B3GNT3
protein-codingUDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3, the group of Beta 3-glycosyltransferases
Gene summary
This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein and contains a signal anchor that is not cleaved. It prefers the substrates of lacto-N-tetraose and lacto-N-neotetraose, and is involved in the biosynthesis of poly-N-acetyllactosamine chains and the biosynthesis of the backbone structure of dimeric sialyl Lewis a. It plays dominant roles in L-selectin ligand biosynthesis, lymphocyte homing and lymphocyte trafficking. [provided by RefSeq, Jul 2008]
- TMEM3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.7 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 B3GNT3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014256.4. 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 | 2 | |||
| missense | 48 | 8 | 1 | 57 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 48 | 9 | 2 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055071.2 | 2 | MANE Select | |
| Ensembl | ENSP00000321874.5 | 2 | MANE Select | |
| Ensembl | ENSP00000472638.1 | 2 | Standard | |
| Ensembl | ENSP00000472638.1 | 2 | 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)
- Metabolism of carbohydrates
- Keratan sulfate biosynthesis
- Keratan sulfate/keratin metabolism
- Glycosaminoglycan metabolism
Biological Process
- protein glycosylation
- O-glycan processing
- keratan sulfate biosynthetic process
- poly-N-acetyllactosamine biosynthetic process
Molecular Function
- acetylgalactosaminyltransferase activity
- UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity
- N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity
- beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity
Cellular Component
- Golgi membrane
- endoplasmic reticulum
- Golgi apparatus
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000318683
- Coding exons
- 2
- Length
- 18255
- Individuals with no LoFs
- 125626
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125640
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.52 | 187 | 255 | 0.733 | 0.0000179 | 2381 |
| Missense (PolyPhen) | 49 | 99.012 | 0.49489 | 997 | ||
| Synonymous | 1.10 | 99 | 114 | 0.869 | 0.00000782 | 807 |
| Loss of Function | 2.43 | 1 | 8.76 | 0.114 | 3.75e-7 | 88 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00012 | 0.00011 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Beta-1,3-N-acetylglucosaminyltransferase involved in the synthesis of poly-N-acetyllactosamine. Has activity for type 2 oligosaccharides (PubMed:11042166). Also acts as a core1-1,3-N- acetylglucosaminyltransferase (Core1-beta3GlcNAcT) to form the 6- sulfo sialyl Lewis x on extended core1 O-glycans (PubMed:11439191). {ECO:0000269|PubMed:11042166, ECO:0000269|PubMed:11439191}.;
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- LoFtool
- 0.435
- RVIS EVS
- 0.53
- RVIS percentile EVS
- 80.82
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.334
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |