GCNT1
protein-codingglucosaminyl (N-acetyl) transferase 1, the group of Glucosaminyl (N-acetyl) transferases/xylosyltransferases
Gene summary
This gene is a member of the beta-1,6-N-acetylglucosaminyltransferase gene family. It is essential to the formation of Gal beta 1-3(GlcNAc beta 1-6)GalNAc structures and the core 2 O-glycan branch. The gene coding this enzyme was originally mapped to 9q21, but was later localized to 9q13. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
- NACGT2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~231.4 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 GCNT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001490.5. 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 | 1 | 1 | 2 | |||
| missense | 50 | 2 | 52 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 50 | 3 | 1 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001481.2 | 1 | MANE Select | |
| Ensembl | ENSP00000365920.4 | 1 | MANE Select | |
| RefSeq | NP_001091102.1 | 1 | Standard | |
| RefSeq | NP_001091103.1 | 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)
- Globo Sphingolipid Metabolism
- Post-translational protein modification
- Metabolism of proteins
- mucin core 1 and core 2 <i>O</i>-glycosylation
Biological Process
- glycoprotein biosynthetic process
- O-glycan processing
- response to insulin
- tissue morphogenesis
- leukocyte tethering or rolling
Molecular Function
- beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity
- protein binding
Cellular Component
- Golgi membrane
- extracellular space
- trans-Golgi network
- integral component of membrane
- Golgi cisterna
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000442371
- Coding exons
- 1
- Length
- 87581
- Individuals with no LoFs
- 125693
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 54
- Defined
- 125747
- p
- 0.000215
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.791 | 201 | 235 | 0.855 | 0.0000131 | 2857 |
| Missense (PolyPhen) | 73 | 96.931 | 0.75311 | 1212 | ||
| Synonymous | -0.189 | 91 | 88.7 | 1.03 | 0.00000523 | 800 |
| Loss of Function | 1.78 | 6 | 12.9 | 0.466 | 7.20e-7 | 165 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00040 | 0.00040 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Glycosyltransferase that catalyzes the transfer of an N- acetylglucosamine moiety onto mucin-type core 1 O-glycan to form the branched mucin-type core 2 O-glycan. Mucin-type core 2 O- glycans play an important role in leukocyte extravasation as they serve as scaffolds for the display of the selectin ligand sialyl Lewis X by leukocytes. {ECO:0000269|PubMed:23027862}.;
Recessive Scores
- pRec
- 0.159
Intolerance Scores
- LoFtool
- 0.658
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 75.43
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.294
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |