HS6ST2

gene
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Also known as HS6ST-2

Summary

HS6ST2 (heparan sulfate 6-O-sulfotransferase 2, HGNC:19133) is a protein-coding gene on chromosome Xq26.2, encoding Heparan-sulfate 6-O-sulfotransferase 2 (Q96MM7). 6-O-sulfation enzyme which catalyzes the transfer of sulfate from 3’-phosphoadenosine 5’-phosphosulfate (PAPS) to position 6 of the N-sulfoglucosamine residue (GlcNS) of heparan sulfate.

Heparan sulfate proteoglycans are ubiquitous components of the cell surface, extracellular matrix, and basement membranes, and interact with various ligands to influence cell growth, differentiation, adhesion, and migration. This gene encodes a member of the heparan sulfate (HS) sulfotransferase gene family, which catalyze the transfer of sulfate to HS. Different family members and isoforms are thought to synthesize heparan sulfates with tissue-specific structures and functions. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 90161 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Paganini-Miozzo syndrome (Limited, GenCC)
  • GWAS associations: 3
  • Clinical variants (ClinVar): 118 total — 1 pathogenic
  • Phenotypes (HPO): 26
  • MANE Select transcript: NM_001394073

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19133
Approved symbolHS6ST2
Nameheparan sulfate 6-O-sulfotransferase 2
LocationXq26.2
Locus typegene with protein product
StatusApproved
AliasesHS6ST-2
Ensembl geneENSG00000171004
Ensembl biotypeprotein_coding
OMIM300545
Entrez90161

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000370833, ENST00000370836, ENST00000406696, ENST00000521489, ENST00000602570, ENST00000640529

RefSeq mRNA: 4 — MANE Select: NM_001394073 NM_001077188, NM_001394073, NM_001394074, NM_147175

CCDS: CCDS48169, CCDS48170

Canonical transcript exons

ENST00000370833 — 5 exons

ExonStartEnd
ENSE00001154195132669113132669199
ENSE00001154202132708462132708494
ENSE00003459518132956808132957326
ENSE00003719920132958175132958629
ENSE00003808713132626015132629093

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 97.50.

FANTOM5 (CAGE): breadth broad, TPM avg 3.7773 / max 334.7052, expressed in 623 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter IDTPM avgSamples expressed
2005431.1502424
2005391.0561297
2005410.4361284
2005420.3292189
2005400.2477162
2005450.1835105
2005440.130052
2005320.127244
2005380.062326
2005470.040312

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011597.50gold quality
Brodmann (1909) area 23UBERON:001355494.50gold quality
lateral nuclear group of thalamusUBERON:000273693.30gold quality
renal medullaUBERON:000036292.16gold quality
esophagus squamous epitheliumUBERON:000692090.92gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.21gold quality
middle temporal gyrusUBERON:000277187.99gold quality
placentaUBERON:000198786.34gold quality
ventricular zoneUBERON:000305385.92gold quality
entorhinal cortexUBERON:000272884.89gold quality
Brodmann (1909) area 46UBERON:000648384.31gold quality
primary visual cortexUBERON:000243684.12gold quality
superior vestibular nucleusUBERON:000722782.95gold quality
ganglionic eminenceUBERON:000402382.75gold quality
gingival epitheliumUBERON:000194982.58gold quality
occipital lobeUBERON:000202182.49gold quality
lateral globus pallidusUBERON:000247682.49gold quality
germinal epithelium of ovaryUBERON:000130482.31gold quality
oral cavityUBERON:000016782.27gold quality
nucleus accumbensUBERON:000188281.57gold quality
postcentral gyrusUBERON:000258180.70gold quality
substantia nigra pars compactaUBERON:000196580.64gold quality
parietal lobeUBERON:000187280.29gold quality
caput epididymisUBERON:000435880.11gold quality
superior frontal gyrusUBERON:000266180.02gold quality
cerebellar vermisUBERON:000472079.94gold quality
left ovaryUBERON:000211979.67gold quality
gingivaUBERON:000182879.09gold quality
ovaryUBERON:000099279.03gold quality
dorsal plus ventral thalamusUBERON:000189778.58gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-CURD-119yes59.29
E-ANND-3yes3.57

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 8)

  • we have characterized HS6ST-2 and HS6ST-1 human isologues, including their chromosomal localizations,HS6STs could also transfer sulfate to N -sulfoglucosamine residues located at the non-reducing terminal of HS with high affinity. (PMID:12492399)
  • HS6ST2 knockdown disrupts epithelial-mesenchymal transition and suggesets that HS6ST2 potentiates Notch signaling in pancreatic cancer cells. (PMID:21443520)
  • HS6ST-1 and HS6ST-2 have roles in regulating the angiogenic program in ovarian cancer cells affecting HB-EGF signaling and subsequent expression of angiogenic cytokines by cancer cells (PMID:24563483)
  • RT-PCR analysis showed that the overall transcriptional activity of the main Heparan Sulfate biosynthesis-involved genes (EXT1, EXT2, NDST1, NDST2, GLCE, HS2ST1, HS3ST1, HS3ST2, HS6ST1, HS6ST2, SULF1, SULF2, HPSE) was decreased by 1.5-2-fold in Grade II-III glioma. (PMID:29104277)
  • downregulated HS6ST2 targeted by miR-23b-3p promotes matrix degradation by activating p38 MAPK in chondrocytes and OA cartilage. (PMID:29899528)
  • we identified a novel c.916G>C variant in the HS6ST2 gene. The mutation caused a significantly reduction in HS6ST2 6-O-sulfotransferase activity and was associated with a previously undescribed form of syndromic XLID with severe congenital myopia (PMID:30471091)
  • Role of lncRNA FAM83H antisense RNA1 (FAM83H-AS1) in the progression of non-small cell lung cancer by regulating the miR-545-3p/heparan sulfate 6-O-sulfotransferase (HS6ST2) axis. (PMID:35260044)
  • Downregulation of HS6ST2 Inhibits Cervical Cancer Cell Migration and Invasion in Vivo and in Vitro. (PMID:38058080)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriohs6st2ENSDARG00000012025
mus_musculusHs6st2ENSMUSG00000062184
rattus_norvegicusHs6st2ENSRNOG00000030880
drosophila_melanogasterHs6stFBGN0038755
caenorhabditis_elegansWBGENE00002031

Paralogs (2): HS6ST1 (ENSG00000136720), HS6ST3 (ENSG00000185352)

Protein

Protein identifiers

Heparan-sulfate 6-O-sulfotransferase 2Q96MM7 (reviewed: Q96MM7)

All UniProt accessions (2): Q96MM7, A0A1W2PQ14

UniProt curated annotations — full annotation on UniProt →

Function. 6-O-sulfation enzyme which catalyzes the transfer of sulfate from 3’-phosphoadenosine 5’-phosphosulfate (PAPS) to position 6 of the N-sulfoglucosamine residue (GlcNS) of heparan sulfate.

Subcellular location. Membrane.

Disease relevance. Paganini-Miozzo syndrome (MRXSPM) [MIM:301025] An X-linked, syndromic, neurodevelopmental disorder characterized by intellectual disability, global developmental delay, severe myopia, and mild facial dysmorphism. The disease may be caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the sulfotransferase 6 family.

Isoforms (4)

UniProt IDNamesCanonical?
Q96MM7-11yes
Q96MM7-22, HS6ST-2S
Q96MM7-33, HS6ST-2
Q96MM7-44

RefSeq proteins (4): NP_001070656, NP_001381002, NP_001381003, NP_671704 (=MANE)

Domains & families (InterPro)

IDNameType
IPR005331SulfotransferaseFamily
IPR010635Heparan_SO4-6-sulfoTrfaseFamily
IPR027417P-loop_NTPaseHomologous_superfamily

Pfam: PF03567

Catalyzed reactions (Rhea), 1 shown:

  • alpha-D-glucosaminyl-heparan sulfate + 3’-phosphoadenylyl sulfate = 6-sulfo-alpha-D-glucosaminyl-heparan sulfate + adenosine 3’,5’-bisphosphate + H(+) (RHEA:56604)

UniProt features (39 total): binding site 11, glycosylation site 8, sequence conflict 6, compositionally biased region 3, topological domain 2, splice variant 2, sequence variant 2, region of interest 2, chain 1, transmembrane region 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96MM7-F174.280.51

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): 290 (proton acceptor)

Ligand- & substrate-binding residues (11): 233–241; 263–264; 280; 285; 290; 325; 333; 337; 344; 457–459; 463–464

Glycosylation sites (8): 209, 404, 460, 544, 556, 564, 589, 592

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2022928HS-GAG biosynthesis

MSigDB gene sets: 212 (showing top): AP1_01, WHITEHURST_PACLITAXEL_SENSITIVITY, GOZGIT_ESR1_TARGETS_DN, CREBP1_Q2, TGACCTY_ERR1_Q2, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, SREBP1_02, IRF7_01, GOBP_HEPARAN_SULFATE_PROTEOGLYCAN_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, TGCTGAY_UNKNOWN, E4F1_Q6, OCT1_07, ATF3_Q6, SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP

GO Biological Process (1): heparan sulfate proteoglycan biosynthetic process (GO:0015012)

GO Molecular Function (3): heparan sulfate 6-sulfotransferase activity (GO:0017095), sulfotransferase activity (GO:0008146), transferase activity (GO:0016740)

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

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

Protein interactions and networks

STRING

820 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HS6ST2HS2ST1Q7LGA3721
HS6ST2NDST2P52849670
HS6ST2HS3ST1O14792662
HS6ST2NDST1P52848652
HS6ST2GLCEO94923645
HS6ST2EXT1Q16394581
HS6ST2SULF2Q8IWU5579
HS6ST2NDST3O95803571
HS6ST2GPC3P51654568
HS6ST2HS3ST3A1Q9Y663557
HS6ST2SULF1Q8IWU6556
HS6ST2HS3ST4Q9Y661547
HS6ST2HS3ST6Q96QI5543
HS6ST2HS3ST5Q8IZT8522
HS6ST2NDST4Q9H3R1518

IntAct

69 interactions, top by confidence:

ABTypeScore
CANXPGRMC1psi-mi:“MI:0914”(association)0.570
YWHAZBLTP3Bpsi-mi:“MI:0914”(association)0.530
PLOD2psi-mi:“MI:0914”(association)0.530
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
OGFOD3CLGNpsi-mi:“MI:0914”(association)0.530
PON2NPC1psi-mi:“MI:0914”(association)0.530
LGALS1LAMA5psi-mi:“MI:0914”(association)0.530
GINM1ADCY9psi-mi:“MI:0914”(association)0.530
ANKHFAM234Bpsi-mi:“MI:0914”(association)0.530
KIF20ANEURL4psi-mi:“MI:0914”(association)0.350
NETO2TIA1psi-mi:“MI:0914”(association)0.350
Pafah1b1ATXN3psi-mi:“MI:0914”(association)0.350
SURF4psi-mi:“MI:0914”(association)0.350
CACNA1CDISP2psi-mi:“MI:0914”(association)0.350
HCN1POTEFpsi-mi:“MI:0914”(association)0.350
CANXHLA-Apsi-mi:“MI:0914”(association)0.350
LDLRAD1GXYLT2psi-mi:“MI:0914”(association)0.350
PDGFRAGXYLT2psi-mi:“MI:0914”(association)0.350
CLEC12BGXYLT2psi-mi:“MI:0914”(association)0.350
GINM1FAM234Bpsi-mi:“MI:0914”(association)0.350
CHRNB2TMEM131Lpsi-mi:“MI:0914”(association)0.350
ST14LIPT2psi-mi:“MI:0914”(association)0.350
SCGB2A2RTL8Cpsi-mi:“MI:0914”(association)0.350
NRSN1FAM171A2psi-mi:“MI:0914”(association)0.350
TMEM59GPR89Apsi-mi:“MI:0914”(association)0.350
CHRNB4GPR89Apsi-mi:“MI:0914”(association)0.350
C1orf54AGRNpsi-mi:“MI:0914”(association)0.350
C1QTNF7AGRNpsi-mi:“MI:0914”(association)0.350

