Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	79709
Gene name	Collagen beta(1-O)galactosyltransferase 1
Gene symbol	COLGALT1
Synonyms (NCBI Gene)	BSVD3ColGalT 1GLT25D1
Chromosome	19
Chromosome location	19p13.11
Summary	The protein encoded by this gene is one of two enzymes that transfers galactose moieties to hydroxylysine residues of collagen and mannose binding lectin. This gene is constitutively expressed and encodes a soluble protein that localizes to the endoplasmi

Show/Hide all (4)

SNP ID	Visualize variation	Clinical significance	Consequence
rs181844791	G>C,T	Pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant
rs1478523191	T>G	Pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant
rs1568481204	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1568481244	G>C	Pathogenic	Coding sequence variant, missense variant

Show/Hide all (37)

miRTarBase ID	miRNA	Experiments	Reference
MIRT020546	hsa-miR-155-5p	Proteomics	18668040
MIRT022180	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT027402	hsa-miR-98-5p	Microarray	19088304
MIRT037931	hsa-miR-532-3p	CLASH	23622248
MIRT037553	hsa-miR-744-5p	CLASH	23622248
MIRT479000	hsa-miR-125a-3p	PAR-CLIP	23592263
MIRT478999	hsa-miR-764	PAR-CLIP	23592263
MIRT478998	hsa-miR-3934-5p	PAR-CLIP	23592263
MIRT478997	hsa-miR-6515-3p	PAR-CLIP	23592263
MIRT478996	hsa-miR-4786-3p	PAR-CLIP	23592263
MIRT478995	hsa-miR-3650	PAR-CLIP	23592263
MIRT478993	hsa-miR-4648	PAR-CLIP	23592263
MIRT478994	hsa-miR-1233-5p	PAR-CLIP	23592263
MIRT478992	hsa-miR-6778-5p	PAR-CLIP	23592263
MIRT478991	hsa-miR-4654	PAR-CLIP	23592263
MIRT478990	hsa-miR-4769-5p	PAR-CLIP	23592263
MIRT478989	hsa-miR-3911	PAR-CLIP	23592263
MIRT478988	hsa-miR-644a	PAR-CLIP	23592263
MIRT478987	hsa-miR-6867-5p	PAR-CLIP	23592263
MIRT478986	hsa-miR-147a	PAR-CLIP	23592263
MIRT020546	hsa-miR-155-5p	HITS-CLIP	22473208
MIRT020546	hsa-miR-155-5p	HITS-CLIP	22473208
MIRT479000	hsa-miR-125a-3p	PAR-CLIP	23592263
MIRT478999	hsa-miR-764	PAR-CLIP	23592263
MIRT478998	hsa-miR-3934-5p	PAR-CLIP	23592263
MIRT478997	hsa-miR-6515-3p	PAR-CLIP	23592263
MIRT478996	hsa-miR-4786-3p	PAR-CLIP	23592263
MIRT478995	hsa-miR-3650	PAR-CLIP	23592263
MIRT478993	hsa-miR-4648	PAR-CLIP	23592263
MIRT478994	hsa-miR-1233-5p	PAR-CLIP	23592263
MIRT478992	hsa-miR-6778-5p	PAR-CLIP	23592263
MIRT478991	hsa-miR-4654	PAR-CLIP	23592263
MIRT478990	hsa-miR-4769-5p	PAR-CLIP	23592263
MIRT478989	hsa-miR-3911	PAR-CLIP	23592263
MIRT478988	hsa-miR-644a	PAR-CLIP	23592263
MIRT478987	hsa-miR-6867-5p	PAR-CLIP	23592263
MIRT478986	hsa-miR-147a	PAR-CLIP	23592263

Show/Hide all (14)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	IDA	20470363
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	TAS
GO:0006493	Process	Protein O-linked glycosylation	IMP	27402836
GO:0016020	Component	Membrane	HDA	19946888
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0030199	Process	Collagen fibril organization	TAS
GO:0050211	Function	Procollagen galactosyltransferase activity	IBA
GO:0050211	Function	Procollagen galactosyltransferase activity	IEA
GO:0050211	Function	Procollagen galactosyltransferase activity	IMP	27402836
GO:0050211	Function	Procollagen galactosyltransferase activity	TAS
GO:1904028	Process	Positive regulation of collagen fibril organization	IMP	27402836

