COLGALT2
protein-codingcollagen beta(1-O)galactosyltransferase 2, the group of Collagen beta(1-O)galactosyltransferases
Gene summary
Predicted to enable procollagen galactosyltransferase activity. Predicted to be involved in collagen fibril organization. Predicted to act upstream of or within T cell apoptotic process. Predicted to be located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Jun 2026]
- C1orf17
- GLT25D2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~107.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0007661
Submitter: Labcorp Genetics (formerly Invitae)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to COLGALT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015101.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 96 | 2 | 98 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 99 | 3 | 0 | 102 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055916.1 | 12 | MANE Select | |
| Ensembl | ENSP00000354960.4 | 12 | MANE Select | |
| RefSeq | NP_001290349.1 | 12 | Standard | |
| RefSeq | NP_001290350.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Lysine degradation - Homo sapiens (human)
- Other types of O-glycan biosynthesis - Homo sapiens (human)
- Collagen biosynthesis and modifying enzymes
- Collagen formation
- Extracellular matrix organization
Molecular Function
- protein binding
- procollagen galactosyltransferase activity
Cellular Component
- endoplasmic reticulum lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000361927
- Coding exons
- 12
- Length
- 108068
- Individuals with no LoFs
- 125708
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 40
- Defined
- 125748
- p
- 0.000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.812 | 304 | 347 | 0.877 | 0.0000186 | 4074 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00014 | 0.00012 | rare |
| Latino/Admixed American | 0.00014 | 0.00014 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00020 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Beta-galactosyltransferase that transfers beta-galactose to hydroxylysine residues of collagen. {ECO:0000269|PubMed:19075007}.;
Recessive Scores
- pRec
- 0.0996
Intolerance Scores
- RVIS EVS
- -0.64
- RVIS percentile EVS
- 16.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |