COLGALT2

collagen beta(1-O)galactosyltransferase 2, the group of Collagen beta(1-O)galactosyltransferases

Basic information

Region (hg38): 1:183929853-184037729

Previous symbols: [ "C1orf17", "GLT25D2" ]

Links

ENSG00000198756 ∙ NCBI:23127 ∙ OMIM:617533 ∙ HGNC:16790 ∙ Uniprot:Q8IYK4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COLGALT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COLGALT2 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						0
missense			51			51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	0	0

Variants in COLGALT2

This is a list of pathogenic ClinVar variants found in the COLGALT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-183938790-C-T		not specified	Uncertain significance (Aug 09, 2021)
1-183938834-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-183938855-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-183938858-G-A		not specified	Uncertain significance (Jun 22, 2024)
1-183938886-C-T		not specified	Uncertain significance (Jul 08, 2022)
1-183938892-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-183938907-C-T		not specified	Uncertain significance (Sep 22, 2023)
1-183938910-A-G		not specified	Uncertain significance (Aug 14, 2023)
1-183938981-G-T		not specified	Uncertain significance (Jan 03, 2024)
1-183939014-T-C		not specified	Uncertain significance (Oct 17, 2023)
1-183939033-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-183940582-C-T		not specified	Uncertain significance (May 09, 2023)
1-183940599-A-G		not specified	Uncertain significance (May 11, 2022)
1-183940662-T-C		not specified	Uncertain significance (Jan 29, 2024)
1-183940711-C-T		not specified	Uncertain significance (Jan 25, 2023)
1-183940777-T-C		not specified	Uncertain significance (Dec 28, 2022)
1-183944274-C-T		not specified	Uncertain significance (May 15, 2023)
1-183944302-T-G		not specified	Uncertain significance (Mar 01, 2024)
1-183944314-G-C		not specified	Uncertain significance (Dec 21, 2023)
1-183944315-A-T		not specified	Uncertain significance (Aug 15, 2023)
1-183945449-A-G		not specified	Uncertain significance (Jan 22, 2024)
1-183945493-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-183945506-C-T		not specified	Uncertain significance (May 18, 2023)
1-183951028-A-T		not specified	Uncertain significance (Feb 28, 2023)
1-183951092-G-C		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COLGALT2	protein_coding	protein_coding	ENST00000361927	12	108068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-10	0.917	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.812	304	347	0.877	0.0000186	4074
Missense in Polyphen		86	95.128	0.90405		1066
Synonymous	0.751	125	136	0.918	0.00000734	1208
Loss of Function	1.94	21	33.1	0.635	0.00000175	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000285	0.000268
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000218	0.000217
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000218	0.000217
South Asian	0.000197	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Beta-galactosyltransferase that transfers beta-galactose to hydroxylysine residues of collagen. {ECO:0000269|PubMed:19075007}.
• 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: 0.0996

Intolerance Scores

• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.63

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.486
• ghis: 0.521

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: Colgalt2

Gene ontology

• Cellular component: endoplasmic reticulum lumen
• Molecular function: protein binding;procollagen galactosyltransferase activity