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GALNT2 polypeptide N-acetylgalactosaminyltransferase 2 [ Homo sapiens (human) ]

Gene ID: 2590, updated on 9-Dec-2018

Summary

Official Symbol
GALNT2provided by HGNC
Official Full Name
polypeptide N-acetylgalactosaminyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:4124
See related
Ensembl:ENSG00000143641 MIM:602274
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
GalNAc-T2
Summary
This gene encodes a member of the glycosyltransferase 2 protein family. Members of this family initiate mucin-type O-glycoslation of peptides in the Golgi apparatus. The encoded protein may be involved in O-linked glycosylation of the immunoglobulin A1 hinge region. This gene may influence triglyceride levels, and may be involved Type 2 diabetes, as well as several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
Expression
Ubiquitous expression in ovary (RPKM 16.5), appendix (RPKM 14.3) and 25 other tissues See more
Orthologs

Genomic context

See GALNT2 in Genome Data Viewer
Location:
1q42.13
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (230057789..230282130)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (230202956..230417875)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373163 Neighboring gene long intergenic non-protein coding RNA 1736 Neighboring gene piggyBac transposable element derived 5 Neighboring gene piggyBac transposable element derived 5

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
NHGRI GWA Catalog
Common variants at 30 loci contribute to polygenic dyslipidemia.
NHGRI GWA Catalog
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog
Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
NHGRI GWA Catalog
Genome-wide and gene-centric analyses of circulating myeloperoxidase levels in the charge and care consortia.
NHGRI GWA Catalog
Genome-wide association study of serum albumin:globulin ratio in Korean populations.
NHGRI GWA Catalog
Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits.
NHGRI GWA Catalog
Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
NHGRI GWA Catalog
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
NHGRI GWA Catalog
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
carbohydrate binding IEA
Inferred from Electronic Annotation
more info
 
manganese ion binding IDA
Inferred from Direct Assay
more info
PubMed 
polypeptide N-acetylgalactosaminyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
polypeptide N-acetylgalactosaminyltransferase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
O-glycan processing IDA
Inferred from Direct Assay
more info
PubMed 
O-glycan processing TAS
Traceable Author Statement
more info
 
immunoglobulin biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
protein O-linked glycosylation IDA
Inferred from Direct Assay
more info
PubMed 
protein O-linked glycosylation via serine IDA
Inferred from Direct Assay
more info
PubMed 
protein O-linked glycosylation via threonine IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi cisterna membrane IEA
Inferred from Electronic Annotation
more info
 
Golgi membrane TAS
Traceable Author Statement
more info
 
Golgi stack IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
integral component of Golgi membrane NAS
Non-traceable Author Statement
more info
PubMed 
membrane HDA PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
polypeptide N-acetylgalactosaminyltransferase 2
Names
UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2
UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)
polypeptide GalNAc transferase 2
pp-GaNTase 2
NP_001278795.1
NP_004472.1
XP_016856452.1
XP_016856453.1
XP_016856454.1
XP_016856455.1

NCBI Reference Sequences (RefSeq)

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_011854.2 RefSeqGene

    Range
    14407..229342
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001291866.1NP_001278795.1  polypeptide N-acetylgalactosaminyltransferase 2 isoform 2

    See identical proteins and their annotated locations for NP_001278795.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 2.
    Source sequence(s)
    AK300453, BC050583, BE328743, X85019
    UniProtKB/Swiss-Prot
    Q10471
    UniProtKB/TrEMBL
    B7Z6K2, G3V1S6
    Conserved Domains (3) summary
    cd02510
    Location:101396
    pp-GalNAc-T; pp-GalNAc-T initiates the formation of mucin-type O-linked glycans
    cd00161
    Location:418527
    RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
    pfam00652
    Location:408525
    Ricin_B_lectin; Ricin-type beta-trefoil lectin domain
  2. NM_004481.5NP_004472.1  polypeptide N-acetylgalactosaminyltransferase 2 precursor

    See identical proteins and their annotated locations for NP_004472.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    BC041120, BC050583, BE328743, X85019
    Consensus CDS
    CCDS1582.1
    UniProtKB/Swiss-Prot
    Q10471
    UniProtKB/TrEMBL
    A0A1L7NY50
    Related
    ENSP00000355632.4, ENST00000366672.4
    Conserved Domains (2) summary
    cd02510
    Location:139434
    pp-GalNAc-T; pp-GalNAc-T initiates the formation of mucin-type O-linked glycans
    pfam00652
    Location:446563
    Ricin_B_lectin; Ricin-type beta-trefoil lectin domain

RNA

  1. NR_120373.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several exons and contains an alternate 3'-terminal exon. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    BC041120, BF727269, BG773173
    Related
    ENST00000488903.1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    230057789..230282130
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000965.1XP_016856454.1  polypeptide N-acetylgalactosaminyltransferase 2 isoform X3

  2. XM_017000963.2XP_016856452.1  polypeptide N-acetylgalactosaminyltransferase 2 isoform X1

  3. XM_017000964.2XP_016856453.1  polypeptide N-acetylgalactosaminyltransferase 2 isoform X2

  4. XM_017000966.1XP_016856455.1  polypeptide N-acetylgalactosaminyltransferase 2 isoform X4

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