U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 2590, updated on 3-Dec-2024

    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; AllianceGenome:HGNC:4124
    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
    CDG2T; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See GALNT2 in Genome Data Viewer
    Location:
    1q42.13
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (230057789..230282122)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (229437364..229661641)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (230193536..230417868)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373163 Neighboring gene MPRA-validated peak757 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:230153835-230154406 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:230155973-230156473 Neighboring gene long intergenic non-protein coding RNA 1736 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230182250-230182750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230194023-230194523 Neighboring gene U7 small nuclear RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2709 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:230207245-230207425 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230220010-230220551 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:230240174-230241373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2713 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230247432-230248098 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:230248997-230250196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2715 Neighboring gene Sharpr-MPRA regulatory region 12256 Neighboring gene Sharpr-MPRA regulatory region 1224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230272664-230273164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230273165-230273665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230276043-230276635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2716 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:230311720-230311947 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:230321452-230322190 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:230322191-230322929 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230334008-230334701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230336117-230336616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230361793-230362294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230362295-230362794 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230387089-230387750 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230387751-230388411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230390520-230391020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230391021-230391521 Neighboring gene uncharacterized LOC124904542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230400862-230401362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230401363-230401863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230402952-230403462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230403463-230403971 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230403972-230404481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:230404482-230404990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230422195-230422694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230423879-230424378 Neighboring gene NANOG hESC enhancer GRCh37_chr1:230431082-230431583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1939 Neighboring gene putative uncharacterized protein FLJ46204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230452427-230452928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230452929-230453428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2718 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:230468147-230468791 and GRCh37_chr1:230468792-230469436 Neighboring gene piggyBac transposable element derived 5 Neighboring gene uncharacterized LOC124904543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:230535746-230536379

    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 Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Congenital disorder of glycosylation, type iit
    MedGen: C5394387 OMIM: 618885 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
    EBI GWAS Catalog
    Genome-wide and gene-centric analyses of circulating myeloperoxidase levels in the charge and care consortia.
    EBI GWAS Catalog
    Genome-wide association study of serum albumin:globulin ratio in Korean populations.
    EBI GWAS 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.
    EBI GWAS Catalog
    Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
    EBI GWAS Catalog
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    EBI GWAS Catalog
    Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables manganese ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables polypeptide N-acetylgalactosaminyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables polypeptide N-acetylgalactosaminyltransferase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables polypeptide N-acetylgalactosaminyltransferase activity TAS
    Traceable Author Statement
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    colocalizes_with Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in Golgi cisterna membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in Golgi membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
     
    located_in Golgi stack IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane HDA PubMed 
    located_in 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_016856453.2
    XP_054191834.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      14450..229334
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001291866.2NP_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/TrEMBL
      B7Z6K2
      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
      A8K1Y3, B7Z8V8, C5HU00, Q10471, Q9NPY4
      UniProtKB/TrEMBL
      A0A1L7NY41, A0A1L7NY50
      Related
      ENSP00000355632.4, ENST00000366672.5
      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_120373.2 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
      Related
      ENST00000488903.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      230057789..230282122
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017000964.3XP_016856453.2  polypeptide N-acetylgalactosaminyltransferase 2 isoform X1

      UniProtKB/TrEMBL
      B7Z6K2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      229437364..229661641
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335859.1XP_054191834.1  polypeptide N-acetylgalactosaminyltransferase 2 isoform X1

      UniProtKB/TrEMBL
      B7Z6K2