B3GNT6
protein-codingUDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6, the group of Beta 3-glycosyltransferases
Gene summary
The protein encoded by this gene is a beta-1,3-N-acetylglucosaminyltransferase that adds an N-acetylglucosamine moiety to N-acetylgalactosamine-modified serine or threonine. The encoded enzyme is responsible for creating the core 3 structure of O-glycans, which are important components of mucin-type glycoproteins. [provided by RefSeq, Dec 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~7.6 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 B3GNT6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_138706.5. 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 | 0 | |||||
| missense | 1 | 61 | 62 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 61 | 0 | 0 | 62 |
Highest pathogenic variant AF is 0.0000034652292
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_619651.3 | 1 | MANE Select | |
| Ensembl | ENSP00000484640.1 | 1 | MANE Select | |
| Ensembl | ENSP00000435628.1 | 1 | Standard | |
| Ensembl | ENSP00000525046.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mucin type O-glycan biosynthesis - Homo sapiens (human)
- Post-translational protein modification
- Metabolism of proteins
- O-Glycan biosynthesis
- O-linked glycosylation of mucins
Biological Process
- protein glycosylation
- glycoprotein biosynthetic process
- O-glycan processing
- O-glycan processing, core 3
- poly-N-acetyllactosamine biosynthetic process
Molecular Function
- acetylgalactosaminyltransferase activity
- galactosyltransferase 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
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000533140
- Coding exons
- 1
- Length
- 7712
- Individuals with no LoFs
- 124594
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 48
- Defined
- 124642
- p
- 0.000193
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.216 | 247 | 238 | 1.04 | 0.0000152 | 2359 |
| Missense (PolyPhen) | 96 | 85.173 | 1.1271 | 918 | ||
| Synonymous | 0.400 | 108 | 113 | 0.952 | 0.00000782 | 826 |
| Loss of Function | -0.935 | 12 | 8.98 | 1.34 | 4.47e-7 | 82 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00040 | 0.00032 | rare |
| Latino/Admixed American | 0.00037 | 0.00035 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00023 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00021 | 0.00019 | rare |
| South Asian | 0.00021 | 0.00020 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Beta-1,3-N-acetylglucosaminyltransferase that synthesizes the core 3 structure of the O-glycan, an important precursor in the biosynthesis of mucin-type glycoproteins. Plays an important role in the synthesis of mucin-type O-glycans in digestive organs.;
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |