Free for academic non-profit institutions. Other users need a Commercial license

Aliases for C1GALT1 Gene

Aliases for C1GALT1 Gene

  • Core 1 Synthase, Glycoprotein-N-Acetylgalactosamine 3-Beta-Galactosyltransferase 1 2 3 5
  • Core 1 UDP-Galactose:N-Acetylgalactosamine-Alpha-R Beta 1,3-Galactosyltransferase 1 3 4
  • Core 1 O-Glycan T-Synthase 3 4
  • Core 1 Beta3-Gal-T1 3 4
  • EC 4 56
  • B3GAL-T8 3 4
  • Glycoprotein-N-Acetylgalactosamine 3-Beta-Galactosyltransferase 1 3
  • Core 1 Beta1,3-Galactosyltransferase 1 4
  • Beta-1,3-Galactosyltransferase 4
  • Core 1 Beta3-Gal-T 2
  • T-Synthase 3
  • C1GalT1 4
  • C1GALT 3

External Ids for C1GALT1 Gene

Previous GeneCards Identifiers for C1GALT1 Gene

  • GC07P006918
  • GC07P007018
  • GC07P007047
  • GC07P007240
  • GC07P007196

Summaries for C1GALT1 Gene

Entrez Gene Summary for C1GALT1 Gene

  • The protein encoded by this gene generates the common core 1 O-glycan structure, Gal-beta-1-3GalNAc-R, by the transfer of Gal from UDP-Gal to GalNAc-alpha-1-R. Core 1 is a precursor for many extended mucin-type O-glycans on cell surface and secreted glycoproteins. Studies in mice suggest that this gene plays a key role in thrombopoiesis and kidney homeostasis.[provided by RefSeq, Sep 2010]

GeneCards Summary for C1GALT1 Gene

C1GALT1 (Core 1 Synthase, Glycoprotein-N-Acetylgalactosamine 3-Beta-Galactosyltransferase 1) is a Protein Coding gene. Diseases associated with C1GALT1 include Iga Glomerulonephritis and Hypersensitivity Vasculitis. Among its related pathways are Ectoderm Differentiation and Metabolism of proteins. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring glycosyl groups and glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity. An important paralog of this gene is C1GALT1C1.

UniProtKB/Swiss-Prot for C1GALT1 Gene

  • Glycosyltransferase that generates the core 1 O-glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins. Plays a central role in many processes, such as angiogenesis, thrombopoiesis and kidney homeostasis development.

Additional gene information for C1GALT1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for C1GALT1 Gene

Genomics for C1GALT1 Gene

GeneHancer (GH) Regulatory Elements for C1GALT1 Gene

Promoters and enhancers for C1GALT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07I007180 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 590.8 +26.4 26383 5.2 PKNOX1 FOXA2 SMAD1 ZFP64 ARID4B SIN3A DMAP1 IRF4 YY1 POLR2B C1GALT1 PIR61695 ENSG00000244167
GH07I007155 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 566.2 +1.3 1262 4.4 SOX13 SMAD1 FOXA2 SAP130 NFIB MAX CEBPG RARA LCORL NR2F6 C1GALT1 ENSG00000244167
GH07I007201 Enhancer 1 Ensembl ENCODE dbSUPER 33.6 +44.9 44949 1.4 EBF1 ATF2 IRF4 ZNF217 GATA3 IKZF1 ZNF444 ETV6 BCLAF1 IKZF2 C1GALT1 ENSG00000272732 PIR37726 PIR61695
GH07I007173 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 17.4 +19.7 19711 5.5 FOXA2 MLX ARID4B SIN3A ETS1 ATF7 FOS DEK SP5 MIER2 ENSG00000244167 C1GALT1 LOC101927354
GH07I007190 Enhancer 0.8 Ensembl dbSUPER 33.5 +33.3 33317 0.5 ZBED1 MAFG CBFA2T3 ZNF316 SKIL NCOR1 HDAC2 IKZF1 PRDM10 MAFK C1GALT1 PIR61695 PIR37726
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around C1GALT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the C1GALT1 gene promoter:

Genomic Locations for C1GALT1 Gene

Genomic Locations for C1GALT1 Gene
91,718 bases
Plus strand

Genomic View for C1GALT1 Gene

Genes around C1GALT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C1GALT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C1GALT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C1GALT1 Gene

Proteins for C1GALT1 Gene

  • Protein details for C1GALT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1
    Protein Accession:
    Secondary Accessions:
    • Q96QH4
    • Q9BTU1

    Protein attributes for C1GALT1 Gene

    363 amino acids
    Molecular mass:
    42203 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Homodimer; disulfide-linked (By similarity). Interacts with the C1GALT1C1 chaperone; required for galactosyltransferase activity.
    • Aberrant O-galactosylation of IgA1 molecules plays a role in the development and progression of IgA nephropathy (IgAN). Genetic interactions of C1GALT1 and ST6GALNAC2 variants influence IgA1 O-glycosylation, disease predisposition, and disease severity, and may contribute to the polygenic nature of IgAN.

    Alternative splice isoforms for C1GALT1 Gene


neXtProt entry for C1GALT1 Gene

Selected DME Specific Peptides for C1GALT1 Gene


Post-translational modifications for C1GALT1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for C1GALT1 Gene

Gene Families for C1GALT1 Gene

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

Protein Domains for C1GALT1 Gene


Suggested Antigen Peptide Sequences for C1GALT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the glycosyltransferase 31 family. Beta3-Gal-T subfamily.
  • Belongs to the glycosyltransferase 31 family. Beta3-Gal-T subfamily.
genes like me logo Genes that share domains with C1GALT1: view

Function for C1GALT1 Gene

Molecular function for C1GALT1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
UDP-alpha-D-galactose + N-acetyl-alpha-D-galactosaminyl-R = UDP + beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl-R.
UniProtKB/Swiss-Prot Function:
Glycosyltransferase that generates the core 1 O-glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins. Plays a central role in many processes, such as angiogenesis, thrombopoiesis and kidney homeostasis development.

Enzyme Numbers (IUBMB) for C1GALT1 Gene

Phenotypes From GWAS Catalog for C1GALT1 Gene

Gene Ontology (GO) - Molecular Function for C1GALT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21496458
GO:0016263 glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity IDA 11677243
GO:0016740 transferase activity IEA --
GO:0016757 transferase activity, transferring glycosyl groups IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with C1GALT1: view
genes like me logo Genes that share phenotypes with C1GALT1: view

Animal Models for C1GALT1 Gene

MGI Knock Outs for C1GALT1:

Animal Model Products

  • Taconic Biosciences Mouse Models for C1GALT1

CRISPR Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for C1GALT1 Gene

Localization for C1GALT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for C1GALT1 Gene

Membrane; Single-pass type II membrane protein.

Subcellular locations from

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 C1GALT1 gene
Compartment Confidence
golgi apparatus 5
extracellular 4
nucleus 2
endoplasmic reticulum 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for C1GALT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IDA,IEA 11677243
genes like me logo Genes that share ontologies with C1GALT1: view

Pathways & Interactions for C1GALT1 Gene

genes like me logo Genes that share pathways with C1GALT1: view

Pathways by source for C1GALT1 Gene

UniProtKB/Swiss-Prot Q9NS00-C1GLT_HUMAN

  • Pathway: Protein modification; protein glycosylation.

Gene Ontology (GO) - Biological Process for C1GALT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IMP 17228361
GO:0001822 kidney development IMP 17228361
GO:0006486 protein glycosylation IEA --
GO:0006493 protein O-linked glycosylation IEA --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with C1GALT1: view

No data available for SIGNOR curated interactions for C1GALT1 Gene

Drugs & Compounds for C1GALT1 Gene

(3) Drugs for C1GALT1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved Nutra 0
Uridine diphosphategalactose Experimental Pharma 0
Uridine-5'-Diphosphate Experimental Pharma 0

(1) Additional Compounds for C1GALT1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 2-Acetamido-2-deoxy-a-D-allopyranose
  • 2-Acetamido-2-deoxy-a-D-glucopyranose
  • 2-Acetamido-2-deoxy-alpha-D-allopyranose
  • 2-Acetamido-2-deoxy-alpha-D-glucopyranose
  • 2-Acetamido-2-deoxy-alpha-delta-allopyranose
genes like me logo Genes that share compounds with C1GALT1: view

Transcripts for C1GALT1 Gene

Unigene Clusters for C1GALT1 Gene

Core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for C1GALT1 Gene

No ASD Table

Relevant External Links for C1GALT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for C1GALT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for C1GALT1 Gene

Protein differential expression in normal tissues from HIPED for C1GALT1 Gene

This gene is overexpressed in Placenta (64.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for C1GALT1 Gene

Protein tissue co-expression partners for C1GALT1 Gene

NURSA nuclear receptor signaling pathways regulating expression of C1GALT1 Gene:


SOURCE GeneReport for Unigene cluster for C1GALT1 Gene:


mRNA Expression by UniProt/SwissProt for C1GALT1 Gene:

Tissue specificity: Widely expressed. Highly expressed in kidney, heart, placenta and liver.

Evidence on tissue expression from TISSUES for C1GALT1 Gene

  • Kidney(4.5)
  • Intestine(2.7)
  • Bone marrow(2)
  • Lung(2)
  • Lymph node(2)
  • Pancreas(2)
  • Spleen(2)
  • Stomach(2)
  • Thyroid gland(2)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with C1GALT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for C1GALT1 Gene

Orthologs for C1GALT1 Gene

This gene was present in the common ancestor of animals.

Orthologs for C1GALT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia C1GALT1 33 34
  • 99.36 (n)
(Canis familiaris)
Mammalia C1GALT1 33 34
  • 92.85 (n)
(Bos Taurus)
Mammalia C1GALT1 33 34
  • 90.5 (n)
(Rattus norvegicus)
Mammalia C1galt1 33
  • 89.16 (n)
(Mus musculus)
Mammalia C1galt1 33 16 34
  • 88.98 (n)
(Ornithorhynchus anatinus)
Mammalia C1GALT1 34
  • 61 (a)
(Gallus gallus)
Aves C1GALT1 33 34
  • 78.32 (n)
(Anolis carolinensis)
Reptilia C1GALT1 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia c1galt1 33
  • 69.8 (n)
(Danio rerio)
Actinopterygii C1GALT1 (4 of 4) 34
  • 58 (a)
c1galt1b 34
  • 54 (a)
C1GALT1 (3 of 4) 34
  • 51 (a)
c1galt1a 34
  • 47 (a)
wufa98f05 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9632 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009979 33
  • 55.22 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG8708 35 34
  • 54 (a)
C1GalTA 33 34
  • 52.46 (n)
CG9520 35
  • 50 (a)
CG13904 35
  • 42 (a)
CG2975 35 34
  • 42 (a)
CG7440 35
  • 41 (a)
CG3119 35 34
  • 38 (a)
CG34056 34
  • 35 (a)
CG2983 35 34
  • 34 (a)
CG34057 34
  • 33 (a)
tgy 34
  • 32 (a)
CG18558 34
  • 18 (a)
(Caenorhabditis elegans)
Secernentea C38H2.2 35 33 34
  • 54.67 (n)
F56H6.1 35
  • 33 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
Species where no ortholog for C1GALT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for C1GALT1 Gene

Gene Tree for C1GALT1 (if available)
Gene Tree for C1GALT1 (if available)

Paralogs for C1GALT1 Gene

Paralogs for C1GALT1 Gene Pseudogenes for C1GALT1 Gene

genes like me logo Genes that share paralogs with C1GALT1: view

Variants for C1GALT1 Gene

Sequence variations from dbSNP and Humsavar for C1GALT1 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs1000070691 -- 7,187,417(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000094874 -- 7,189,793(+) A/T genic_upstream_transcript_variant, intron_variant
rs1000173015 -- 7,214,558(+) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000195289 -- 7,207,922(+) C/A genic_upstream_transcript_variant, intron_variant
rs1000292464 -- 7,207,753(+) G/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for C1GALT1 Gene

Variant ID Type Subtype PubMed ID
dgv6249n100 CNV gain 25217958
esv2752174 CNV gain 17911159
esv2759505 CNV loss 17122850
esv3571612 CNV loss 25503493
esv3576288 CNV gain 25503493
esv3612065 CNV gain 21293372
esv3612067 CNV gain 21293372
esv3891032 CNV gain 25118596
nsv1020929 CNV gain 25217958
nsv1023133 CNV gain 25217958
nsv1032974 CNV loss 25217958
nsv464300 CNV gain 19166990
nsv464301 CNV gain 19166990
nsv469770 CNV loss 16826518
nsv477417 CNV novel sequence insertion 20440878
nsv508445 CNV deletion 20534489
nsv606033 CNV gain 21841781
nsv606035 CNV gain 21841781
nsv606036 CNV loss 21841781
nsv8041 CNV loss 18304495

Variation tolerance for C1GALT1 Gene

Residual Variation Intolerance Score: 16.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.22; 39.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for C1GALT1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C1GALT1 Gene

Disorders for C1GALT1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for C1GALT1 Gene - From: HGMD, DISEASES, and Novoseek

Disorder Aliases PubMed IDs
iga glomerulonephritis
  • berger's iga or igg nephropathy
hypersensitivity vasculitis
  • vasculitis hypersensitivity
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for C1GALT1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with C1GALT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for C1GALT1 Gene

Publications for C1GALT1 Gene

  1. Variants of C1GALT1 gene are associated with the genetic susceptibility to IgA nephropathy. (PMID: 17228361) Li GS … Wang HY (Kidney international 2007) 3 4 22 44 58
  2. Interaction between variants of two glycosyltransferase genes in IgA nephropathy. (PMID: 19357720) Zhu L … Wang H (Kidney international 2009) 3 4 44 58
  3. No evidence for a role of cosmc-chaperone mutations in European IgA nephropathy patients. (PMID: 18840896) Malycha F … Eitner F (Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association 2009) 3 22 44 58
  4. Cloning and expression of human core 1 beta1,3-galactosyltransferase. (PMID: 11677243) Ju T … Canfield WM (The Journal of biological chemistry 2002) 2 3 4 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for C1GALT1 Gene

Sources for C1GALT1 Gene

Loading form....