MGAT5
protein-codingalpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase, the group of MicroRNA protein coding host genes|Mannosyl-glycoprotein N-acetylglucosaminyltransferases
Gene summary
The protein encoded by this gene belongs to the glycosyltransferase family. It catalyzes the addition of beta-1,6-N-acetylglucosamine to the alpha-linked mannose of biantennary N-linked oligosaccharides present on the newly synthesized glycoproteins. It is one of the most important enzymes involved in the regulation of the biosynthesis of glycoprotein oligosaccharides. Alterations of the oligosaccharides on cell surface glycoproteins cause significant changes in the adhesive or migratory behavior of a cell. Increase in the activity of this enzyme has been correlated with the progression of invasive malignancies. [provided by RefSeq, Oct 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~334.6 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 MGAT5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002410.5. 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 | 2 | 3 | |||
| missense | 51 | 51 | ||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 58 | 2 | 0 | 60 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002401.1 | 16 | MANE Select | |
| Ensembl | ENSP00000281923.2 | 16 | MANE Select | |
| RefSeq | NP_001358386.1 | 16 | Standard | |
| Ensembl | ENSP00000386377.1 | 16 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- N-Glycan biosynthesis - Homo sapiens (human)
- Post-translational protein modification
- N-Glycan antennae elongation
- N-glycan antennae elongation in the medial/trans-Golgi
- Metabolism of proteins
Biological Process
- protein N-linked glycosylation
- protein N-linked glycosylation via asparagine
- positive regulation of cell migration
- negative regulation of protein tyrosine phosphatase activity
- positive regulation of STAT cascade
Molecular Function
- protein phosphatase inhibitor activity
- alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity
- manganese ion binding
Cellular Component
- Golgi membrane
- Golgi apparatus
- membrane
- integral component of membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000409645
- Coding exons
- 16
- Length
- 334639
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 125747
- p
- 0.0000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.56 | 263 | 408 | 0.644 | 0.0000215 | 4924 |
| Missense (PolyPhen) | 48 | 126.79 | 0.37857 | 1606 | ||
| Synonymous | -0.135 | 155 | 153 | 1.01 | 0.00000873 | 1364 |
| Loss of Function | 5.69 | 3 | 43.6 | 0.0689 | 0.00000236 | 475 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the addition of N-acetylglucosamine in beta 1- 6 linkage to the alpha-linked mannose of biantennary N-linked oligosaccharides. It is one of the most important enzymes involved in the regulation of the biosynthesis of glycoprotein oligosaccharides.;
Recessive Scores
- pRec
- 0.585
Intolerance Scores
- LoFtool
- 0.00779
- RVIS EVS
- -1.27
- RVIS percentile EVS
- 5.24
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.645
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |