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NDST1 N-deacetylase and N-sulfotransferase 1 [ Homo sapiens (human) ]

Gene ID: 3340, updated on 10-Dec-2024

Summary

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Official Symbol
NDST1provided by HGNC
Official Full Name
N-deacetylase and N-sulfotransferase 1provided by HGNC
Primary source
HGNC:HGNC:7680
See related
Ensembl:ENSG00000070614 MIM:600853; AllianceGenome:HGNC:7680
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HSST; NST1; MRT46
Summary
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. The encoded protein catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to nitrogen of glucosamine in heparan sulfate. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Expression
Ubiquitous expression in spleen (RPKM 12.3), lung (RPKM 12.2) and 25 other tissues See more
Orthologs
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Genomic context

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See NDST1 in Genome Data Viewer
Location:
5q33.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (150497779..150558211)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (151034321..151094757)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149877341..149937773)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak5537 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149828819-149829757 Neighboring gene MPRA-validated peak5538 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149840208-149840834 Neighboring gene ribosomal protein S14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149843737-149844462 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82371 Neighboring gene NDST1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:149865131-149865786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23420 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149872150-149872771 Neighboring gene Sharpr-MPRA regulatory region 285 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149881034-149881594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149881595-149882153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149889677-149890250 Neighboring gene Sharpr-MPRA regulatory region 361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149891552-149892205 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149902065-149902942 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149905099-149905839 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149916701-149917473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149919751-149920250 Neighboring gene Sharpr-MPRA regulatory region 2793 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149926039-149926554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149953456-149954442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149956181-149956887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149969781-149970280 Neighboring gene synaptopodin Neighboring gene uncharacterized LOC124901108 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149995691-149995878 Neighboring gene uncharacterized LOC124901107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23423 Neighboring gene Sharpr-MPRA regulatory region 14746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150003601-150004100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150005713-150006428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150006429-150007142

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Altered expression of NDST-1 messenger RNA in puromycin aminonucleoside nephrosis. Nakayama K, et al. J Lab Clin Med, 2004 Feb. PMID 14966466
  2. Role of Deacetylase Activity of N-Deacetylase/N-Sulfotransferase 1 in Forming N-Sulfated Domain in Heparan Sulfate. Dou W, et al. J Biol Chem, 2015 Aug 14. PMID 26109066, Free PMC Article
  3. Crystal structure of the sulfotransferase domain of human heparan sulfate N-deacetylase/ N-sulfotransferase 1. Kakuta Y, et al. J Biol Chem, 1999 Apr 16. PMID 10196134
  4. A girl with developmental delay, ataxia, cranial nerve palsies, severe respiratory problems in infancy-Expanding NDST1 syndrome. Armstrong L, et al. Am J Med Genet A, 2017 Mar. PMID 28211985
  5. A role of Lys614 in the sulfotransferase activity of human heparan sulfate N-deacetylase/N-sulfotransferase. Sueyoshi T, et al. FEBS Lett, 1998 Aug 21. PMID 9744796

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Two Cases of Recessive Intellectual Disability Caused by NDST1 and METTL23 Variants.
    Title: Two Cases of Recessive Intellectual Disability Caused by NDST1 and METTL23 Variants.
  2. MiRNA-191 functions as an oncogene in primary glioblastoma by directly targeting NDST1.
    Title: MiRNA-191 functions as an oncogene in primary glioblastoma by directly targeting NDST1.
  3. Compound heterozygous mutations in NDST1 were identified, in the heparan sulfate N deacetylatase domain of one allele and the sulfotransferase domain of the other allele. This report expands the phenotypic spectrum of Ndst1 deficiency in humans.
    Title: A girl with developmental delay, ataxia, cranial nerve palsies, severe respiratory problems in infancy-Expanding NDST1 syndrome.
  4. Among the genes enriched in this screening, the authors found that TM9SF2 is critical for N-sulfation of heparan sulfate and therefore for chikungunya virus infection because it is involved in the proper localization and stability of NDST1.
    Title: Genome-Wide Screening Uncovers the Significance of N-Sulfation of Heparan Sulfate as a Host Cell Factor for Chikungunya Virus Infection.
  5. Our data confirm NDST1 mutations as a cause of autosomal recessive intellectual disability with a distinctive phenotype, and support an important function of NDST1 in human development.
    Title: NDST1 missense mutations in autosomal recessive intellectual disability.
  6. demonstrate the essential role of domain cooperation within NDST-1 in producing HS with specific domain structures
    Title: Role of Deacetylase Activity of N-Deacetylase/N-Sulfotransferase 1 in Forming N-Sulfated Domain in Heparan Sulfate.
  7. Upregulation of NDST1 is associated with chemoresistance in breast cancer.
    Title: Methylation-regulated miR-149 modulates chemoresistance by targeting GlcNAc N-deacetylase/N-sulfotransferase-1 in human breast cancer.
  8. These findings establish NDST1 as a target of miR-24 and demonstrate how such NDST1 suppression in endothelial cells results in reduced responsiveness to VEGFA
    Title: MicroRNA-24 suppression of N-deacetylase/N-sulfotransferase-1 (NDST1) reduces endothelial cell responsiveness to vascular endothelial growth factor A (VEGFA).
  9. MicroRNA-191 targets N-deacetylase/N-sulfotransferase 1 and promotes cell growth in human gastric carcinoma cell line MGC803
    Title: MicroRNA-191 targets N-deacetylase/N-sulfotransferase 1 and promotes cell growth in human gastric carcinoma cell line MGC803.
  10. Inhibitory peptides of the sulfotransferase domain of the heparan sulfate enzyme, N-deacetylase-N-sulfotransferase-1.
    Title: Inhibitory peptides of the sulfotransferase domain of the heparan sulfate enzyme, N-deacetylase-N-sulfotransferase-1.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Intellectual disability, autosomal recessive 46
MedGen: C4015283 OMIM: 616116 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat FITC-labeled Tat 47-59 peptide downregulates gene expression of N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 (NDST1) in U-937 macrophages PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables N-acetylglucosamine deacetylase activity TAS
Traceable Author Statement
more info
  
