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

Gene ID: 79695, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (98807670..98850081)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (110979352..111021780)
105.20220307 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
  • 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. Evidence for GALNT12 as a moderate penetrance gene for colorectal cancer. Evans DR, et al. Hum Mutat, 2018 Aug. PMID 29749045, Free PMC Article
  3. Role of GALNT12 in the genetic predisposition to attenuated adenomatous polyposis syndrome. Lorca V, et al. PLoS One, 2017. PMID 29095867, Free PMC Article
  4. GALNT12 is not a major contributor of familial colorectal cancer type X. Seguí N, et al. Hum Mutat, 2014 Jan. PMID 24115450
  5. Inherited deleterious variants in GALNT12 are associated with CRC susceptibility. Clarke E, et al. Hum Mutat, 2012 Jul. PMID 22461326

See all (24) 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
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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
  
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_2023_10

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

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