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NDST3 N-deacetylase and N-sulfotransferase 3 [ Homo sapiens (human) ]

Gene ID: 9348, updated on 14-Nov-2024

Summary

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Official Symbol
NDST3provided by HGNC
Official Full Name
N-deacetylase and N-sulfotransferase 3provided by HGNC
Primary source
HGNC:HGNC:7682
See related
Ensembl:ENSG00000164100 MIM:603950; AllianceGenome:HGNC:7682
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
HSST3
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. 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. [provided by RefSeq, Nov 2008]
Expression
Low expression observed in reference dataset See more
Orthologs
all
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Genomic context

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See NDST3 in Genome Data Viewer
Location:
4q26
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (118033322..118258634)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (121338213..121564058)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (118954477..119179789)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1378 Neighboring gene NT5C3A pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:118694015-118694515 Neighboring gene uncharacterized LOC102723914 Neighboring gene long intergenic non-protein coding RNA 2264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:118862351-118863022 Neighboring gene uncharacterized LOC107986307 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:119112107-119112789 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:119115072-119115572 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:119115573-119116073 Neighboring gene FKBP prolyl isomerase 4 pseudogene 1 Neighboring gene uncharacterized LOC105377392 Neighboring gene uncharacterized LOC124900765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21845 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15649 Neighboring gene small nucleolar RNA, H/ACA box 24 Neighboring gene small nucleolar RNA host gene 8

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 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. NDST3 deacetylates α-tubulin and suppresses V-ATPase assembly and lysosomal acidification. Tang Q, et al. EMBO J, 2021 Oct 1. PMID 34435379, Free PMC Article
  2. Glycanogenomics: a qPCR-approach to investigate biological glycan function. Krenn EC, et al. Biochem Biophys Res Commun, 2008 Oct 24. PMID 18692483
  3. Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder. Lencz T, et al. Nat Commun, 2013. PMID 24253340, Free PMC Article
  4. rs11098403 polymorphism near NDST3 is associated with a reduced risk of schizophrenia in a Han Chinese population. Gu LZ, et al. Neurosci Lett, 2014 Oct 3. PMID 25139529
  5. A comprehensive analysis of NDST3 for schizophrenia and bipolar disorder in Han Chinese. Zhang C, et al. Transl Psychiatry, 2016 Jan 5. PMID 26731438, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic Variance in Heparan Sulfation Is Associated With Salt Sensitivity.
    Title: Genetic Variance in Heparan Sulfation Is Associated With Salt Sensitivity.
  2. Hsa_circ_0001017 inhibits proliferation and metastasis via regulating the let-7g-3p/NDST3 axis in glioma.
    Title: Hsa_circ_0001017 inhibits proliferation and metastasis via regulating the let-7g-3p/NDST3 axis in glioma.
  3. NDST3 deacetylates alpha-tubulin and suppresses V-ATPase assembly and lysosomal acidification.
    Title: NDST3 deacetylates α-tubulin and suppresses V-ATPase assembly and lysosomal acidification.
  4. 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.
    Title: Association study of NDST3 gene for schizophrenia, bipolar disorder, major depressive disorder in the Han Chinese population.
  5. A genome-wide association study provided suggestive evidence that the NDST3 variation predisposed patients to schizophrenia and bipolar disorder.
    Title: A comprehensive analysis of NDST3 for schizophrenia and bipolar disorder in Han Chinese.
  6. 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
    Title: rs11098403 polymorphism near NDST3 is associated with a reduced risk of schizophrenia in a Han Chinese population.
  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.
    Title: Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder.
  8. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Genome-wide searching of rare genetic variants in WTCCC data.
  9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Clone Names

  • MGC130028, MGC130029

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 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 
Process Evidence Code Pubs
involved_in heparan sulfate proteoglycan biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in heparin biosynthetic process 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 IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3
Names
GlcNAc N-deacetylase/ N-sulfotransferase 3
N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3
N-deacetylase/N-sulfotransferase 3
N-heparan sulfate sulfotransferase 3
glucosaminyl N-deacetylase/N-sulfotransferase 3
NP_004775.1
XP_006714479.1
XP_011530717.1
XP_011530718.1
XP_016864328.1
XP_016864329.1
XP_016864330.1
XP_016864332.1
XP_016864333.1
XP_047272370.1
XP_047272371.1
XP_054207227.1
XP_054207228.1
XP_054207229.1
XP_054207230.1
XP_054207231.1
XP_054207232.1
XP_054207233.1
XP_054207234.1
XP_054207235.1
XP_054207236.1

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.

mRNA and Protein(s)

  1. NM_004784.3 → NP_004775.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3

    See identical proteins and their annotated locations for NP_004775.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the protein-coding transcript.
    Source sequence(s)
    AF074924, BC034037, BE348441
    Consensus CDS
    CCDS3708.1
    UniProtKB/Swiss-Prot
    B4DI67, O95803, Q4W5C1, Q4W5D0, Q6UWC5, Q9UP21
    Related
    ENSP00000296499.5, ENST00000296499.6
    Conserved Domains (2) summary
    pfam00685
    Location:595 → 846
    Sulfotransfer_1; Sulfotransferase domain
    pfam12062
    Location:20 → 506
    HSNSD; heparan sulfate-N-deacetylase

RNA

  1. NR_146513.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC096762, AC108201, AC110999, BC034037

  2. NR_146514.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC096762, AC108201, AC110999, BC034037

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    118033322..118258634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714416.4 → XP_006714479.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X2

    See identical proteins and their annotated locations for XP_006714479.1

    UniProtKB/Swiss-Prot
    B4DI67, O95803, Q4W5C1, Q4W5D0, Q6UWC5, Q9UP21
    Conserved Domains (2) summary
    pfam00685
    Location:595 → 846
    Sulfotransfer_1; Sulfotransferase domain
    pfam12062
    Location:20 → 506
    HSNSD; heparan sulfate-N-deacetylase

  2. XM_017008840.3 → XP_016864329.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X1

  3. XM_047416415.1 → XP_047272371.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X5

  4. XM_017008839.3 → XP_016864328.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X1

  5. XM_011532415.4 → XP_011530717.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X3

    Conserved Domains (1) summary
    pfam12062
    Location:20 → 506
    HSNSD; heparan sulfate-N-deacetylase

  6. XM_011532416.4 → XP_011530718.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X5

    Conserved Domains (1) summary
    pfam12062
    Location:20 → 506
    HSNSD; heparan sulfate-N-deacetylase

  7. XM_017008844.2 → XP_016864333.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X4

  8. XM_047416414.1 → XP_047272370.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X4

  9. XM_017008841.2 → XP_016864330.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X4

  10. XM_017008843.2 → XP_016864332.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    121338213..121564058
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351253.1 → XP_054207228.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X1

  2. XM_054351254.1 → XP_054207229.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X2

    UniProtKB/Swiss-Prot
    B4DI67, O95803, Q4W5C1, Q4W5D0, Q6UWC5, Q9UP21

  3. XM_054351259.1 → XP_054207234.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X5

  4. XM_054351252.1 → XP_054207227.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X1

  5. XM_054351255.1 → XP_054207230.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X3

  6. XM_054351258.1 → XP_054207233.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X5

  7. XM_054351261.1 → XP_054207236.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X4

  8. XM_054351257.1 → XP_054207232.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X4

  9. XM_054351256.1 → XP_054207231.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X4

  10. XM_054351260.1 → XP_054207235.1  bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 3 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95803.1 GenPept UniProtKB/Swiss-Prot:O95803

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