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CSGALNACT2 chondroitin sulfate N-acetylgalactosaminyltransferase 2 [ Homo sapiens (human) ]

Gene ID: 55454, updated on 5-Mar-2024

Summary

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Official Symbol
CSGALNACT2provided by HGNC
Official Full Name
chondroitin sulfate N-acetylgalactosaminyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:24292
See related
Ensembl:ENSG00000169826 MIM:616616; AllianceGenome:HGNC:24292
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
CHGN2; ChGn-2; PRO0082; GALNACT2; GALNACT-2; beta4GalNAcT
Summary
This gene encodes a member of the chondroitin N-acetylgalactosaminyltransferase family. The encoded protein is involved in elongation during chondroitin sulfate synthesis. Alternative splicing of this gene results in multiple transcript variants. Two related pseudogenes have been identified on chromosome X. [provided by RefSeq, Feb 2016]
Expression
Broad expression in bone marrow (RPKM 48.3), gall bladder (RPKM 16.8) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
10q11.21
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (43138445..43185308)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (44015942..44064232)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (43633893..43680756)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene RET 5' regulatory region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:43572872-43573862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43580156-43580656 Neighboring gene VISTA enhancer hs2326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43596873-43597372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43600219-43600970 Neighboring gene RET intron 1 enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3282 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:43604510-43604673 Neighboring gene ret proto-oncogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3286 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:43625782-43626382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43626383-43626983 Neighboring gene CSGALNACT2 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2318 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:43655229-43656428 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12290 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:43686663-43686892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43696895-43697396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2319 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43700051-43700884 Neighboring gene RasGEF domain family member 1A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43707013-43707615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43711759-43712514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43712515-43713270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43723488-43724298 Neighboring gene uncharacterized LOC107984225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43726130-43726684 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_12309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43744792-43745584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43745585-43746376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43754815-43755598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43761143-43762018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43778224-43778748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43781282-43781790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43789145-43789646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43789647-43790146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43812626-43813176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43813177-43813727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:43813728-43814277 Neighboring gene uncharacterized LOC105378271 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:43815195-43816027 Neighboring gene long intergenic non-protein coding RNA 2633

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. Expression of the functional recombinant human glycosyltransferase GalNAcT2 in Escherichia coli. Lauber J, et al. Microb Cell Fact, 2015 Jan 13. PMID 25582753, Free PMC Article
  2. The prognostic role of intragenic copy number breakpoints and identification of novel fusion genes in paediatric high grade glioma. Carvalho D, et al. Acta Neuropathol Commun, 2014 Feb 18. PMID 24548782, Free PMC Article
  3. Simultaneous siRNA-mediated silencing of pairs of genes coding for enzymes involved in glycosaminoglycan synthesis. Dziedzic D, et al. Acta Biochim Pol, 2012. PMID 22590693
  4. [Genetic bases of Hirschsprung's disease]. Passarge E, et al. Pathologe, 2007 Mar. PMID 17285323
  5. Persistence of Golgi matrix distribution exhibits the same dependence on Sar1p activity as a Golgi glycosyltransferase. Stroud WJ, et al. Traffic, 2003 Sep. PMID 12911817

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Chondroitin sulfate N-acetylgalactosaminyltransferase 2 is functionally involved in the progression of atherosclerosis both in its early and advanced stages.
    Title: Chondroitin sulfate N-acetylgalactosaminyltransferase-2 deletion alleviates lipoprotein retention in early atherosclerosis and attenuates aortic smooth muscle cell migration.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
  3. plays a role in the initiation and elongation in the synthesis of chondroitin sulfate
    Title: Differential roles of two N-acetylgalactosaminyltransferases, CSGalNAcT-1, and a novel enzyme, CSGalNAcT-2. Initiation and elongation in synthesis of chondroitin sulfate.
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 identifies potential susceptibility Loci for hirschsprung disease.
EBI GWAS Catalog
Genome-wide association study identifies NRG1 as a susceptibility locus for Hirschsprung's disease.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ43310, MGC40204, DKFZp686H13226

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables acetylgalactosaminyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity TAS
Traceable Author Statement
more info
  
enables glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chondroitin sulfate biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chondroitin sulfate biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in chondroitin sulfate proteoglycan biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in dermatan sulfate proteoglycan biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in proteoglycan biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi cisterna membrane IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 

General protein information

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Preferred Names
chondroitin sulfate N-acetylgalactosaminyltransferase 2
Names
beta 4 GalNAcT-2
chondroitin beta1,4 N-acetylgalactosaminyltransferase 2
glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase 2
NP_001306583.1
NP_001306585.1
NP_061060.3
XP_011538240.1
XP_016871877.1
XP_016871880.1
XP_047281394.1
XP_047281395.1
XP_047281396.1
XP_047281397.1
XP_054222214.1
XP_054222215.1
XP_054222216.1
XP_054222217.1
XP_054222218.1
XP_054222219.1
XP_054222220.1

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_001319654.1 → NP_001306583.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon, which results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1. The 5' UTR is incomplete because no 5'-complete transcripts exist for this variant, and there is splice pattern ambiguity further upstream.
    Source sequence(s)
    AA721408, AK074474, AK125300, KU178705
    UniProtKB/TrEMBL
    A0A0S2Z5K4
    Conserved Domains (1) summary
    cl11394
    Location:122 → 389
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  2. NM_001319656.1 → NP_001306585.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate exons, which results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (3) has a distinct and shorter C-terminus, compared to isoform 1. The 5' UTR is incomplete because no 5'-complete transcripts exist for this variant, and there is splice pattern ambiguity further upstream.
    Source sequence(s)
    AA721408, AK074474, AK125300, KU178706
    UniProtKB/TrEMBL
    A0A0S2Z5F9
    Conserved Domains (1) summary
    cl11394
    Location:122 → 327
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  3. NM_018590.5 → NP_061060.3  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform 1

    See identical proteins and their annotated locations for NP_061060.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC030268, BX102005, DA674683, DB291068
    Consensus CDS
    CCDS7201.1
    UniProtKB/Swiss-Prot
    B3KWL7, Q6MZJ5, Q6MZP6, Q8N6G5, Q8TCH4, Q9P1I6
    UniProtKB/TrEMBL
    A0A0S2Z5F5
    Related
    ENSP00000363590.3, ENST00000374466.4
    Conserved Domains (1) summary
    cl11394
    Location:122 → 516
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

RNA

  1. NR_135077.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) includes an additional exon in the central region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA721408, BX640967, CT003455, DB291068

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
    43138445..43185308
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017016388.3 → XP_016871877.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z5K4
    Conserved Domains (1) summary
    cl11394
    Location:122 → 389
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  2. XM_011539938.3 → XP_011538240.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X5

    Conserved Domains (1) summary
    cl11394
    Location:140 → 414
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  3. XM_047425440.1 → XP_047281396.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X3

  4. XM_017016391.3 → XP_016871880.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X4

  5. XM_047425439.1 → XP_047281395.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X1

    UniProtKB/Swiss-Prot
    B3KWL7, Q6MZJ5, Q6MZP6, Q8N6G5, Q8TCH4, Q9P1I6
    UniProtKB/TrEMBL
    A0A0S2Z5F5

  6. XM_047425441.1 → XP_047281397.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z5K4

  7. XM_047425438.1 → XP_047281394.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X1

    UniProtKB/Swiss-Prot
    B3KWL7, Q6MZJ5, Q6MZP6, Q8N6G5, Q8TCH4, Q9P1I6
    UniProtKB/TrEMBL
    A0A0S2Z5F5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    44015942..44064232
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054366240.1 → XP_054222215.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z5K4

  2. XM_054366244.1 → XP_054222219.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X5

  3. XM_054366242.1 → XP_054222217.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X3

  4. XM_054366243.1 → XP_054222218.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X4

  5. XM_054366241.1 → XP_054222216.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X1

  6. XM_054366245.1 → XP_054222220.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z5K4

  7. XM_054366239.1 → XP_054222214.1  chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N6G5.1 GenPept UniProtKB/Swiss-Prot:Q8N6G5

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