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B3GALNT2 beta-1,3-N-acetylgalactosaminyltransferase 2 [ Homo sapiens (human) ]

Gene ID: 148789, updated on 11-Apr-2024

Summary

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Official Symbol
B3GALNT2provided by HGNC
Official Full Name
beta-1,3-N-acetylgalactosaminyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:28596
See related
Ensembl:ENSG00000162885 MIM:610194; AllianceGenome:HGNC:28596
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
MDDGA11; B3GalNAc-T2
Summary
This gene encodes a member of the glycosyltransferase 31 family. The encoded protein synthesizes GalNAc:beta-1,3GlcNAc, a novel carbohydrate structure, on N- and O-glycans. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Mar 2013]
Expression
Ubiquitous expression in prostate (RPKM 6.9), esophagus (RPKM 6.9) and 25 other tissues See more
Orthologs
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Genomic context

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See B3GALNT2 in Genome Data Viewer
Location:
1q42.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (235439796..235504452, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (234835690..234900322, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (235610505..235667752, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904559 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235530449-235531162 Neighboring gene tubulin folding cofactor E Neighboring gene MPRA-validated peak773 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235563413-235563946 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:235605546-235606745 Neighboring gene ribosomal protein S21 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:235639769-235640268 Neighboring gene MPRA-validated peak774 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:235667854-235668530 Neighboring gene MT-CYB pseudogene 14 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:235695340-235696539 Neighboring gene MT-ND6 pseudogene 14

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. [Genetic analysis of a Chinese family affected with α-dystroglycanopathy due to variant of B3GALNT2 gene]. Zeng L, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2023 Jul 10. PMID 37368380
  2. Prenatal diagnosis of Walker-Warburg syndrome due to compound mutations in the B3GALNT2 gene. Wang P, et al. J Gene Med, 2022 May. PMID 35338537, Free PMC Article
  3. Novel mutations in B3GALNT2 gene causing α-dystroglycanopathy in Chinese patients. Chen XY, et al. Chin Med J (Engl), 2020 Dec 7. PMID 33290285, Free PMC Article
  4. Identification of mammalian glycoproteins with type-I LacdiNAc structures synthesized by the glycosyltransferase B3GALNT2. Nakane T, et al. J Biol Chem, 2019 May 3. PMID 30898876, Free PMC Article
  5. Increased B3GALNT2 in hepatocellular carcinoma promotes macrophage recruitment via reducing acetoacetate secretion and elevating MIF activity. Yang T, et al. J Hematol Oncol, 2018 Apr 4. PMID 29618368, Free PMC Article

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. [Genetic analysis of a Chinese family affected with alpha-dystroglycanopathy due to variant of B3GALNT2 gene].
    Title: [Genetic analysis of a Chinese family affected with α-dystroglycanopathy due to variant of B3GALNT2 gene].
  2. Prenatal diagnosis of Walker-Warburg syndrome due to compound mutations in the B3GALNT2 gene.
    Title: Prenatal diagnosis of Walker-Warburg syndrome due to compound mutations in the B3GALNT2 gene.
  3. Novel mutations in B3GALNT2 gene causing alpha-dystroglycanopathy in Chinese patients.
    Title: Novel mutations in B3GALNT2 gene causing α-dystroglycanopathy in Chinese patients.
  4. B3GALNT2 primarily transferred LDN to intracellular glycoproteins, thereby clearly delineating proteins that carry type-I or type-II LacdiNAcs
    Title: Identification of mammalian glycoproteins with type-I LacdiNAc structures synthesized by the glycosyltransferase B3GALNT2.
  5. B3GALNT2 reduced expression of some metabolic enzymes and thus downregulated levels of secreted acetoacetate. This relieved the activity of MIF and enhanced macrophage recruitment to promote tumor growth.
    Title: Increased B3GALNT2 in hepatocellular carcinoma promotes macrophage recruitment via reducing acetoacetate secretion and elevating MIF activity.
  6. Mutations in B3GALNT2 give rise to a novel muscular dystrophy-dystroglycanopathies syndrome presentation, characterized by intellectual disability and seizure, but without any apparent muscular involvement.
    Title: B3GALNT2 mutations associated with non-syndromic autosomal recessive intellectual disability reveal a lack of genotype-phenotype associations in the muscular dystrophy-dystroglycanopathies.
  7. B3GALNT2 is a gene associated with congenital muscular dystrophy with brain malformations.
    Title: B3GALNT2 is a gene associated with congenital muscular dystrophy with brain malformations.
  8. B3GALNT2 overexpression is associated with breast cancer.
    Title: Involvement of B3GALNT2 overexpression in the cell growth of breast cancer.
  9. Results demonstrate a role for B3GALNT2 in the glycosylation of alpha-DG and show that B3GALNT2 mutations can cause dystroglycanopathy with muscle and brain involvement.
    Title: Mutations in B3GALNT2 cause congenital muscular dystrophy and hypoglycosylation of α-dystroglycan.
  10. Although the GalNAcbeta1-3GlcNAcbeta1-R structure has not been reported in humans or other mammals, we have discovered a novel human glycosyltransferase producing this structure on N- and O-glycans.
    Title: A novel human beta1,3-N-acetylgalactosaminyltransferase that synthesizes a unique carbohydrate structure, GalNAcbeta1-3GlcNAc.
Submit: New GeneRIF Correction

