B3GAT1
protein-codingbeta-1,3-glucuronyltransferase 1, the group of Beta-1,3-glucuronyltransferases|CD molecules
Gene summary
The protein encoded by this gene is a member of the glucuronyltransferase gene family. These enzymes exhibit strict acceptor specificity, recognizing nonreducing terminal sugars and their anomeric linkages. This gene product functions as the key enzyme in a glucuronyl transfer reaction during the biosynthesis of the carbohydrate epitope HNK-1 (human natural killer-1, also known as CD57 and LEU7). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]
- CD57
- LEU7
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.7 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 B3GAT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_054025.3. 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 | 1 | 1 | ||||
| missense | 34 | 34 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 0 | 1 | 35 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_473366.1 | 4 | MANE Select | |
| Ensembl | ENSP00000307875.4 | 4 | MANE Select | |
| RefSeq | NP_001354902.1 | 5 | Standard | |
| RefSeq | NP_061114.2 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mannose type O-glycan biosynthesis - Homo sapiens (human)
- Metabolism of carbohydrates
- A tetrasaccharide linker sequence is required for GAG synthesis
- Heparan sulfate/heparin (HS-GAG) metabolism
- Chondroitin sulfate/dermatan sulfate metabolism
Biological Process
- carbohydrate metabolic process
- protein glycosylation
- glycosaminoglycan metabolic process
- chondroitin sulfate proteoglycan biosynthetic process
Molecular Function
- UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity
- galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity
- metal ion binding
Cellular Component
- Golgi membrane
- extracellular region
- endoplasmic reticulum membrane
- integral component of membrane
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000524765
- Coding exons
- 4
- Length
- 33415
- Individuals with no LoFs
- 125719
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125729
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.42 | 138 | 244 | 0.565 | 0.0000182 | 2087 |
| Missense (PolyPhen) | 33 | 90.189 | 0.3659 | 860 | ||
| Synonymous | -0.411 | 121 | 115 | 1.05 | 0.00000922 | 734 |
| Loss of Function | 2.51 | 4 | 14.2 | 0.281 | 9.24e-7 | 124 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000059 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0.000064 | 0.000046 | rare |
| European (Non-Finnish) | 0.000037 | 0.000035 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00019 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on glycoproteins. Can also play a role in glycosaminoglycan biosynthesis. Substrates include asialo- orosomucoid (ASOR), asialo-fetuin, and asialo-neural cell adhesion molecule. Requires sphingomyelin for activity: stearoyl- sphingomyelin was the most effective, followed by palmitoyl- sphingomyelin and lignoceroyl-sphingomyelin. Activity was demonstrated only for sphingomyelin with a saturated fatty acid and not for that with an unsaturated fatty acid, regardless of the length of the acyl group. {ECO:0000250|UniProtKB:O35789}.;
Recessive Scores
- pRec
- 0.448
Intolerance Scores
- LoFtool
- 0.375
- RVIS EVS
- -0.21
- RVIS percentile EVS
- 38.58
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.383
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |