COLGALT1

collagen beta(1-O)galactosyltransferase 1, the group of Collagen beta(1-O)galactosyltransferases

Basic information

Region (hg38): 19:17555649-17583162

Previous symbols: [ "GLT25D1" ]

Links

ENSG00000130309 ∙ NCBI:79709 ∙ OMIM:617531 ∙ HGNC:26182 ∙ Uniprot:Q8NBJ5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• brain small vessel disease 3 (Limited), mode of inheritance: AR
• brain small vessel disease 3 (Moderate), mode of inheritance: AR
• brain small vessel disease 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Brain small vessel disease 3	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	30412317

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COLGALT1 gene.

• not_provided (162 variants)
• Inborn_genetic_diseases (125 variants)
• COLGALT1-related_disorder (22 variants)
• Brain_small_vessel_disease_3 (10 variants)
• Vascular_dementia (1 variants)
• Dilated_cardiomyopathy_1NN (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COLGALT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024656.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				51	11	62
missense	3	1	159	7		170
nonsense			2			2
start loss						0
frameshift	3					3
splice donor/acceptor (+/-2bp)			1			1
Total	6	1	162	58	11

Highest pathogenic variant AF is 0.000006565902

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COLGALT1	protein_coding	protein_coding	ENST00000252599	12	27569

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.91e-8	0.967	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.523	337	365	0.923	0.0000253	3993
Missense in Polyphen		107	113.27	0.94464		1087
Synonymous	0.221	146	149	0.977	0.0000105	1254
Loss of Function	2.06	16	27.7	0.578	0.00000134	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000610	0.000605
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.000218	0.000217
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: 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 (PubMed:27402836). {ECO:0000269|PubMed:19075007, ECO:0000269|PubMed:22216269, ECO:0000269|PubMed:27402836}.
• Pathway: Lysine degradation - Homo sapiens (human);Other types of O-glycan biosynthesis - Homo sapiens (human);Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: -1.5
• rvis_percentile_EVS: 3.57

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.476
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Colgalt1
• Phenotype: skeleton phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: positive regulation of collagen fibril organization
• Cellular component: endoplasmic reticulum lumen;membrane
• Molecular function: procollagen galactosyltransferase activity