MIM	HGNC	e!Ensembl
617531	26182	ENSG00000130309

Q8NBJ5

Protein name

Procollagen galactosyltransferase 1 (EC 2.4.1.50) (Collagen beta(1-O)galactosyltransferase 1) (ColGalT 1) (Glycosyltransferase 25 family member 1) (Hydroxylysine galactosyltransferase 1)

Protein function

Beta-galactosyltransferase that transfers beta-galactose to hydroxylysine residues of type I collagen (PubMed:19075007, PubMed:22216269, PubMed:27402836). By acting on collagen glycosylation, facilitates the formation of collagen triple helix (P

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13704	Glyco_tranf_2_4	61 → 181		Family
PF01755	Glyco_transf_25	340 → 525	Glycosyltransferase family 25 (LPS biosynthesis protein)	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous with higher levels in placenta, heart, lung and spleen. {ECO:0000269|PubMed:19075007}.

Sequence

MAAAPRAGRRRGQPLLALLLLLLAPLPPGAPPGADAYFPEERWSPESPLQAPRVLIALLA
RNAAHALPTTLGALERLRHPRERTALWVATDHNMDNTSTVLREWLVAVKSLYHSVEWRPA
EEPRSYPDEEGPKHWSDSRYEHVMKLRQAALKSARDMWADYILFVDADNLILNPDTLSLL
IAENKTVVAPMLDSRAAYSNFWCGMTSQGYYKRTPAYIPIRKRDRRGCFAVPMVHSTFLI
DLRKAASRNLAFYPPHPDYTWSFDDIIVFAFSCKQAEVQMYVCNKEEYGFLPVPLRAHST
LQDEAESFMHVQLEVMVKHPPAEPSRFISAPTKTPDKMGFDEVFMINLRRRQDRRERMLR
ALQAQEIECRLVEAVDGKAMNTSQVEALGIQMLPGYRDPYHGRPLTKGELGCFLSHYNIW
KEVVDRGLQKSLVFEDDLRFEIFFKRRLMNLMRDVEREGLDWDLIYVGRKRMQVEHPEKA
VPRVRNLVEADYSYWTLAYVISLQGARKLLAAEPLSKMLPVDEFLPVMFDKHPVSEYKAH
FSLRNLHAFSVEPLLIYPTHYTGDDGYVSDTETSVVWNNEHVKTDWDRAKSQKMREQQAL
SREAKNSDVLQSPLDSAARDEL

Sequence length

622

Interactions

View interactions

	KEGG		Reactome
	Lysine degradation Other types of O-glycan biosynthesis Metabolic pathways		Collagen biosynthesis and modifying enzymes

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Brain small vessel disease 3	Pathogenic; Likely pathogenic	rs1478523191, rs1568481204, rs181844791, rs1568481244, rs2076207767	RCV000761581 RCV000761582 RCV000761583 RCV000761584 RCV001175209	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLGALT1-related disorder	Benign; Uncertain significance; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA, VASCULAR	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Vascular dementia	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (17)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Acquired porencephaly	Acquired Porencephaly	BEFREE	30822656		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	35842702	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral Small Vessel Diseases	Cerebral Microangiopathy	BEFREE	30412317		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral Small Vessel Diseases	Cerebral microangiopathy	Pubtator	35307828	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	35307828	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital porencephaly	Congenital Porencephaly	BEFREE	30822656		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukoencephalopathy	Leukoencephalopathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Narcolepsy	Narcolepsy	GWASDB_DG	19629137		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	27402836		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	Pubtator	27402836	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Porencephaly	Porencephaly	BEFREE	30822656		★★★★★ ★☆☆☆☆ Found in Text Mining only
SIMPSON-GOLABI-BEHMEL SYNDROME, TYPE 1	Simpson-Golabi-Behmel Syndrome	BEFREE	28428430		★★★★★ ★☆☆☆☆ Found in Text Mining only
Spastic Quadriplegia	Spastic Quadriplegia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Stroke	Stroke	Pubtator	32106772	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	40312703	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

COLGALT1 (collagen beta(1-O)galactosyltransferase 1)