BioGRID (76): HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-RNA), HS6ST2 (Affinity Capture-MS), HS6ST2 (Affinity Capture-MS)

ESM2 similar proteins: A0A8C2LVE3, A0MGZ5, A0MGZ7, A4IID1, A5D7I4, A9X1C8, O08889, O12971, O60243, O93336, O97583, P0DJQ9, P52849, P52850, P61642, P69478, P97464, Q16394, Q56UJ5, Q5IGR7, Q5IGR8, Q5R621, Q5RBC3, Q5U4X8, Q6GQK9, Q6KFX9, Q6ZXD2, Q76KB1, Q76KB2, Q7LFX5, Q7LGA3, Q7T3S3, Q800H9, Q80UW0, Q86V40, Q8CHI9, Q8IZP7, Q8R3H7, Q91XQ5, Q91ZB4

Diamond homologs: A0MGZ5, A0MGZ7, O60243, Q56UJ5, Q76KB2, Q76LW2, Q800H9, Q80UW0, Q8IZP7, Q91ZB4, Q96MM7, Q9QYK4, Q9QYK5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance80
Likely benign9
Benign5

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
633697NM_001394073.1(HS6ST2):c.916G>C (p.Gly306Arg)Pathogenic

SpliceAI

3682 predictions. Top by Δscore:

VariantEffectΔscore
X:132629092:TCC:Tacceptor_loss1.0000
X:132629093:CCT:Cacceptor_loss1.0000
X:132629094:C:CCacceptor_gain1.0000
X:132629095:T:Gacceptor_loss1.0000
X:132629100:A:ACacceptor_gain1.0000
X:132710259:G:Cacceptor_gain1.0000
X:132629090:GTTC:Gacceptor_gain0.9900
X:132629091:TTC:Tacceptor_gain0.9900
X:132629092:TC:Tacceptor_gain0.9900
X:132629093:CC:Cacceptor_gain0.9900
X:132629100:A:Cacceptor_gain0.9900
X:132710247:CA:Cacceptor_gain0.9900
X:132710248:A:ACacceptor_gain0.9900
X:132710248:A:Cacceptor_gain0.9900
X:132710259:G:GCacceptor_gain0.9900
X:132758254:A:ACdonor_gain0.9900
X:132758255:C:CCdonor_gain0.9900
X:132841263:C:Tacceptor_gain0.9900
X:132956805:CACC:Cdonor_loss0.9900
X:132956806:A:ACdonor_gain0.9900
X:132956806:ACCT:Adonor_loss0.9900
X:132956807:C:Adonor_loss0.9900
X:132956807:C:CCdonor_gain0.9900
X:132957325:CG:Cacceptor_gain0.9900
X:132629089:AGTTC:Aacceptor_gain0.9800
X:132639632:A:ACdonor_gain0.9800
X:132639633:C:CCdonor_gain0.9800
X:132710240:CAAAG:Cacceptor_gain0.9800
X:132710241:A:Tacceptor_gain0.9800
X:132841263:C:CTacceptor_gain0.9800

AlphaMissense

4241 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:132628547:C:AR498S1.000
X:132628547:C:GR498S1.000
X:132628548:C:AR498M1.000
X:132628548:C:GR498T1.000
X:132628560:A:GL494P1.000
X:132628569:G:TA491D1.000
X:132628570:C:GA491P1.000
X:132628590:T:AD484V1.000
X:132628590:T:GD484A1.000
X:132628591:C:AD484Y1.000
X:132628591:C:GD484H1.000
X:132628598:A:CN481K1.000
X:132628598:A:TN481K1.000
X:132628673:A:CF456L1.000
X:132628673:A:TF456L1.000
X:132628674:A:CF456C1.000
X:132628674:A:GF456S1.000
X:132628675:A:GF456L1.000
X:132628685:A:CF452L1.000
X:132628685:A:TF452L1.000
X:132628686:A:CF452C1.000
X:132628686:A:GF452S1.000
X:132628687:A:GF452L1.000
X:132628698:A:GF448S1.000
X:132628699:A:TF448I1.000
X:132628706:C:AE445D1.000
X:132628706:C:GE445D1.000
X:132628707:T:AE445V1.000
X:132628709:A:CF444L1.000
X:132628709:A:TF444L1.000

