COLGALT2 collagen beta(1-O)galactosyltransferase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: COLGALT2provided by HGNC
Official Full Name: collagen beta(1-O)galactosyltransferase 2provided by HGNC
Primary source: HGNC:HGNC:16790
See related: Ensembl:ENSG00000198756 MIM:617533; AllianceGenome:HGNC:16790
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: C1orf17; GLT25D2; ColGalT 2
Summary: Predicted to enable procollagen galactosyltransferase activity. Predicted to be involved in collagen fibril organization. Predicted to be located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in brain (RPKM 11.8), adrenal (RPKM 2.5) and 7 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q25.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (183929662..184037728, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (183289012..183400897, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (183898796..184006862, complement)

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 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?

Mediation of the Same Epigenetic and Transcriptional Effect by Independent Osteoarthritis Risk-Conferring Alleles on a Shared Target Gene, COLGALT2.
Title: Mediation of the Same Epigenetic and Transcriptional Effect by Independent Osteoarthritis Risk-Conferring Alleles on a Shared Target Gene, COLGALT2.
Osteoarthritis genetic risk acting on the galactosyltransferase gene COLGALT2 has opposing functional effects in articulating joint tissues.
Title: Osteoarthritis genetic risk acting on the galactosyltransferase gene COLGALT2 has opposing functional effects in articulating joint tissues.
COLGALT2 is overexpressed in ovarian cancer and interacts with PLOD3.
Title: COLGALT2 is overexpressed in ovarian cancer and interacts with PLOD3.
Genetic and Epigenetic Interplay Within a COLGALT2 Enhancer Associated With Osteoarthritis.
Title: Genetic and Epigenetic Interplay Within a COLGALT2 Enhancer Associated With Osteoarthritis.
Observational study of gene-disease association. (HuGE Navigator)
Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Two collagen beta(1-O)galactosyltransferases corresponding to the GLT25D1 and GLT25D2 proteins were identified.
Title: Core glycosylation of collagen is initiated by two beta(1-O)galactosyltransferases.

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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

EBI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. 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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Addition of peripheral sugar residues such as galactose, N-acetylglucosamine, and sialic acid to HIV-1 gp120 is processed by specific glycosyltransferase	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S1821E (e-PCR)
- UniSTS:150794

SHGC-76043 (e-PCR)
- UniSTS:1293

D1S3425 (e-PCR)
- UniSTS:14145

SHGC-76030 (e-PCR)
- UniSTS:15946

RH122702 (e-PCR)
- UniSTS:133980

SHGC-86155 (e-PCR)
- UniSTS:104803

SHGC-156106 (e-PCR)
- UniSTS:182117

SHGC-142028 (e-PCR)
- UniSTS:171204

D1S1769E (e-PCR)
- UniSTS:77798

SHGC-148815 (e-PCR)
- UniSTS:176626

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables procollagen galactosyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables procollagen galactosyltransferase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in collagen fibril organization	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info

General protein information

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Preferred Names: procollagen galactosyltransferase 2

Names: glycosyltransferase 25 domain containing 2; glycosyltransferase 25 family member 2; hydroxylysine galactosyltransferase 2

NP_001290349.1

EC 2.4.1.50

NP_001290350.1

EC 2.4.1.50

NP_055916.1

EC 2.4.1.50

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.

mRNA and Protein(s)

NM_001303420.2 → NP_001290349.1 procollagen galactosyltransferase 2 isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate 3' terminal exon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK293973, BC035672

Consensus CDS

CCDS91126.1

UniProtKB/TrEMBL

A0A3B3IT37, B4DF84

Related

ENSP00000497601.1, ENST00000649786.1

Conserved Domains (2) summary

cl01298
Location:341 → 526

Glyco_transf_25; Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of ...

cl11394
Location:62 → 175

Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold
NM_001303421.2 → NP_001290350.1 procollagen galactosyltransferase 2 isoform 3

See identical proteins and their annotated locations for NP_001290350.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' terminal exon, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AB011156, AK095192, BQ477485

UniProtKB/TrEMBL

B3KT92

Conserved Domains (1) summary

cl01298
Location:221 → 406

Glyco_transf_25; Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of ...
NM_015101.4 → NP_055916.1 procollagen galactosyltransferase 2 isoform 1precursor

See identical proteins and their annotated locations for NP_055916.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AB011156, BC035672, BQ477485

Consensus CDS

CCDS1360.1

UniProtKB/Swiss-Prot

O60327, Q8IYK4, Q9BZR0

UniProtKB/TrEMBL

B4DF84

Related

ENSP00000354960.4, ENST00000361927.9

Conserved Domains (2) summary

pfam13704
Location:62 → 175

Glyco_tranf_2_4; Glycosyl transferase family 2

cl01298
Location:341 → 526

Glyco_transf_25; Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of ...