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CHST9 carbohydrate sulfotransferase 9 [ Homo sapiens (human) ]

Gene ID: 83539, updated on 3-Apr-2024

Summary

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Official Symbol
CHST9provided by HGNC
Official Full Name
carbohydrate sulfotransferase 9provided by HGNC
Primary source
HGNC:HGNC:19898
See related
Ensembl:ENSG00000154080 MIM:610191; AllianceGenome:HGNC:19898
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
GalNAc4ST2; GALNAC4ST-2
Summary
The protein encoded by this gene belongs to the sulfotransferase 2 family. It is localized to the golgi membrane, and catalyzes the transfer of sulfate to position 4 of non-reducing N-acetylgalactosamine (GalNAc) residues in both N-glycans and O-glycans. Sulfate groups on carbohydrates confer highly specific functions to glycoproteins, glycolipids, and proteoglycans, and are critical for cell-cell interaction, signal transduction, and embryonic development. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Aug 2011]
Expression
Biased expression in spleen (RPKM 1.3), testis (RPKM 1.2) and 13 other tissues See more
Orthologs
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Genomic context

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Location:
18q11.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (26906481..27185308, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (27100538..27379358, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (24486445..24765272, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ubiquitin recognition factor in ER associated degradation 1 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:24442920-24443420 Neighboring gene AQP4 antisense RNA 1 Neighboring gene aquaporin 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:24507672-24508283 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:24536524-24537111 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:24537112-24537698 Neighboring gene ATPase H+ transporting V1 subunit E1 pseudogene 2 Neighboring gene uncharacterized LOC124904275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13195 Neighboring gene uncharacterized LOC105372036 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:24743020-24744219 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24803365-24803888 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:24812317-24813029 Neighboring gene long intergenic non-protein coding RNA 1908 Neighboring gene uncharacterized LOC105372038

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. A Frameshift Variant in the CHST9 Gene Identified by Family-Based Whole Genome Sequencing Is Associated with Schizophrenia in Chinese Population. Chen J, et al. Sci Rep, 2019 Sep 3. PMID 31481703, Free PMC Article
  2. CHST9 rs1436904 genetic variant contributes to prognosis of triple-negative breast cancer. Yuan J, et al. Sci Rep, 2017 Sep 18. PMID 28924212, Free PMC Article
  3. Examination of copy number variations of CHST9 in multiple types of hematologic malignancies. Zhao X, et al. Cancer Genet Cytogenet, 2010 Dec. PMID 21156230
  4. Molecular cloning and expression of an N-acetylgalactosamine-4-O-sulfotransferase that transfers sulfate to terminal and non-terminal beta 1,4-linked N-acetylgalactosamine. Kang HG, et al. J Biol Chem, 2001 Apr 6. PMID 11139592
  5. Molecular cloning and expression of two distinct human N-acetylgalactosamine 4-O-sulfotransferases that transfer sulfate to GalNAc beta 1-->4GlcNAc beta 1-->R in both N- and O-glycans. Hiraoka N, et al. Glycobiology, 2001 Jun. PMID 11445554

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A Frameshift Variant in the CHST9 Gene Identified by Family-Based Whole Genome Sequencing Is Associated with Schizophrenia in Chinese Population.
    Title: A Frameshift Variant in the CHST9 Gene Identified by Family-Based Whole Genome Sequencing Is Associated with Schizophrenia in Chinese Population.
  2. CHST9 rs1436904 polymorphism significantly contributes to prognosis of early-stage TNBC, suggesting its clinical potential in the screening of high-risk TNBC patients for recurrence and the possibility of patient-tailored therapeutic decisions.
    Title: CHST9 rs1436904 genetic variant contributes to prognosis of triple-negative breast cancer.
  3. the copy number variations of CHST9 have been shown to associate with hematologic malignancies
    Title: Examination of copy number variations of CHST9 in multiple types of hematologic malignancies.
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
A genome-wide association study (GWAS) for bronchopulmonary dysplasia.
EBI GWAS Catalog
Genome-wide association scan of dental caries in the permanent dentition.
EBI GWAS Catalog
Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.
EBI GWAS Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
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