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

Associated conditions

Description Tests
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11
MedGen: C3554638 OMIM: 615181 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC39558

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables UDP-glycosyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables acetylgalactosaminyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables acetylgalactosaminyltransferase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein O-linked glycosylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein O-linked glycosylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein O-linked glycosylation TAS
Traceable Author Statement
more info
  
involved_in protein glycosylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2
Names
UDP-GalNAc:betaGlcNAc beta-1,3-galactosaminyltransferase, polypeptide 2
beta-1,3-GalNAc-T2
NP_001264084.1
NP_689703.1
XP_006711812.1
XP_016855883.1
XP_047302958.1
XP_047302959.1
XP_047302960.1
XP_047302961.1
XP_054187907.1
XP_054187908.1
XP_054187909.1
XP_054187910.1
XP_054187911.1
XP_054187912.1
XP_054190572.1
XP_054190573.1
XP_054190574.1
XP_054190575.1
XP_054190576.1
XP_054190577.1

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.

Genomic

  1. NG_033219.3 RefSeqGene

    Range
    5000..62262
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001277155.3 → NP_001264084.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform 2

    See identical proteins and their annotated locations for NP_001264084.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate in-frame exon in the 5' coding region, and its transcription extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR compared to variant 1. The encoded protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC016974, BC029564, FO393422
    Consensus CDS
    CCDS60453.1
    UniProtKB/Swiss-Prot
    Q8NCR0
    Related
    ENSP00000315678.3, ENST00000313984.3
    Conserved Domains (1) summary
    PLN03133
    Location:93 → 142
    PLN03133; beta-1,3-galactosyltransferase; Provisional

  2. NM_152490.5 → NP_689703.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform 1

    See identical proteins and their annotated locations for NP_689703.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
    Source sequence(s)
    AB209046, AW513183, BC029564, BQ221255, FO393422
    Consensus CDS
    CCDS1606.1
    UniProtKB/Swiss-Prot
    Q59GR3, Q5TCI3, Q8NCR0, Q96AL7
    UniProtKB/TrEMBL
    A0A6Q8PEZ9
    Related
    ENSP00000355559.3, ENST00000366600.8
    Conserved Domains (2) summary
    PLN03133
    Location:52 → 101
    PLN03133; beta-1,3-galactosyltransferase; Provisional
    cl21608
    Location:307 → 457
    Galactosyl_T; Galactosyltransferase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    235439796..235504452 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006711749.4 → XP_006711812.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X1

    Conserved Domains (1) summary
    cl21608
    Location:307 → 457
    Galactosyl_T; Galactosyltransferase

  2. XM_017000394.2 → XP_016855883.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X2

    UniProtKB/TrEMBL
    A0A6Q8PGQ3
    Related
    ENSP00000502392.1, ENST00000676288.1

  3. XM_047447005.1 → XP_047302961.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X6

  4. XM_047447004.1 → XP_047302960.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X5

  5. XM_047447002.1 → XP_047302958.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X3

  6. XM_047447003.1 → XP_047302959.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X4

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_014040927.1 Reference GRCh38.p14 PATCHES

    Range
    83388..148044 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331932.1 → XP_054187907.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X1

  2. XM_054331933.1 → XP_054187908.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X2

  3. XM_054331937.1 → XP_054187912.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X6

  4. XM_054331934.1 → XP_054187909.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X3

  5. XM_054331936.1 → XP_054187911.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X5

  6. XM_054331935.1 → XP_054187910.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    234835690..234900322 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334597.1 → XP_054190572.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X1

  2. XM_054334598.1 → XP_054190573.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X2

  3. XM_054334602.1 → XP_054190577.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X6

  4. XM_054334599.1 → XP_054190574.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X3

  5. XM_054334601.1 → XP_054190576.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X5

  6. XM_054334600.1 → XP_054190575.1  UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NCR0.1 GenPept UniProtKB/Swiss-Prot:Q8NCR0

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