dbSNP variants (sampled 300 via entrez): RS1000013089 (X:132780340 T>A), RS1000024263 (X:132879453 T>C,G), RS1000037374 (X:132668198 G>A,C), RS1000046375 (X:132946632 C>G,T), RS1000046849 (X:132798084 A>G), RS1000047775 (X:132857412 A>G), RS1000063846 (X:132934705 T>C), RS1000076982 (X:132661063 C>T), RS1000115174 (X:132724662 A>C), RS1000115883 (X:132634029 T>C), RS1000140273 (X:132826430 C>G), RS1000154441 (X:132698352 C>G), RS1000162888 (X:132733560 A>T), RS1000166672 (X:132916453 T>C), RS1000171051 (X:132696379 C>T)

Disease associations

OMIM: gene MIM:300545 | disease phenotypes: MIM:301025

GenCC curated gene-disease

DiseaseClassificationInheritance
Paganini-Miozzo syndromeLimitedX-linked

Mondo (1): Paganini-Miozzo syndrome (MONDO:0026724)

Orphanet (0):

HPO phenotypes

26 total (26 of 26 shown, HPO-id order):

HPOTerm
HP:0000020Urinary incontinence
HP:0000233Thin vermilion border
HP:0000272Malar flattening
HP:0000303Mandibular prognathia
HP:0000325Triangular face
HP:0000341Narrow forehead
HP:0000358Posteriorly rotated ears
HP:0000369Low-set ears
HP:0000490Deeply set eye
HP:0000494Downslanted palpebral fissures
HP:0000750Delayed speech and language development
HP:0001263Global developmental delay
HP:0001419X-linked recessive inheritance
HP:0002003Large forehead
HP:0002151Increased circulating lactate concentration
HP:0002373Febrile seizure (within the age range of 3 months to 6 years)
HP:0002465Poor speech
HP:0002714Downturned corners of mouth
HP:0003348Hyperalaninemia
HP:0006956Lateral ventricle dilatation
HP:0008551Microtia
HP:0011003High myopia
HP:0011463Childhood onset
HP:0011968Feeding difficulties
HP:0031936Delayed ability to walk
HP:0032653Elevated lactate:pyruvate ratio

GWAS associations

3 associations (top):

StudyTraitp-value
GCST002127_28Periodontitis (Mean PAL)9.000000e-06
GCST006442_462Educational attainment (years of education)9.000000e-13
GCST90000050_86Age at first birth4.000000e-13

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004784self reported educational attainment
EFO:0009101age at first birth measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases methylation, affects expression, increases expression6
methylmercuric chloridedecreases expression, increases expression, affects cotreatment3
trichostatin Aincreases expression2
Benzo(a)pyreneaffects expression, affects methylation2
Estradioldecreases expression, affects cotreatment2
Tobacco Smoke Pollutiondecreases methylation, increases expression2
Tretinoindecreases expression2
aristolochic acid Idecreases expression1
propionaldehydeincreases expression1
arseniteincreases methylation1
sodium arsenitedecreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
beta-methylcholineaffects expression1
glycidamidedecreases expression1
CGP 52608affects binding, increases reaction1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
incobotulinumtoxinAdecreases expression1
(+)-JQ1 compounddecreases expression1
Temozolomideincreases expression1
Vorinostatincreases expression1
Calcitriolincreases expression1
Coumestrolaffects cotreatment, decreases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Fluorouracildecreases expression1
Leadaffects expression1
Methotrexateincreases expression1

Clinical trials (associated diseases)

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