GALNT5
protein-codingpolypeptide N-acetylgalactosaminyltransferase 5, the group of Polypeptide N-acetylgalactosaminyltransferases
Gene summary
The protein encoded by this gene is a membrane-bound polypeptide N-acetylgalactosaminyltransferase that is found in the Golgi. The encoded protein catalyzes the first step in the mucin-type O-glycosylation of Golgi proteins, transfering an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. [provided by RefSeq, Aug 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~60.8 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 GALNT5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014568.3. 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 | 1 | 1 | ||||
| missense | 135 | 12 | 147 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 137 | 12 | 0 | 149 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055383.1 | 10 | MANE Select | |
| Ensembl | ENSP00000259056.4 | 10 | MANE Select | |
| RefSeq | NP_001316797.1 | 10 | Standard | |
| Ensembl | ENSP00000570047.1 | 10 | 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
- O-Glycan biosynthesis
Biological Process
- glycosaminoglycan biosynthetic process
- O-glycan processing
Molecular Function
- polypeptide N-acetylgalactosaminyltransferase activity
- carbohydrate binding
- metal ion binding
Cellular Component
- Golgi membrane
- cellular_component
- Golgi apparatus
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000259056
- Coding exons
- 10
- Length
- 56614
- Individuals with no LoFs
- 125608
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 139
- Defined
- 125747
- p
- 0.000553
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.478 | 455 | 485 | 0.939 | 0.0000240 | 6172 |
| Missense (PolyPhen) | 157 | 161.69 | 0.971 | 2044 | ||
| Synonymous | -0.380 | 182 | 176 | 1.04 | 0.00000880 | 1788 |
| Loss of Function | 1.64 | 26 | 36.8 | 0.707 | 0.00000196 | 460 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00050 | 0.00049 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0.00069 | 0.00069 | rare |
| European (Non-Finnish) | 0.00087 | 0.00085 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D- galactosamine residue to a serine or threonine residue on the protein receptor. Has activity toward EA2 peptide substrate, but has a weak activity toward Muc2 or Muc1b substrates (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0799
Intolerance Scores
- LoFtool
- 0.861
- RVIS EVS
- -0.33
- RVIS percentile EVS
- 30.9
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.707
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |