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CHST3 carbohydrate sulfotransferase 3 [ Homo sapiens (human) ]

Gene ID: 9469, updated on 23-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (71964395..72013558)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (72835220..72884391)
105.20220307 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 uncharacterized LOC124902447 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. Biallelic variants in CHST3 cause Spondyloepiphyseal dysplasia with joint dislocations in three Pakistani kindreds. Kausar M, et al. BMC Musculoskelet Disord, 2022 Aug 30. PMID 36042462, Free PMC Article
  2. Chondroitin 6-sulfate represses keratinocyte proliferation in mouse skin, which is associated with psoriasis. Kitazawa K, et al. Commun Biol, 2021 Jan 25. PMID 33495490, Free PMC Article
  3. 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
  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. Craniosynostosis: a previously unreported association with CHST3-related skeletal dysplasia (autosomal recessive Larsen syndrome). Searle C, et al. Clin Dysmorphol, 2014 Jan. PMID 24300290

See all (38) 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)

Genotypes

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
  
is_active_in trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
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_2023_10

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

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