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

Summary

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: mouse all
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Genomic context

Location:: 10q11.21

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (43138445..43185308)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (44015942..44064232)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (43633893..43680756)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CSGALNACT2 restricts ovarian cancer migration and invasion by modulating MAPK/ERK pathway through DUSP1.
Title: CSGALNACT2 restricts ovarian cancer migration and invasion by modulating MAPK/ERK pathway through DUSP1.
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.
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.
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.

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Phenotypes

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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 EBI GWAS CatalogPubMed
Genome-wide association study identifies NRG1 as a susceptibility locus for Hirschsprung's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:51004

A008J24 (e-PCR)
- UniSTS:29110

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 more info	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

EC 2.4.1.174

NP_001306585.1

EC 2.4.1.174

NP_061060.3

EC 2.4.1.174

XP_011538240.1

EC 2.4.1.174

XP_016871877.1

EC 2.4.1.174

XP_016871880.1

EC 2.4.1.174

XP_047281394.1

EC 2.4.1.174

XP_047281395.1

EC 2.4.1.174

XP_047281396.1

EC 2.4.1.174

XP_047281397.1

EC 2.4.1.174

XP_054222214.1

EC 2.4.1.174

XP_054222215.1

EC 2.4.1.174

XP_054222216.1

EC 2.4.1.174

XP_054222217.1

EC 2.4.1.174

XP_054222218.1

EC 2.4.1.174

XP_054222219.1

EC 2.4.1.174

XP_054222220.1

EC 2.4.1.174

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)

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
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
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

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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

43138445..43185308

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
XM_047425440.1 → XP_047281396.1 chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X3
XM_017016391.3 → XP_016871880.1 chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X4
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
XM_047425441.1 → XP_047281397.1 chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X2

UniProtKB/TrEMBL

A0A0S2Z5K4
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

NC_060934.1 Alternate T2T-CHM13v2.0

Range

44015942..44064232

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0S2Z5K4
XM_054366244.1 → XP_054222219.1 chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X5
XM_054366242.1 → XP_054222217.1 chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X3
XM_054366243.1 → XP_054222218.1 chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X4
XM_054366241.1 → XP_054222216.1 chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X1
XM_054366245.1 → XP_054222220.1 chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X2

UniProtKB/TrEMBL

A0A0S2Z5K4
XM_054366239.1 → XP_054222214.1 chondroitin sulfate N-acetylgalactosaminyltransferase 2 isoform X1