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    GALNT12 polypeptide N-acetylgalactosaminyltransferase 12 [ Homo sapiens (human) ]

    Gene ID: 79695, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GALNT12provided by HGNC
    Official Full Name
    polypeptide N-acetylgalactosaminyltransferase 12provided by HGNC
    Primary source
    HGNC:HGNC:19877
    See related
    Ensembl:ENSG00000119514 MIM:610290; AllianceGenome:HGNC:19877
    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
    CRCS1; GalNAc-T12
    Summary
    This gene encodes a member of a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases, which catalyze the transfer of N-acetylgalactosamine (GalNAc) from UDP-GalNAc to a serine or threonine residue on a polypeptide acceptor in the initial step of O-linked protein glycosylation. Mutations in this gene are associated with an increased susceptibility to colorectal cancer.[provided by RefSeq, Mar 2011]
    Expression
    Biased expression in colon (RPKM 24.5), stomach (RPKM 17.8) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GALNT12 in Genome Data Viewer
    Location:
    9q22.33
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (98807670..98850081)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (110979352..111021780)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (101569952..101612363)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ankyrin repeat and sterile alpha motif domain containing 6 Neighboring gene Sharpr-MPRA regulatory region 9654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20120 Neighboring gene H3K27ac hESC enhancers GRCh37_chr9:101558100-101558600 and GRCh37_chr9:101558601-101559101 Neighboring gene uncharacterized LOC124902229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20123 Neighboring gene Sharpr-MPRA regulatory region 15412 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:101622227-101622437 Neighboring gene uncharacterized LOC102724684 Neighboring gene NME2 pseudogene 3

    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 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. GALNT12 is associated with the malignancy of glioma and promotes glioblastoma multiforme in vitro by activating Akt signaling. Zheng Y, et al. Biochem Biophys Res Commun, 2022 Jun 25. PMID 35461073
    2. Inactivating germ-line and somatic mutations in polypeptide N-acetylgalactosaminyltransferase 12 in human colon cancers. Guda K, et al. Proc Natl Acad Sci U S A, 2009 Aug 4. PMID 19617566, Free PMC Article
    3. Inherited deleterious variants in GALNT12 are associated with CRC susceptibility. Clarke E, et al. Hum Mutat, 2012 Jul. PMID 22461326
    4. GALNT12 is not a major contributor of familial colorectal cancer type X. Seguí N, et al. Hum Mutat, 2014 Jan. PMID 24115450
    5. Expression of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-12 in gastric and colonic cancer cell lines and in human colorectal cancer. Guo JM, et al. Oncology, 2004. PMID 15557789

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. GALNT12 is associated with the malignancy of glioma and promotes glioblastoma multiforme in vitro by activating Akt signaling.
      Title: GALNT12 is associated with the malignancy of glioma and promotes glioblastoma multiforme in vitro by activating Akt signaling.
    2. Interaction between G ALNT12 and C1GALT1 Associates with Galactose-Deficient IgA1 and IgA Nephropathy.
      Title: Interaction between GALNT12 and C1GALT1 Associates with Galactose-Deficient IgA1 and IgA Nephropathy.
    3. The findings provide strong, independent evidence for the association of GALNT12 defects with CRC-susceptibility; underscoring implications for glycosylation pathway defects in CRC.
      Title: Evidence for GALNT12 as a moderate penetrance gene for colorectal cancer.
    4. LOH analyses, glycosylation pattern tests and case-control studies, our results did not support the role of c.907G>A, p.(D303N) as a high-penetrance risk allele for polyposis CRC
      Title: Role of GALNT12 in the genetic predisposition to attenuated adenomatous polyposis syndrome.
    5. Results rule out GALNT12 as a major high familial colorectal cancer susceptibility gene. Additional studies are required to provide further evidence about its role as a moderate/low susceptibility gene in familial aggregation of cancer.
      Title: GALNT12 is not a major contributor of familial colorectal cancer type X.
    6. we integrated different computational tools to perform the in silico analysis of clinically significant mutations (nsSNPs/single amino acid change) at both functional and structural levels, found in human GALNT3, GALNT8, GALNT12, and GALNT13 genes.
      Title: Clinically significant missense variants in human GALNT3, GALNT8, GALNT12, and GALNT13 genes: intriguing in silico findings.
    7. Inherited deleterious variants in GALNT12 are associated with CRC susceptibility.
      Title: Inherited deleterious variants in GALNT12 are associated with CRC susceptibility.
    8. inactivating GALNT12 mutations were identified as acquired somatic mutations in a set of 30 microsatellite stable colon tumors.
      Title: Inactivating germ-line and somatic mutations in polypeptide N-acetylgalactosaminyltransferase 12 in human colon cancers.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Inactivating germ-line and somatic mutations in polypeptide N-acetylgalactosaminyltransferase 12 in human colon cancers.
    10. cloning and characterization
      Title: Molecular cloning and characterization of a novel member of the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase family, pp-GalNAc-T12.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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
    Colorectal cancer, susceptibility to, 1
    MedGen: C1837315 OMIM: 608812 GeneReviews: Not available
    		not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2019-09-09)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2019-09-09)

    ClinGen Genome Curation PagePubMed

    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

    • FLJ21212

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables polypeptide N-acetylgalactosaminyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables polypeptide N-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 O-glycan processing TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein O-linked glycosylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Golgi apparatus 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
    polypeptide N-acetylgalactosaminyltransferase 12
    Names
    UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 12
    UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)
    colorectal cancer, susceptibility to 1
    polypeptide GalNAc transferase 12
    pp-GaNTase 12
    protein-UDP acetylgalactosaminyltransferase 12
    NP_078918.3
    XP_006717350.1
    XP_011517320.1
    XP_011517322.1
    XP_016870622.1
    XP_047279827.1
    XP_054219783.1
    XP_054219784.1
    XP_054219785.1
    XP_054219786.1
    XP_054219787.1

    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_028218.1 RefSeqGene

      Range
      4972..47383
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_024642.5 → NP_078918.3  polypeptide N-acetylgalactosaminyltransferase 12

      See identical proteins and their annotated locations for NP_078918.3

      Status: REVIEWED

      Source sequence(s)
      AB078146, AJ132365, AK024865, AL136084, CB243715
      Consensus CDS
      CCDS6737.1
      UniProtKB/Swiss-Prot
      Q5TCF7, Q8IXK2, Q8NG54, Q96CT9, Q9H771
      UniProtKB/TrEMBL
      Q58A70
      Related
      ENSP00000364150.3, ENST00000375011.4
      Conserved Domains (4) summary
      cd02510
      Location:139 → 433
      pp-GalNAc-T; pp-GalNAc-T initiates the formation of mucin-type O-linked glycans
      COG0463
      Location:134 → 429
      WcaA; Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]
      cd00161
      Location:447 → 576
      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:445 → 574
      Ricin_B_lectin; Ricin-type beta-trefoil lectin domain

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      98807670..98850081
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006717287.1 → XP_006717350.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X4

      See identical proteins and their annotated locations for XP_006717350.1

      UniProtKB/Swiss-Prot
      Q8IXK2
      Conserved Domains (3) summary
      cd00161
      Location:150 → 279
      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:148 → 277
      Ricin_B_lectin; Ricin-type beta-trefoil lectin domain
      cl11394
      Location:2 → 136
      Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

    2. XM_011519018.3 → XP_011517320.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X1

      UniProtKB/TrEMBL
      Q58A70
      Conserved Domains (4) summary
      cd02510
      Location:65 → 359
      pp-GalNAc-T; pp-GalNAc-T initiates the formation of mucin-type O-linked glycans
      COG0463
      Location:60 → 355
      WcaA; Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]
      cd00161
      Location:373 → 502
      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:371 → 500
      Ricin_B_lectin; Ricin-type beta-trefoil lectin domain

    3. XM_047423871.1 → XP_047279827.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X4

    4. XM_017015133.1 → XP_016870622.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X2

    5. XM_011519020.2 → XP_011517322.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X3

      Conserved Domains (3) summary
      cd00161
      Location:211 → 340
      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:209 → 338
      Ricin_B_lectin; Ricin-type beta-trefoil lectin domain
      cl11394
      Location:8 → 197
      Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      110979352..111021780
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363811.1 → XP_054219786.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X4

    2. XM_054363808.1 → XP_054219783.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X1

    3. XM_054363812.1 → XP_054219787.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X4

    4. XM_054363809.1 → XP_054219784.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X2

    5. XM_054363810.1 → XP_054219785.1  polypeptide N-acetylgalactosaminyltransferase 12 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IXK2.3 GenPept UniProtKB/Swiss-Prot:Q8IXK2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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