enables [heparan sulfate]-glucosamine N-sulfotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables [heparan sulfate]-glucosamine N-sulfotransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables [heparan sulfate]-glucosamine N-sulfotransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables [heparan sulfate]-glucosamine N-sulfotransferase activity TAS
Traceable Author Statement
more info
  
enables deacetylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables heparan sulfate N-deacetylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables heparan sulfate N-deacetylase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in aorta development IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac septum development IEA
Inferred from Electronic Annotation
more info
  
involved_in cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in coronary vasculature development IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic neurocranium morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic viscerocranium morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in fibroblast growth factor receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in forebrain development IEA
Inferred from Electronic Annotation
more info
  
involved_in heparan sulfate proteoglycan biosynthetic process, enzymatic modification TAS
Traceable Author Statement
more info
  
involved_in heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in heparin biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in midbrain development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of MAPK cascade IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in respiratory gaseous exchange by respiratory system IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in trans-Golgi network membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
Names
HSNST 1
N-Deacetylase-N-sulfotransferase 1
N-HSST 1
N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1
N-deacetylase/N-sulfotransferase 1
N-heparan sulfate sulfotransferase 1
NDST-1
[Heparan sulfate]-glucosamine N-sulfotransferase 1
glucosaminyl N-deacetylase/N-sulfotransferase 1
heparan sulfate-N-deacetylase/N-sulfotransferase
heparan sulfate/heparin GlcNAc N-deacetylase/GlcN N-sulfotransferase 1
NP_001287992.1
NP_001534.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_041806.1 RefSeqGene

    Range
    15354..65434
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301063.2 → NP_001287992.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 isoform 2

    See identical proteins and their annotated locations for NP_001287992.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AC011383, AK293746, ES315645, U18918
    Consensus CDS
    CCDS75358.1
    UniProtKB/TrEMBL
    A8K8T3
    Related
    ENSP00000428604.1, ENST00000523767.5
    Conserved Domains (2) summary
    pfam00685
    Location:605 → 798
    Sulfotransfer_1; Sulfotransferase domain
    pfam12062
    Location:30 → 515
    HSNSD; heparan sulfate-N-deacetylase

  2. NM_001543.5 → NP_001534.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 isoform 1

    See identical proteins and their annotated locations for NP_001534.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC011383, AK292448, U18918, U36600
    Consensus CDS
    CCDS34277.1
    UniProtKB/Swiss-Prot
    B7Z1Q0, E7EVJ3, P52848, Q96E57
    UniProtKB/TrEMBL
    A8K8T3
    Related
    ENSP00000261797.6, ENST00000261797.7
    Conserved Domains (2) summary
    pfam00685
    Location:605 → 855
    Sulfotransfer_1; Sulfotransferase domain
    pfam12062
    Location:30 → 515
    HSNSD; heparan sulfate-N-deacetylase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    150497779..150558211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    151034321..151094757
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P52848.1 GenPept UniProtKB/Swiss-Prot:P52848

Gene LinkOut

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