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    CHST3 carbohydrate sulfotransferase 3 [ Homo sapiens (human) ]

    Gene ID: 9469, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CHST3provided by HGNC
    Official Full Name
    carbohydrate sulfotransferase 3provided by HGNC
    Primary source
    HGNC:HGNC:1971
    See related
    Ensembl:ENSG00000122863 MIM:603799; AllianceGenome:HGNC:1971
    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
    HSD; C6ST; C6ST1
    Summary
    This gene encodes an enzyme which catalyzes the sulfation of chondroitin, a proteoglycan found in the extracellular matrix and most cells which is involved in cell migration and differentiation. Mutations in this gene are associated with spondylepiphyseal dysplasia and humerospinal dysostosis. [provided by RefSeq, Mar 2009]
    Expression
    Broad expression in testis (RPKM 10.9), ovary (RPKM 8.0) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CHST3 in Genome Data Viewer
    Location:
    10q22.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (71964395..72013558)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (72835220..72884391)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (73724153..73773316)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene prosaposin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73609267-73609766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:73610158-73610688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73610689-73611219 Neighboring gene RNA, U7 small nuclear 38 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73619612-73619846 Neighboring gene NFE2L2 motif-containing MPRA enhancers 43 and 138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3524 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73635755-73636635 Neighboring gene long intergenic non-protein coding RNA 3139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2467 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:73665425-73665924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3525 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73698038-73698194 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73715248-73715463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2468 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73716485-73716704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73729339-73729882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73729883-73730426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73733189-73733688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73738687-73739188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3527 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73751377-73751550 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73757484-73758436 Neighboring gene uncharacterized LOC124902448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73828839-73829346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73829527-73830028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73840535-73841319 Neighboring gene SPARC (osteonectin), cwcv and kazal like domains proteoglycan 2

    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. Omani-type spondyloepiphyseal dysplasia with cardiac involvement caused by a missense mutation in CHST3. Tuysuz B, et al. Clin Genet, 2009 Apr. PMID 19320654
    2. Lumbar disc degeneration is linked to a carbohydrate sulfotransferase 3 variant. Song YQ, et al. J Clin Invest, 2013 Nov. PMID 24216480, Free PMC Article
    3. Craniosynostosis: a previously unreported association with CHST3-related skeletal dysplasia (autosomal recessive Larsen syndrome). Searle C, et al. Clin Dysmorphol, 2014 Jan. PMID 24300290
    4. A novel CHST3 allele associated with spondyloepiphyseal dysplasia and hearing loss in Pakistani kindred. Waryah AM, et al. Clin Genet, 2016 Jul. PMID 26572954, Free PMC Article
    5. Spondyloepiphyseal dysplasia Omani type: CHST3 mutation spectrum and phenotypes in three Indian families. Srivastava P, et al. Am J Med Genet A, 2017 Jan. PMID 27753269

    See all (42) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Indian patients with CHST3-related chondrodysplasia with congenital joint dislocations.
      Title: Indian patients with CHST3-related chondrodysplasia with congenital joint dislocations.
    2. Dampening HOTAIR sensitizes the gastric cancer cells to oxaliplatin through miR-195-5p and ABCG2 pathway.
      Title: Dampening HOTAIR sensitizes the gastric cancer cells to oxaliplatin through miR-195-5p and ABCG2 pathway.
    3. CHST3-related skeletal dysplasia in 14 patients: Identification of 8 novel variants and further expansion of the phenotypic spectrum.
      Title: CHST3-related skeletal dysplasia in 14 patients: Identification of 8 novel variants and further expansion of the phenotypic spectrum.
    4. Biallelic variants in CHST3 cause Spondyloepiphyseal dysplasia with joint dislocations in three Pakistani kindreds.
      Title: Biallelic variants in CHST3 cause Spondyloepiphyseal dysplasia with joint dislocations in three Pakistani kindreds.
    5. Chondroitin 6-sulfate represses keratinocyte proliferation in mouse skin, which is associated with psoriasis.
      Title: Chondroitin 6-sulfate represses keratinocyte proliferation in mouse skin, which is associated with psoriasis.
    6. Lysophosphatidic acid receptor 5 transactivation of TGFBR1 stimulates the mRNA expression of proteoglycan synthesizing genes XYLT1 and CHST3.
      Title: Lysophosphatidic acid receptor 5 transactivation of TGFBR1 stimulates the mRNA expression of proteoglycan synthesizing genes XYLT1 and CHST3.
    7. Abnormal expression of chondroitin sulfate sulfotransferases in the articular cartilage of pediatric patients with Kashin-Beck disease.
      Title: Abnormal expression of chondroitin sulfate sulfotransferases in the articular cartilage of pediatric patients with Kashin-Beck disease.
    8. We show that the CHST3 and CHST13 alleles are significantly more frequent in pulmonary arterial hypertension patients with elevated aminotransferases during therapy with bosentan than those in patients without liver injury. This is the first pharmacogenomics study linking proteoglycan sulfating genes to drug-induced liver dysfunction.
      Title: CHST3 and CHST13 polymorphisms as predictors of bosentan-induced liver toxicity in Japanese patients with pulmonary arterial hypertension.
    9. We describe three consanguineous Indian families with a distinct form of spondyloepiphyseal dysplasia (SED Omani type). It is an autosomal recessive disorder due to mutation in CHST3 gene.
      Title: Spondyloepiphyseal dysplasia Omani type: CHST3 mutation spectrum and phenotypes in three Indian families.
    10. A novel CHST3 allele associated with spondyloepiphyseal dysplasia and hearing loss has been described in a consanguineous Pakistani pedigree.
      Title: A novel CHST3 allele associated with spondyloepiphyseal dysplasia and hearing loss in Pakistani kindred.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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
    Lumbar disc degeneration is linked to a carbohydrate sulfotransferase 3 variant.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env Sulfate is linked to the carbohydrate chains of HIV-1 glycoproteins gp160, gp120, and gp41 during the endoplasmic reticulum to Golgi transport of the glycoproteins 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 6-O-sulfotransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chondroitin 6-sulfotransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chondroitin 6-sulfotransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chondroitin 6-sulfotransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables proteoglycan sulfotransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in N-acetylglucosamine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in T cell homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chondroitin sulfate biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chondroitin sulfate biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chondroitin sulfate biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chondroitin sulfate biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in sulfur compound metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    carbohydrate sulfotransferase 3
    Names
    C6ST-1
    GST-0
    carbohydrate (chondroitin 6) sulfotransferase 3
    chondroitin 6 sulfotransferase 1
    chondroitin 6-O-sulfotransferase 1
    galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 0
    NP_004264.2
    XP_006718138.1
    XP_011538671.1
    XP_047281978.1
    XP_054223177.1
    XP_054223178.1
    XP_054223179.1

    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_012635.1 RefSeqGene

      Range
      5034..54197
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_004273.5 → NP_004264.2  carbohydrate sulfotransferase 3

      See identical proteins and their annotated locations for NP_004264.2

      Status: REVIEWED

      Source sequence(s)
      AB017915, AC022392, AI041015
      Consensus CDS
      CCDS7312.1
      UniProtKB/Swiss-Prot
      O75099, Q52M30, Q7LGC8
      Related
      ENSP00000362207.4, ENST00000373115.5
      Conserved Domains (1) summary
      pfam00685
      Location:265 → 452
      Sulfotransfer_1; Sulfotransferase domain

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      71964395..72013558
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426022.1 → XP_047281978.1  carbohydrate sulfotransferase 3 isoform X1

      UniProtKB/Swiss-Prot
      O75099, Q52M30, Q7LGC8

    2. XM_006718075.5 → XP_006718138.1  carbohydrate sulfotransferase 3 isoform X1

      See identical proteins and their annotated locations for XP_006718138.1

      UniProtKB/Swiss-Prot
      O75099, Q52M30, Q7LGC8
      Conserved Domains (1) summary
      pfam00685
      Location:265 → 452
      Sulfotransfer_1; Sulfotransferase domain

    3. XM_011540369.3 → XP_011538671.1  carbohydrate sulfotransferase 3 isoform X1

      See identical proteins and their annotated locations for XP_011538671.1

      UniProtKB/Swiss-Prot
      O75099, Q52M30, Q7LGC8
      Conserved Domains (1) summary
      pfam00685
      Location:265 → 452
      Sulfotransfer_1; Sulfotransferase domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      72835220..72884391
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367202.1 → XP_054223177.1  carbohydrate sulfotransferase 3 isoform X1

      UniProtKB/Swiss-Prot
      O75099, Q52M30, Q7LGC8

    2. XM_054367204.1 → XP_054223179.1  carbohydrate sulfotransferase 3 isoform X1

      UniProtKB/Swiss-Prot
      O75099, Q52M30, Q7LGC8

    3. XM_054367203.1 → XP_054223178.1  carbohydrate sulfotransferase 3 isoform X1

      UniProtKB/Swiss-Prot
      O75099, Q52M30, Q7LGC8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7LGC8.3 GenPept UniProtKB/Swiss-Prot:Q7LGC8

    Gene LinkOut

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

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