2Q93063558
NDST3K7EP71K7EP71547
NDST3EXTL2Q9UBQ6544
NDST3USTQ9Y2C2544

IntAct

4 interactions, top by confidence:

ABTypeScore
NDST2CLGNpsi-mi:“MI:0914”(association)0.350
NDST3PYGBpsi-mi:“MI:0914”(association)0.350
NDST3B3GAT3psi-mi:“MI:0914”(association)0.350

BioGRID (9): NDST3 (Affinity Capture-MS), NDST4 (Affinity Capture-MS), PYGB (Affinity Capture-MS), NDST3 (Affinity Capture-MS), KCTD13 (Affinity Capture-MS), LMF1 (Affinity Capture-MS), TUBB2B (Affinity Capture-MS), B3GAT3 (Affinity Capture-MS), RTFDC1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A1D5PUP4, A2AFS3, M0R7X9, O70472, O75882, O95803, P01134, P26012, P52799, P52848, P69849, Q02353, Q05204, Q0VCJ8, Q12841, Q13635, Q15155, Q3UHN9, Q3ZBS2, Q58D84, Q5EA46, Q5JPE7, Q5R9Y1, Q5U4X8, Q5VV63, Q5ZJB7, Q5ZMH6, Q61115, Q62356, Q62632, Q6A051, Q6GQK9, Q6GQT9, Q6P988, Q6UXG2, Q7Z5A7, Q86TD4, Q90693, Q91WE9, Q96CW9

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

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance77
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3214 predictions. Top by Δscore:

VariantEffectΔscore
4:118053755:GACT:Gacceptor_gain1.0000
4:118114802:A:AGacceptor_gain1.0000
4:118114802:AAAG:Aacceptor_gain1.0000
4:118114956:CCTTA:Cdonor_gain1.0000
4:118114957:CTTA:Cdonor_gain1.0000
4:118114958:TTA:Tdonor_gain1.0000
4:118114959:TA:Tdonor_gain1.0000
4:118114959:TAG:Tdonor_loss1.0000
4:118114960:AGTAA:Adonor_loss1.0000
4:118114961:G:Adonor_loss1.0000
4:118114961:G:GGdonor_gain1.0000
4:118114962:T:Adonor_loss1.0000
4:118114963:A:ATdonor_loss1.0000
4:118114964:AGTAA:Adonor_loss1.0000
4:118143551:TTCA:Tacceptor_loss1.0000
4:118143552:TCAG:Tacceptor_loss1.0000
4:118143553:CAG:Cacceptor_loss1.0000
4:118143554:A:AGacceptor_gain1.0000
4:118143555:G:GGacceptor_gain1.0000
4:118143555:G:GTacceptor_loss1.0000
4:118143680:ACCCT:Adonor_gain1.0000
4:118143681:CCCT:Cdonor_gain1.0000
4:118143682:CCT:Cdonor_gain1.0000
4:118143682:CCTG:Cdonor_loss1.0000
4:118143683:CT:Cdonor_gain1.0000
4:118143685:G:GGdonor_gain1.0000
4:118143686:TAAG:Tdonor_loss1.0000
4:118143687:AA:Adonor_loss1.0000
4:118224489:A:AGacceptor_gain1.0000
4:118224490:G:GAacceptor_gain1.0000

AlphaMissense

5795 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:118054841:G:CD311H1.000
4:118054842:A:CD311A1.000
4:118054842:A:TD311V1.000
4:118114886:C:GH384D1.000
4:118114888:T:AH384Q1.000
4:118114888:T:GH384Q1.000
4:118138094:C:AP422H1.000
4:118138096:C:GH423D1.000
4:118138099:C:GH424D1.000
4:118138101:T:AH424Q1.000
4:118138101:T:GH424Q1.000
4:118138141:T:AW438R1.000
4:118138141:T:CW438R1.000
4:118138171:A:CS448R1.000
4:118138173:C:AS448R1.000
4:118138173:C:GS448R1.000
4:118143557:T:AV471D1.000
4:118143566:G:CR474T1.000
4:118143583:T:CF480L1.000
4:118143585:C:AF480L1.000
4:118143585:C:GF480L1.000
4:118253570:A:TK824I1.000
4:118253571:A:CK824N1.000
4:118253571:A:TK824N1.000
4:118053983:A:CS25R0.999
4:118053985:C:AS25R0.999
4:118053985:C:GS25R0.999
4:118054838:G:CD310H0.999
4:118054839:A:CD310A0.999
4:118054839:A:TD310V0.999

dbSNP variants (sampled 300 via entrez): RS1000012600 (4:118073755 A>C), RS1000016608 (4:118200178 T>A), RS1000019507 (4:118102031 C>A,G,T), RS1000033086 (4:118061734 A>G), RS1000053498 (4:118201754 T>G), RS1000092522 (4:118119317 T>C), RS1000101895 (4:118161538 C>T), RS1000108517 (4:118201573 G>A), RS1000114086 (4:118170687 C>T), RS10001247 (4:118170438 A>G), RS1000133194 (4:118150998 C>A,T), RS10001520 (4:118140673 A>G), RS1000175081 (4:118254175 G>A), RS10001926 (4:118215739 A>T), RS1000204379 (4:118149319 A>G)

Disease associations

OMIM: gene MIM:603950 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST002277_1Schizophrenia3.000000e-08
GCST006218_54Erosive tooth wear (severe vs non-severe)3.000000e-08
GCST006950_9Feeling worry4.000000e-08
GCST007201_468Schizophrenia4.000000e-08
GCST008395_4End-stage kidney disease9.000000e-07
GCST009391_427Metabolite levels6.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0009589worry measurement
EFO:0010384phosphatidylcholine 38:2 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases methylation, increases expression2
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
entinostatdecreases expression1
2,2’,4,4’,5-brominated diphenyl etherdecreases expression1
Arsenic Trioxidedecreases expression1
Vorinostatdecreases expression1
Cadmiumincreases abundance, decreases expression1
Carbamazepineaffects expression1
Methapyrileneincreases methylation1
Phthalic Acidsincreases methylation1
Valproic Acidaffects expression1
Aflatoxin B1decreases methylation1
Asbestos, Crocidoliteincreases methylation1
Cadmium Chloridedecreases expression, increases abundance1
Okadaic Acidincreases 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.