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] See more...

Aliases for CSGALNACT2 Gene

Aliases for CSGALNACT2 Gene

  • Chondroitin Sulfate N-Acetylgalactosaminyltransferase 2 2 3 4 5
  • GALNACT2 2 3 4
  • Glucuronylgalactosylproteoglycan 4-Beta-N-Acetylgalactosaminyltransferase 2 2 3
  • Chondroitin Beta1,4 N-Acetylgalactosaminyltransferase 2 2 3
  • GALNACT-2 2 3
  • PRO0082 2 3
  • CHGN2 3 4
  • Chondroitin Beta-1,4-N-Acetylgalactosaminyltransferase 2 4
  • Beta 4 GalNAcT-2 3
  • Beta4GalNAcT-2 4
  • Beta4GalNAcT 3
  • EC 2.4.1.174 4
  • CSGALNACT2 5
  • GalNAcT-2 4
  • MGC40204 2
  • ChGn-2 3

External Ids for CSGALNACT2 Gene

Previous GeneCards Identifiers for CSGALNACT2 Gene

  • GC10P042954
  • GC10P043633
  • GC10P040176

Summaries for CSGALNACT2 Gene

Entrez Gene Summary for CSGALNACT2 Gene

  • 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]

GeneCards Summary for CSGALNACT2 Gene

CSGALNACT2 (Chondroitin Sulfate N-Acetylgalactosaminyltransferase 2) is a Protein Coding gene. Diseases associated with CSGALNACT2 include Coffin-Siris Syndrome 1 and Coffin-Siris Syndrome 2. Among its related pathways are Chondroitin sulfate/dermatan sulfate metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include acetylgalactosaminyltransferase activity and glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity. An important paralog of this gene is CSGALNACT1.

UniProtKB/Swiss-Prot Summary for CSGALNACT2 Gene

  • Transfers 1,4-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of glucuronic acid (GlcUA). Required for addition of the first GalNAc to the core tetrasaccharide linker and for elongation of chondroitin chains.

Additional gene information for CSGALNACT2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CSGALNACT2 Gene

Genomics for CSGALNACT2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CSGALNACT2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J043136 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 690.3 +1.1 1056 5.8 CREB1 GATAD2A HNRNPL PRDM10 ZNF629 TFE3 ZNF692 POLR2A BACH1 LARP7 CSGALNACT2 ENSG00000273008 HNRNPF RASGEF1A piR-44858-002
GH10J043201 Promoter/Enhancer 1.5 Ensembl ENCODE CraniofacialAtlas 76.1 +64.7 64669 2.7 CTCF ZBTB33 HNRNPL IKZF1 ZNF143 MTA2 PKNOX1 MTA1 REST TRIM22 CSGALNACT2 piR-57387-005 lnc-CSGALNACT2-1 LOC107984225 RASGEF1A
GH10J043166 Enhancer 0.8 Ensembl ENCODE dbSUPER 79.2 +28.2 28156 4 SCRT2 ARID3A ELF1 JUNB BATF FOS MTA2 lnc-RET-1 CSGALNACT2 RASGEF1A lnc-CSGALNACT2-1
GH10J043120 Enhancer 1 FANTOM5 ENCODE dbSUPER 63.5 -16.9 -16934 2.3 PRDM10 RELA ZIC2 YY1 EED RELB RUNX3 CBFB ELF1 NFIC CSGALNACT2 HNRNPF ENSG00000273008 piR-37551 RET
GH10J043104 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE CraniofacialAtlas 32.1 -33.1 -33144 1.8 CTCF LARP7 ZNF143 ZIC2 PATZ1 REST RAD21 TRIM22 EZH2 ZNF600 CSGALNACT2 RET RASGEF1A piR-37551 ENSG00000273008
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CSGALNACT2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CSGALNACT2

Top Transcription factor binding sites by QIAGEN in the CSGALNACT2 gene promoter:
  • AhR
  • AML1a
  • CUTL1
  • MZF-1
  • NF-1
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • RFX1

Genomic Locations for CSGALNACT2 Gene

Genomic Locations for CSGALNACT2 Gene
chr10:43,138,445-43,185,308
(GRCh38/hg38)
Size:
46,864 bases
Orientation:
Plus strand
chr10:43,633,934-43,680,756
(GRCh37/hg19)
Size:
46,823 bases
Orientation:
Plus strand

Genomic View for CSGALNACT2 Gene

Genes around CSGALNACT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CSGALNACT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CSGALNACT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CSGALNACT2 Gene

Proteins for CSGALNACT2 Gene

  • Protein details for CSGALNACT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N6G5-CGAT2_HUMAN
    Recommended name:
    Chondroitin sulfate N-acetylgalactosaminyltransferase 2
    Protein Accession:
    Q8N6G5
    Secondary Accessions:
    • B3KWL7
    • Q6MZJ5
    • Q6MZP6
    • Q8TCH4
    • Q9P1I6

