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

    Gene ID: 9348, updated on 10-Dec-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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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