Clone Names

  • FLJ42328

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables N-acetylgalactosamine 4-O-sulfotransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables N-acetylgalactosamine 4-O-sulfotransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables chondroitin 4-sulfotransferase activity TAS
Traceable Author Statement
more info
  
enables sulfotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in carbohydrate biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in chondroitin sulfate biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in glycosaminoglycan metabolic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in hormone biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in proteoglycan biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteoglycan biosynthetic process ISS
Inferred from Sequence or Structural Similarity
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
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
carbohydrate sulfotransferase 9
Names
GalNAc-4-sulfotransferase 2
N-acetylgalactosamine 4-O-sulfotransferase 2
carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9
galNAc-4-O-sulfotransferase 2
NP_001243245.1
NP_001385422.1
NP_113610.2
XP_005258419.1
XP_006722618.1
XP_047293837.1
XP_054175228.1
XP_054175229.1

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_029856.2 RefSeqGene

    Range
    5000..283827
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001256316.2 → NP_001243245.1  carbohydrate sulfotransferase 9 isoform 2

    See identical proteins and their annotated locations for NP_001243245.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct and significantly shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AC010854, AF239821, BI710997, BM919514, KF456359
    Consensus CDS
    CCDS58618.1
    UniProtKB/TrEMBL
    A0A0S2Z5U9
    Related
    ENSP00000464655.1, ENST00000580774.2

  2. NM_001398493.1 → NP_001385422.1  carbohydrate sulfotransferase 9 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC010854, AC023575, AC116017, KF456359
    Consensus CDS
    CCDS42422.1
    UniProtKB/Swiss-Prot
    Q6UX69, Q7L1S5, Q9BXH3, Q9BXH4, Q9BZW9
    Related
    ENSP00000462852.1, ENST00000581714.5
    Conserved Domains (1) summary
    pfam03567
    Location:209 → 438
    Sulfotransfer_2; Sulfotransferase family

  3. NM_031422.6 → NP_113610.2  carbohydrate sulfotransferase 9 isoform 1

    See identical proteins and their annotated locations for NP_113610.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC010854, AF239821, AY358488, KF456359
    Consensus CDS
    CCDS42422.1
    UniProtKB/Swiss-Prot
    Q6UX69, Q7L1S5, Q9BXH3, Q9BXH4, Q9BZW9
    UniProtKB/TrEMBL
    A0A0S2Z5P0
    Related
    ENSP00000480991.1, ENST00000618847.5
    Conserved Domains (1) summary
    pfam03567
    Location:209 → 438
    Sulfotransfer_2; Sulfotransferase family

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    26906481..27185308 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047437881.1 → XP_047293837.1  carbohydrate sulfotransferase 9 isoform X1

  2. XM_005258362.5 → XP_005258419.1  carbohydrate sulfotransferase 9 isoform X2

    See identical proteins and their annotated locations for XP_005258419.1

    UniProtKB/TrEMBL
    A0A0S2Z5P0
    Conserved Domains (1) summary
    pfam03567
    Location:124 → 353
    Sulfotransfer_2; Sulfotransferase family

  3. XM_006722555.5 → XP_006722618.1  carbohydrate sulfotransferase 9 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    27100538..27379358 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319253.1 → XP_054175228.1  carbohydrate sulfotransferase 9 isoform X1

  2. XM_054319254.1 → XP_054175229.1  carbohydrate sulfotransferase 9 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001243848.1: Suppressed sequence

    Description
    NM_001243848.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, which appears to retain intronic sequence at its 5' end.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7L1S5.2 GenPept UniProtKB/Swiss-Prot:Q7L1S5

Gene LinkOut

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