    Protein attributes for CSGALNACT2 Gene

    Size:
    542 amino acids
    Molecular mass:
    62572 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF71068.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CSGALNACT2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CSGALNACT2 Gene

Post-translational modifications for CSGALNACT2 Gene

  • Glycosylation at Asn41 and Asn333
  • Modification sites at PhosphoSitePlus

Other Protein References for CSGALNACT2 Gene

No data available for DME Specific Peptides for CSGALNACT2 Gene

Domains & Families for CSGALNACT2 Gene

Gene Families for CSGALNACT2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for CSGALNACT2 Gene

Suggested Antigen Peptide Sequences for CSGALNACT2 Gene

GenScript: Design optimal peptide antigens:
  • Chondroitin beta-1,4-N-acetylgalactosaminyltransferase 2 (CGAT2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N6G5

UniProtKB/Swiss-Prot:

CGAT2_HUMAN :
  • Belongs to the chondroitin N-acetylgalactosaminyltransferase family.
Family:
  • Belongs to the chondroitin N-acetylgalactosaminyltransferase family.
genes like me logo Genes that share domains with CSGALNACT2: view

Function for CSGALNACT2 Gene

Molecular function for CSGALNACT2 Gene

UniProtKB/Swiss-Prot Function:
Transfers 1,4-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of glucuronic acid (GlcUA). Required for addition of the first GalNAc to the core tetrasaccharide linker and for elongation of chondroitin chains.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=3-O-(beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-(beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + H(+) + UDP; Xref=Rhea:RHEA:23464, Rhea:RHEA-COMP:12573, Rhea:RHEA-COMP:12575, ChEBI:CHEBI:15378, ChEBI:CHEBI:58223, ChEBI:CHEBI:67138, ChEBI:CHEBI:132093, ChEBI:CHEBI:132105; EC=2.4.1.174;.

Enzyme Numbers (IUBMB) for CSGALNACT2 Gene

Phenotypes From GWAS Catalog for CSGALNACT2 Gene

Gene Ontology (GO) - Molecular Function for CSGALNACT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0008376 acetylgalactosaminyltransferase activity IDA 11788602
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0047237 glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity IEA --
genes like me logo Genes that share ontologies with CSGALNACT2: view
genes like me logo Genes that share phenotypes with CSGALNACT2: view

Animal Models for CSGALNACT2 Gene

MGI Knock Outs for CSGALNACT2:

Animal Model Products

  • Taconic Biosciences Mouse Models for CSGALNACT2

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CSGALNACT2

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CSGALNACT2 Gene

Localization for CSGALNACT2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CSGALNACT2 Gene

Golgi apparatus, Golgi stack membrane. Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CSGALNACT2 gene
Compartment Confidence
golgi apparatus 5
endoplasmic reticulum 3
mitochondrion 2
plasma membrane 1
extracellular 1
peroxisome 1
nucleus 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CSGALNACT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA,HDA 19946888
GO:0016021 integral component of membrane IEA --
GO:0030173 integral component of Golgi membrane NAS 11788602
genes like me logo Genes that share ontologies with CSGALNACT2: view

Pathways & Interactions for CSGALNACT2 Gene

genes like me logo Genes that share pathways with CSGALNACT2: view

Gene Ontology (GO) - Biological Process for CSGALNACT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030166 proteoglycan biosynthetic process IDA 11788602
GO:0030206 chondroitin sulfate biosynthetic process TAS --
GO:0050650 chondroitin sulfate proteoglycan biosynthetic process IDA 11788602
GO:0050651 dermatan sulfate proteoglycan biosynthetic process IDA 11788602
GO:0050652 dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process TAS 11788602
genes like me logo Genes that share ontologies with CSGALNACT2: view

No data available for SIGNOR curated interactions for CSGALNACT2 Gene

Drugs & Compounds for CSGALNACT2 Gene

(2) Drugs for CSGALNACT2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Manganese Approved Nutra 56
Uridine 5'-diphosphate Experimental Pharma 0

(1) Additional Compounds for CSGALNACT2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Uridine diphosphate-N-acetylgalactosamine
  • UDP-N-Acetyl-D-galactosamine
  • UDP-N-Acetyl-delta-galactosamine
  • UDP-N-Acetylgalactosamine
  • Uridine 5'-diphospho-N-acetylgalactosamine
  • Uridine diphosphate-N-acetyl-D-galactosamine
7277-98-7
genes like me logo Genes that share compounds with CSGALNACT2: view

Transcripts for CSGALNACT2 Gene

mRNA/cDNA for CSGALNACT2 Gene

3 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CSGALNACT2

Alternative Splicing Database (ASD) splice patterns (SP) for CSGALNACT2 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11
SP1: - -
SP2: -
SP3: - -
SP4: -
SP5: - - -
SP6:
SP7: -

Relevant External Links for CSGALNACT2 Gene

GeneLoc Exon Structure for
CSGALNACT2

Expression for CSGALNACT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CSGALNACT2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CSGALNACT2 Gene

This gene is overexpressed in Whole Blood (x8.5).

Protein differential expression in normal tissues from HIPED for CSGALNACT2 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (53.1) and Pancreas (15.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CSGALNACT2 Gene



Protein tissue co-expression partners for CSGALNACT2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CSGALNACT2

SOURCE GeneReport for Unigene cluster for CSGALNACT2 Gene:

Hs.657569

mRNA Expression by UniProt/SwissProt for CSGALNACT2 Gene:

Q8N6G5-CGAT2_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for CSGALNACT2 Gene

  • Intestine(4.4)
  • Lung(4.3)
  • Heart(4.3)
  • Pancreas(4.1)
  • Nervous system(3.9)
  • Bone marrow(2.2)
genes like me logo Genes that share expression patterns with CSGALNACT2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CSGALNACT2 Gene

Orthologs for CSGALNACT2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CSGALNACT2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CSGALNACT2 30 31
  • 99.69 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CSGALNACT2 30 31
  • 94.59 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CSGALNACT2 30 31
  • 94.03 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Csgalnact2 30 17 31
  • 90.53 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Csgalnact2 30
  • 90.34 (n)
Oppossum
(Monodelphis domestica)
Mammalia CSGALNACT2 31
  • 90 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CSGALNACT2 31
  • 88 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CSGALNACT2 30 31
  • 78.69 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CSGALNACT2 31
  • 85 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii csgalnact2 31
  • 73 (a)
OneToOne
LOC560826 30
  • 68.35 (n)
-- 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG12913 31
  • 37 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6775 31
  • 35 (a)
OneToMany
Species where no ortholog for CSGALNACT2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CSGALNACT2 Gene

ENSEMBL:
Gene Tree for CSGALNACT2 (if available)
TreeFam:
Gene Tree for CSGALNACT2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CSGALNACT2: view image

Paralogs for CSGALNACT2 Gene

Paralogs for CSGALNACT2 Gene

(2) SIMAP similar genes for CSGALNACT2 Gene using alignment to 1 proteins:

  • CGAT2_HUMAN

Pseudogenes.org Pseudogenes for CSGALNACT2 Gene

genes like me logo Genes that share paralogs with CSGALNACT2: view

Variants for CSGALNACT2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CSGALNACT2 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
rs11238456 - p.Glu215Lys
rs2435381 - p.Pro479Ser

Additional dbSNP identifiers (rs#s) for CSGALNACT2 Gene

Structural Variations from Database of Genomic Variants (DGV) for CSGALNACT2 Gene

Variant ID Type Subtype PubMed ID
esv1015880 CNV insertion 17803354
esv28818 CNV gain 19812545
esv3578784 CNV loss 25503493
esv3623038 CNV loss 21293372
nsv1038102 CNV gain 25217958
nsv1042310 CNV loss 25217958
nsv513008 CNV insertion 21212237
nsv947896 CNV duplication 23825009
nsv951565 CNV duplication 24416366

Variation tolerance for CSGALNACT2 Gene

Residual Variation Intolerance Score: 42.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.79; 83.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CSGALNACT2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CSGALNACT2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CSGALNACT2 Gene

Disorders for CSGALNACT2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CSGALNACT2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
coffin-siris syndrome 1
  • css1
coffin-siris syndrome 2
  • css2
coffin-siris syndrome 3
  • css3
autosomal dominant non-syndromic intellectual disability
  • autosomal dominant mental retardation
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CSGALNACT2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CSGALNACT2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CSGALNACT2 Gene

Publications for CSGALNACT2 Gene

  1. Differential roles of two N-acetylgalactosaminyltransferases, CSGalNAcT-1, and a novel enzyme, CSGalNAcT-2. Initiation and elongation in synthesis of chondroitin sulfate. (PMID: 12446672) Sato T … Narimatsu H (The Journal of biological chemistry 2003) 2 3 4
  2. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 41
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Molecular cloning and expression of a second chondroitin N-acetylgalactosaminyltransferase involved in the initiation and elongation of chondroitin/dermatan sulfate. (PMID: 12433924) Uyama T … Sugahara K (The Journal of biological chemistry 2003) 3 4

Products for CSGALNACT2 Gene

  • Signalway Proteins for CSGALNACT2

Sources for CSGALNACT2 Gene