B3GALT2
protein-codingbeta-1,3-galactosyltransferase 2, the group of Beta 3-glycosyltransferases
Gene summary
This gene is a member of the beta-1,3-galactosyltransferase (beta3GalT) gene family. This family encodes type II membrane-bound glycoproteins with diverse enzymatic functions using different donor substrates (UDP-galactose and UDP-N-acetylglucosamine) and different acceptor sugars (N-acetylglucosamine, galactose, N-acetylgalactosamine). The beta3GalT genes are distantly related to the Drosophila Brainiac gene and have the protein coding sequence contained in a single exon. The beta3GalT proteins also contain conserved sequences not found in the beta4GalT or alpha3GalT proteins. The carbohydrate chains synthesized by these enzymes are designated as type 1, whereas beta4GalT enzymes synthesize type 2 carbohydrate chains. The ratio of type 1:type 2 chains changes during embryogenesis. By sequence similarity, the beta3GalT genes fall into at least two groups: beta3GalT4 and 4 other beta3GalT genes (beta3GalT1-3, beta3GalT5). This gene encodes a protein that functions in N-linked glycoprotein glycosylation and shows strict donor substrate specificity for UDP-galactose. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~7.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to B3GALT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003783.3. 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 | 2 | 3 | 5 | |||
| missense | 42 | 1 | 43 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 4 | 0 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003774.1 | 1 | MANE Select | |
| Ensembl | ENSP00000356404.4 | 1 | MANE Select | |
| Ensembl | ENSP00000628499.1 | 1 | Standard | |
| Ensembl | ENSP00000628499.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human)
Biological Process
- protein glycosylation
- protein N-linked glycosylation
- galactosylceramide biosynthetic process
- oligosaccharide biosynthetic process
Molecular Function
- acetylgalactosaminyltransferase activity
- UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity
- glucosaminylgalactosylglucosylceramide beta-galactosyltransferase activity
Cellular Component
- Golgi membrane
- endoplasmic reticulum
- Golgi apparatus
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000367434
- Coding exons
- 1
- Length
- 7610
- Individuals with no LoFs
- 125724
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 125730
- p
- 0.0000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.62 | 163 | 232 | 0.701 | 0.0000121 | 2787 |
| Missense (PolyPhen) | 37 | 79.159 | 0.46741 | 914 | ||
| Synonymous | -0.643 | 85 | 77.8 | 1.09 | 0.00000362 | 806 |
| Loss of Function | 3.26 | 2 | 16.1 | 0.124 | 0.00000100 | 179 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Beta-1,3-galactosyltransferase that transfers galactose from UDP-galactose to substrates with a terminal beta-N- acetylglucosamine (beta-GlcNAc) residue. Can also utilize substrates with a terminal galactose residue, albeit with lower efficiency. Involved in the biosynthesis of the carbohydrate moieties of glycolipids and glycoproteins. Inactive towards substrates with terminal alpha-N-acetylglucosamine (alpha-GlcNAc) or alpha-N-acetylgalactosamine (alpha-GalNAc) residues. {ECO:0000269|PubMed:9417100, ECO:0000269|PubMed:9582303}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- LoFtool
- 0.257
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 34.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.394
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |