B3GAT2 beta-1,3-glucuronyltransferase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: B3GAT2provided by HGNC
Official Full Name: beta-1,3-glucuronyltransferase 2provided by HGNC
Primary source: HGNC:HGNC:922
See related: Ensembl:ENSG00000112309 MIM:607497; AllianceGenome:HGNC:922
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: GLCATS
Summary: The product of this gene is a transmembrane protein belonging to the glucuronyltransferase family, and catalyzes the transfer of a beta-1,3 linked glucuronic acid to a terminal galactose in different glycoproteins or glycolipids containing a Gal-beta-1-4GlcNAc or Gal-beta-1-3GlcNAc residue. The encoded protein is involved in the synthesis of the human natural killer-1 (HNK-1) carbohydrate epitope, a sulfated trisaccharide implicated in cellular migration and adhesion in the nervous system. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in brain (RPKM 8.3), duodenum (RPKM 3.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q13

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (70856679..70957060, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (72037217..72137607, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (71566382..71666763, complement)

Chromosome 6 - NC_000006.12 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?

The study identified a region on chromosome 6 comprising the genes SMAP1, B3GAT2, and RIMS1 as novel susceptibility locus for pediatric venous thromboembolism.
Title: Rare genetic variants in SMAP1, B3GAT2, and RIMS1 contribute to pediatric venous thromboembolism.
B3GAT2 and ZNF793 are hypermethylated in BE, and the methylation status of these genes can be used to detect BE in tissue samples.
Title: Methylated B3GAT2 and ZNF793 Are Potential Detection Biomarkers for Barrett's Esophagus.
results suggest that effects on biosynthesis of the neuronal epitope HNK-1, through common B3GAT2 variation, could increase the risk of SCZ, possibly by decreasing cortical area.
Title: Candidate gene analysis of the human natural killer-1 carbohydrate pathway and perineuronal nets in schizophrenia: B3GAT2 is associated with disease risk and cortical surface area.
Observational study and meta-analysis of gene-disease association. (HuGE Navigator)
Title: Candidate gene analysis of the human natural killer-1 carbohydrate pathway and perineuronal nets in schizophrenia: B3GAT2 is associated with disease risk and cortical surface area.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Residues interacting with UDP molecule, which is a part of the donor substrate, are highly conserved between GlcAT-P and GlcAT-S
Title: Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope.
human GlcAT-S gene-located on human chromosome 6 encodes a protein involved in biosynthesis of HNK-1 carbohydrate epitope on glycoproteins.
Title: Cloning, characterization, and chromosome mapping of the human GlcAT-S gene.

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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
Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. 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

WI-13200 (e-PCR)
- UniSTS:74500

RH18293 (e-PCR)
- UniSTS:38158

D20S768 (e-PCR)
- UniSTS:154152

SHGC-30828 (e-PCR)
- UniSTS:20032

D6S1180E.1 (e-PCR)
- UniSTS:39262

D6S1413 (e-PCR)
- UniSTS:26503

RH75302 (e-PCR)
- UniSTS:91801

D6S1220E (e-PCR)
- UniSTS:40861

A003B38 (e-PCR)
- UniSTS:21662

RH15822 (e-PCR)
- UniSTS:82399

NoName (e-PCR)
- UniSTS:484092

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in carbohydrate biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in carbohydrate metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in chondroitin sulfate proteoglycan biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein glycosylation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in Golgi membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2

Names: UDP-glucuronosyltransferase S; UDP-glucuronyltransferase S; glcAT-D; glucuronosyltransferase S; uridine diphosphate glucuronic acid:acceptor glucuronosyltransferase

NP_542780.1

EC 2.4.1.135

XP_047274165.1

EC 2.4.1.135

XP_054210276.1

EC 2.4.1.135

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_080742.3 → NP_542780.1 galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 2 precursor

See identical proteins and their annotated locations for NP_542780.1

Status: REVIEWED

Source sequence(s)

AB075843, AL121961, DA782678

Consensus CDS

CCDS4974.1

UniProtKB/Swiss-Prot

Q5JS09, Q8TF38, Q96NK4, Q9NPZ5

Related

ENSP00000230053.6, ENST00000230053.11

Conserved Domains (1) summary

cd00218
Location:81 → 305

GlcAT-I; Beta1,3-glucuronyltransferase I (GlcAT-I) is involved in the initial steps of proteoglycan synthesis