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

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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

GALNT2 expression is associated with glucose control and serum metabolites in patients with type 2 diabetes.
Title: GALNT2 expression is associated with glucose control and serum metabolites in patients with type 2 diabetes.
GALNT2, an O-glycosylating enzyme, is a critical regulator of radioresistance of non-small cell lung cancer: evidence from an integrated multi-omics analysis.
Title: GALNT2, an O-glycosylating enzyme, is a critical regulator of radioresistance of non-small cell lung cancer: evidence from an integrated multi-omics analysis.
Leveraging Genetics to Address the Role of GALNT2 on Atherogenic Dyslipidemia.
Title: Leveraging Genetics to Address the Role of GALNT2 on Atherogenic Dyslipidemia.
GALNT2 sustains glioma stem cells by promoting CD44 expression.
Title: GALNT2 sustains glioma stem cells by promoting CD44 expression.
GALNT2 promotes invasiveness of colorectal cancer cells partly through AXL.
Title: GALNT2 promotes invasiveness of colorectal cancer cells partly through AXL.
O-Glycosylating Enzyme GALNT2 Predicts Worse Prognosis in Cervical Cancer.
Title: O-Glycosylating Enzyme GALNT2 Predicts Worse Prognosis in Cervical Cancer.
GALNT2 rs4846914 SNP Is Associated with Obesity, Atherogenic Lipid Traits, and ANGPTL3 Plasma Level.
Title: GALNT2 rs4846914 SNP Is Associated with Obesity, Atherogenic Lipid Traits, and ANGPTL3 Plasma Level.
Role of GALNT2 on Insulin Sensitivity, Lipid Metabolism and Fat Homeostasis.
Title: Role of GALNT2 on Insulin Sensitivity, Lipid Metabolism and Fat Homeostasis.
Maternal GALNT2 Variations Affect Blood Pressure, Atherogenic Index, and Fetal Growth, Depending on BMI in Gestational Diabetes Mellitus.
Title: Maternal GALNT2 Variations Affect Blood Pressure, Atherogenic Index, and Fetal Growth, Depending on BMI in Gestational Diabetes Mellitus.
GALNT2 Gene Variant rs4846914 Is Associated with Insulin and Insulin Resistance Depending on BMI in PCOS Patients: a Case-Control Study.
Title: GALNT2 Gene Variant rs4846914 Is Associated with Insulin and Insulin Resistance Depending on BMI in PCOS Patients: a Case-Control Study.

Submit: New GeneRIF Correction See all GeneRIFs (49)

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
Congenital disorder of glycosylation, type iit MedGen: C5394387 OMIM: 618885 GeneReviews: Not available	not available

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL009628 (e-PCR)
- UniSTS:9225

G19686 (e-PCR)
- UniSTS:27929

A001V25 (e-PCR)
- UniSTS:27930

RH64521 (e-PCR)
- UniSTS:33865

AL034013 (e-PCR)
- UniSTS:93527

RH18350 (e-PCR)
- UniSTS:17806

AL009748 (e-PCR)
- UniSTS:39066

RH12675 (e-PCR)
- UniSTS:7332

D13S1146E (e-PCR)
- UniSTS:153786

SHGC-79753 (e-PCR)
- UniSTS:101080

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

Process	Evidence Code	Pubs
involved_in O-glycan processing	IDA Inferred from Direct Assay more info	PubMed
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
involved_in protein O-linked glycosylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein O-linked glycosylation via serine	IDA Inferred from Direct Assay more info	PubMed
involved_in protein O-linked glycosylation via threonine	IDA Inferred from Direct Assay more info	PubMed
involved_in protein maturation	IDA Inferred from Direct Assay 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 more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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

EC 2.4.1.41

NP_004472.1

EC 2.4.1.41

XP_016856453.2

EC 2.4.1.41

XP_054191834.1

EC 2.4.1.41

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

NG_011854.2 RefSeqGene

Range

14450..229334

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001291866.2 → NP_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:101 → 396

pp-GalNAc-T; pp-GalNAc-T initiates the formation of mucin-type O-linked glycans

cd00161
Location:418 → 527

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:408 → 525

Ricin_B_lectin; Ricin-type beta-trefoil lectin domain
NM_004481.5 → NP_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:139 → 434

pp-GalNAc-T; pp-GalNAc-T initiates the formation of mucin-type O-linked glycans

pfam00652
Location:446 → 563

Ricin_B_lectin; Ricin-type beta-trefoil lectin domain

RNA

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