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 (Strong), mode of inheritance: AR
• brain small vessel disease 3 (Moderate), 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 (1 variants)
• Inborn genetic diseases (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				41	10	51
missense			102	3		105
nonsense			1			1
start loss						0
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			9	11		20
non coding			2	15	2	19
Total	2	0	105	59	12

Highest pathogenic variant AF is 0.00000661

Variants in COLGALT1

This is a list of pathogenic ClinVar variants found in the COLGALT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-17555711-G-A			Uncertain significance (Jul 01, 2024)
19-17555726-C-T		Inborn genetic diseases	Uncertain significance (May 09, 2022)
19-17555729-CGCGCGGGCCGGCG-C		Inborn genetic diseases	Pathogenic (Sep 16, 2021)
19-17555733-C-G			Uncertain significance (Jul 26, 2022)
19-17555742-G-C		Inborn genetic diseases	Uncertain significance (Oct 16, 2024)
19-17555744-C-G			Uncertain significance (Aug 04, 2023)
19-17555747-G-C		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
19-17555753-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 11, 2023)
19-17555778-T-C		Inborn genetic diseases	Uncertain significance (Oct 02, 2023)
19-17555785-G-C			Likely benign (Aug 04, 2023)
19-17555799-G-T			Uncertain significance (Aug 10, 2023)
19-17555809-G-A		COLGALT1-related disorder	Likely benign (Dec 30, 2021)
19-17555811-G-T		Inborn genetic diseases	Benign/Likely benign (Jan 04, 2024)
19-17555823-A-C		Inborn genetic diseases	Uncertain significance (Apr 29, 2024)
19-17555827-C-T			Benign (Jan 31, 2024)
19-17555845-C-G		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
19-17555848-G-A		COLGALT1-related disorder	Likely benign (Mar 10, 2023)
19-17555854-G-A			Likely benign (Jan 22, 2024)
19-17555867-C-T			Uncertain significance (Aug 08, 2022)
19-17555875-G-A			Likely benign (Jul 26, 2023)
19-17555875-G-T			Likely benign (Oct 22, 2023)
19-17555881-C-T			Likely benign (Apr 01, 2022)
19-17555882-G-C		Inborn genetic diseases	Uncertain significance (Aug 20, 2024)
19-17555886-T-C		Brain small vessel disease 3	Likely pathogenic (-)
19-17555930-G-T			Uncertain significance (Feb 22, 2022)

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