GCNT3
protein-codingglucosaminyl (N-acetyl) transferase 3, mucin type, the group of Glucosaminyl (N-acetyl) transferases/xylosyltransferases
Gene summary
This gene encodes a member of the N-acetylglucosaminyltransferase family. The encoded protein is a beta-6-N-acetylglucosamine-transferase that catalyzes the formation of core 2 and core 4 O-glycans on mucin-type glycoproteins.[provided by RefSeq, Apr 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~45.4 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 GCNT3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004751.3. 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 | 0 | |||||
| missense | 79 | 2 | 81 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 79 | 2 | 1 | 82 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004742.1 | 1 | MANE Select | |
| Ensembl | ENSP00000379377.1 | 1 | MANE Select | |
| Ensembl | ENSP00000453453.1 | 1 | Standard | |
| Ensembl | ENSP00000453774.1 | 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
- mucin core 1 and core 2 <i>O</i>-glycosylation
- terminal <i>O</i>-glycans residues modification
Biological Process
- immunoglobulin production in mucosal tissue
- carbohydrate metabolic process
- protein O-linked glycosylation
- O-glycan processing
- tissue morphogenesis
Molecular Function
- beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
- N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity
- acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
Cellular Component
- Golgi membrane
- membrane
- integral component of membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000396065
- Coding exons
- 1
- Length
- 45365
- Individuals with no LoFs
- 124852
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 892
- Defined
- 125746
- p
- 0.00356
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.65 | 300 | 230 | 1.31 | 0.0000123 | 2904 |
| Missense (PolyPhen) | 106 | 92.782 | 1.1425 | 1186 | ||
| Synonymous | -4.10 | 137 | 88.1 | 1.56 | 0.00000466 | 831 |
| Loss of Function | 0.339 | 13 | 14.4 | 0.904 | 8.94e-7 | 170 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0031 | 0.0031 | notable |
| Latino/Admixed American | 0.0020 | 0.0020 | notable |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.010 | 0.010 | notable |
| European (Non-Finnish) | 0.0041 | 0.0040 | notable |
| South Asian | 0.0019 | 0.0019 | notable |
| Other | 0.0042 | 0.0041 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Glycosyltransferase that can synthesize all known mucin beta 6 N-acetylglucosaminides. Mediates core 2 and core 4 O-glycan branching, 2 important steps in mucin-type biosynthesis. Has also I-branching enzyme activity by converting linear into branched poly-N-acetyllactosaminoglycans, leading to introduce the blood group I antigen during embryonic development. {ECO:0000269|PubMed:9915862}.;
Recessive Scores
- pRec
- 0.0979
Intolerance Scores
- LoFtool
- 0.881
- RVIS EVS
- 0.45
- RVIS percentile EVS
- 77.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.258
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |