The protein encoded by this gene is one of two enzymes that transfers galactose moieties to hydroxylysine residues of collagen and mannose binding lectin. This gene is constitutively expressed and encodes a soluble protein that localizes to the endoplasmic reticulum. [provided by RefSeq, Dec 2015] See more...

Aliases for COLGALT1 Gene

Aliases for COLGALT1 Gene

  • Collagen Beta(1-O)Galactosyltransferase 1 2 3 4 5
  • Glycosyltransferase 25 Domain Containing 1 2 3
  • Glycosyltransferase 25 Family Member 1 3 4
  • Hydroxylysine Galactosyltransferase 1 3 4
  • Procollagen Galactosyltransferase 1 3 4
  • ColGalT 1 3 4
  • GLT25D1 3 4
  • Hydroxylysine Galactosyltransferase 2
  • Procollagen Galactosyltransferase 2
  • EC 2.4.1.50 4
  • COLGALT1 5
  • FLJ22329 2
  • BSVD3 3

External Ids for COLGALT1 Gene

Previous HGNC Symbols for COLGALT1 Gene

  • GLT25D1

Previous GeneCards Identifiers for COLGALT1 Gene

  • GC19P017747
  • GC19P017916

Summaries for COLGALT1 Gene

Entrez Gene Summary for COLGALT1 Gene

  • The protein encoded by this gene is one of two enzymes that transfers galactose moieties to hydroxylysine residues of collagen and mannose binding lectin. This gene is constitutively expressed and encodes a soluble protein that localizes to the endoplasmic reticulum. [provided by RefSeq, Dec 2015]

GeneCards Summary for COLGALT1 Gene

COLGALT1 (Collagen Beta(1-O)Galactosyltransferase 1) is a Protein Coding gene. Diseases associated with COLGALT1 include Brain Small Vessel Disease 3 and Porencephaly. Among its related pathways are Degradation of the extracellular matrix and Collagen chain trimerization. Gene Ontology (GO) annotations related to this gene include procollagen galactosyltransferase activity. An important paralog of this gene is COLGALT2.

UniProtKB/Swiss-Prot Summary for COLGALT1 Gene

  • Beta-galactosyltransferase that transfers beta-galactose to hydroxylysine residues of type I collagen (PubMed:19075007, PubMed:22216269, PubMed:27402836). By acting on collagen glycosylation, facilitates the formation of collagen triple helix (PubMed:27402836). Also involved in the biosynthesis of collagen type IV (PubMed:30412317).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COLGALT1 Gene

Genomics for COLGALT1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for COLGALT1 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
GH19J017552 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 275.7 -0.6 -631 4.8 SP1 ZNF654 MYC IKZF1 JUND ZNF580 ZNF592 ZMYM3 ATF2 BRCA1 COLGALT1 HSALNG0124537 MVB12A ENSG00000269578 ENSG00000267904 ENSG00000268087 ENSG00000268743 ENSG00000268938 ENSG00000269191 PGLS
GH19J017333 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 54.2 -219.6 -219556 6.2 BCLAF1 SP1 ZNF654 ZNF207 MYC IKZF1 NCOR1 ZNF600 SIX5 ZNF580 GTPBP3 ANO8 lnc-DDA1-1 CHERP ENSG00000269578 ENSG00000268743 IQCN C19orf44 SIN3B MED26
GH19J018289 Promoter/Enhancer 2.4 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 38.7 +736.6 736587 6.1 BCLAF1 SP1 MYC NCOR1 IKZF1 ZNF600 ZNF580 ZNF592 ZMYM3 ATF2 HSALNG0124607 HSALNG0124608 ENSG00000268030 IQCN NR2C2AP UPF1 COLGALT1 ENSG00000268938 PGLS-DT SUGP2
GH19J018414 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 31.1 +863.0 862986 9.3 ZNF207 NCOR1 IKZF1 MYC ZNF600 SSRP1 ZNF580 ZNF592 ZMYM3 ATF2 SSBP4 HSALNG0124621 NONHSAG025131.2 MAU2 ENSG00000268030 NR2C2AP UPF1 IQCN ENSG00000268938 ENSG00000269191
GH19J017859 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 37.8 +307.1 307097 7.5 BCLAF1 SP1 ZNF654 ZNF207 MYC ZNF600 SIX5 SSRP1 ZNF580 ZNF592 RPL18A SNORA68 NONHSAG025111.2 MN297184-002 piR-38446-002 piR-33407-002 ENSG00000268030 UPF1 ENSG00000268938 IQCN
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COLGALT1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COLGALT1

Genomic Locations for COLGALT1 Gene

Latest Assembly
chr19:17,555,649-17,583,162
(GRCh38/hg38)
Size:
27,514 bases
Orientation:
Plus strand

Previous Assembly
chr19:17,666,458-17,693,966
(GRCh37/hg19 by Entrez Gene)
Size:
27,509 bases
Orientation:
Plus strand

chr19:17,666,403-17,693,971
(GRCh37/hg19 by Ensembl)
Size:
27,569 bases
Orientation:
Plus strand

Genomic View for COLGALT1 Gene

Genes around COLGALT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COLGALT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COLGALT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COLGALT1 Gene

Proteins for COLGALT1 Gene

  • Protein details for COLGALT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NBJ5-GT251_HUMAN
    Recommended name:
    Procollagen galactosyltransferase 1
    Protein Accession:
    Q8NBJ5
    Secondary Accessions:
    • Q8NC64

    Protein attributes for COLGALT1 Gene

    Size:
    622 amino acids
    Molecular mass:
    71636 Da
    Quaternary structure:
    No Data Available

neXtProt entry for COLGALT1 Gene

Post-translational modifications for COLGALT1 Gene

  • N-glycosylated.
  • Glycosylation at Asn96, Asn184, and Asn381
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • GT251_HUMAN (1631)

Other Protein References for COLGALT1 Gene

No data available for DME Specific Peptides for COLGALT1 Gene

Domains & Families for COLGALT1 Gene

Gene Families for COLGALT1 Gene

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

Protein Domains for COLGALT1 Gene

Suggested Antigen Peptide Sequences for COLGALT1 Gene

GenScript: Design optimal peptide antigens:
  • Hydroxylysine galactosyltransferase 1 (GT251_HUMAN)
  • GLT25D1 protein (Q6IPW8_HUMAN)
  • GLT25D1 protein (Q8WUI9_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NBJ5

UniProtKB/Swiss-Prot:

GT251_HUMAN :
  • Belongs to the glycosyltransferase 25 family.
Family:
  • Belongs to the glycosyltransferase 25 family.
genes like me logo Genes that share domains with COLGALT1: view

Function for COLGALT1 Gene

Molecular function for COLGALT1 Gene

UniProtKB/Swiss-Prot Function:
Beta-galactosyltransferase that transfers beta-galactose to hydroxylysine residues of type I collagen (PubMed:19075007, PubMed:22216269, PubMed:27402836). By acting on collagen glycosylation, facilitates the formation of collagen triple helix (PubMed:27402836). Also involved in the biosynthesis of collagen type IV (PubMed:30412317).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(5R)-5-hydroxy-L-lysyl-[procollagen] + UDP-alpha-D-galactose = (5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysyl-[procollagen] + H(+) + UDP; Xref=Rhea:RHEA:12637, Rhea:RHEA-COMP:12752, Rhea:RHEA-COMP:12753, ChEBI:CHEBI:15378, ChEBI:CHEBI:58223, ChEBI:CHEBI:66914, ChEBI:CHEBI:133442, ChEBI:CHEBI:133443; EC=2.4.1.50; Evidence={ECO:0000269|PubMed:19075007};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=18.7 uM for UDP-galactose (at 37 degrees Celsius and pH 7.4) {ECO:0000269|PubMed:19075007}; KM=29.9 uM for UDP-galactose (at 37 degrees Celsius and pH 7.4) {ECO:0000269|PubMed:22216269};

Enzyme Numbers (IUBMB) for COLGALT1 Gene

Phenotypes From GWAS Catalog for COLGALT1 Gene

Gene Ontology (GO) - Molecular Function for COLGALT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016740 transferase activity IEA --
GO:0016757 transferase activity, transferring glycosyl groups IEA --
GO:0050211 procollagen galactosyltransferase activity IBA,TAS --
genes like me logo Genes that share ontologies with COLGALT1: view
genes like me logo Genes that share phenotypes with COLGALT1: view

Human Phenotype Ontology for COLGALT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for COLGALT1 Gene

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COLGALT1

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for COLGALT1 Gene

Localization for COLGALT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COLGALT1 Gene

Endoplasmic reticulum lumen. Note=Colocalized with PLOD3 and mannose binding lectin/MBL2. {ECO:0000269 PubMed:20470363}.

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 COLGALT1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 2
plasma membrane 1
mitochondrion 1
nucleus 1
cytosol 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for COLGALT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with COLGALT1: view

Pathways & Interactions for COLGALT1 Gene

genes like me logo Genes that share pathways with COLGALT1: view

Pathways by source for COLGALT1 Gene

SIGNOR curated interactions for COLGALT1 Gene

Gene Ontology (GO) - Biological Process for COLGALT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0018215 protein phosphopantetheinylation IEA --
GO:1904028 positive regulation of collagen fibril organization IMP 27402836
genes like me logo Genes that share ontologies with COLGALT1: view

Drugs & Compounds for COLGALT1 Gene

(2) Drugs for COLGALT1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Uridine 5'-diphosphate Experimental Pharma 0
Uridine diphosphategalactose Experimental Pharma 0
genes like me logo Genes that share compounds with COLGALT1: view

Transcripts for COLGALT1 Gene

mRNA/cDNA for COLGALT1 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COLGALT1

Alternative Splicing Database (ASD) splice patterns (SP) for COLGALT1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c · 13d · 13e ^ 14a · 14b
SP1: - - - - -
SP2: - -
SP3: - - - - -
SP4: -
SP5:
SP6:

Relevant External Links for COLGALT1 Gene

GeneLoc Exon Structure for
COLGALT1

Expression for COLGALT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COLGALT1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COLGALT1 Gene

This gene is overexpressed in Whole Blood (x4.4).

Protein differential expression in normal tissues from HIPED for COLGALT1 Gene

This gene is overexpressed in Lymph node (12.4), Peripheral blood mononuclear cells (10.1), and Bone marrow stromal cell (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for COLGALT1 Gene



Protein tissue co-expression partners for COLGALT1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COLGALT1

SOURCE GeneReport for Unigene cluster for COLGALT1 Gene:

Hs.418795

mRNA Expression by UniProt/SwissProt for COLGALT1 Gene:

Q8NBJ5-GT251_HUMAN
Tissue specificity: Ubiquitous with higher levels in placenta, heart, lung and spleen.

Evidence on tissue expression from TISSUES for COLGALT1 Gene

  • Liver(4.4)
  • Nervous system(2.1)
genes like me logo Genes that share expression patterns with COLGALT1: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for COLGALT1 Gene

Orthologs for COLGALT1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COLGALT1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia GLT25D1 29 30
  • 98.79 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Colgalt1 16 30
  • 92 (a)
OneToOne
Glt25d1 29
  • 86.79 (n)
Dog
(Canis familiaris)
Mammalia COLGALT1 29 30
  • 90.73 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia COLGALT1 29 30
  • 89.66 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia COLGALT1 30
  • 89 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Colgalt1 29
  • 86.05 (n)
Oppossum
(Monodelphis domestica)
Mammalia COLGALT1 30
  • 85 (a)
OneToOne
Chicken
(Gallus gallus)
Aves -- 30
  • 84 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia COLGALT1 30
  • 76 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100488616 29
  • 69.34 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13613 29
Zebrafish
(Danio rerio)
Actinopterygii COLGALT1 (3 of 3) 30
  • 75 (a)
OneToMany
COLGALT1 (1 of 3) 30
  • 73 (a)
OneToMany
colgalt1 29 30
  • 68.37 (n)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4024 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG31915 30
  • 41 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea D2045.9 30
  • 34 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 47 (a)
OneToMany
Species where no ortholog for COLGALT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • Wheat (Triticum aestivum)

Evolution for COLGALT1 Gene

ENSEMBL:
Gene Tree for COLGALT1 (if available)
TreeFam:
Gene Tree for COLGALT1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for COLGALT1: view image
Alliance of Genome Resources:
Additional Orthologs for COLGALT1

Paralogs for COLGALT1 Gene

Paralogs for COLGALT1 Gene

(5) SIMAP similar genes for COLGALT1 Gene using alignment to 3 proteins:

  • GT251_HUMAN
  • M0QX72_HUMAN
  • M0QYH0_HUMAN
genes like me logo Genes that share paralogs with COLGALT1: view

Variants for COLGALT1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COLGALT1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
1013147 Likely Benign: not provided 17,572,541(+) C/T
NM_024656.4(COLGALT1):c.888C>T (p.Arg296=)
SYNONYMOUS
917942 Likely Pathogenic: Brain small vessel disease 3 17,555,886(+) T/C
NM_024656.4(COLGALT1):c.173T>C (p.Leu58Pro)
MISSENSE
rs118174667 Uncertain Significance: not provided 17,559,323(+) C/T
NM_024656.4(COLGALT1):c.273C>T (p.Asp91=)
SYNONYMOUS
rs147852319 Brain small vessel disease 3 (BSVD3) [MIM:618360] p.Leu151Arg
rs1478523191 Pathogenic: Brain small vessel disease 3 17,560,428(+) T/G
NM_024656.4(COLGALT1):c.452T>G (p.Leu151Arg)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for COLGALT1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for COLGALT1 Gene

Variant ID Type Subtype PubMed ID
esv2422429 CNV duplication 17116639
nsv138503 CNV insertion 16902084
nsv952419 CNV deletion 24416366

Variation tolerance for COLGALT1 Gene

Residual Variation Intolerance Score: 33.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.27; 52.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COLGALT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
COLGALT1
Leiden Open Variation Database (LOVD)
COLGALT1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COLGALT1 Gene

Disorders for COLGALT1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for COLGALT1 Gene - From: OMI, CVR, GTR, SWI, COP, and GCD

Disorder Aliases PubMed IDs
brain small vessel disease 3
  • bsvd3
porencephaly
achilles bursitis
  • achilles bursitis or tendinitis
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

GT251_HUMAN
  • Brain small vessel disease 3 (BSVD3) [MIM:618360]: An autosomal recessive form of brain small vessel disease, a cerebrovascular disorder with variable manifestations reflecting the location and severity of the vascular defect. BSVD3 patients may have disease onset in utero or early infancy with subsequent global developmental delay, spasticity, and porencephaly on brain imaging. Other patients may have normal or mildly delayed development with sudden onset of intracranial hemorrhage causing acute neurologic deterioration. {ECO:0000269 PubMed:30412317}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for COLGALT1

genes like me logo Genes that share disorders with COLGALT1: view

No data available for Genatlas for COLGALT1 Gene

Publications for COLGALT1 Gene

  1. Core glycosylation of collagen is initiated by two beta(1-O)galactosyltransferases. (PMID: 19075007) Schegg B … Hennet T (Molecular and cellular biology 2009) 2 3 4
  2. Biallelic COLGALT1 variants are associated with cerebral small vessel disease. (PMID: 30412317) Miyatake S … Matsumoto N (Annals of neurology 2018) 4 72
  3. Collagen Accumulation in Osteosarcoma Cells lacking GLT25D1 Collagen Galactosyltransferase. (PMID: 27402836) Baumann S … Hennet T (The Journal of biological chemistry 2016) 3 4
  4. Identification of domains and amino acids essential to the collagen galactosyltransferase activity of GLT25D1. (PMID: 22216269) Perrin-Tricaud C … Hennet T (PloS one 2011) 3 4
  5. The human collagen beta(1-O)galactosyltransferase, GLT25D1, is a soluble endoplasmic reticulum localized protein. (PMID: 20470363) Liefhebber JM … van Leeuwen HC (BMC cell biology 2010) 3 4

Products for COLGALT1 Gene

Sources for COLGALT1 Gene