GALNT11
protein-codingpolypeptide N-acetylgalactosaminyltransferase 11, the group of Polypeptide N-acetylgalactosaminyltransferases
Gene summary
Enables Notch binding activity and polypeptide N-acetylgalactosaminyltransferase activity. Predicted to be involved in several processes, including Notch receptor processing; Notch signaling involved in heart development; and regulation of Notch signaling pathway. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~96.7 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 GALNT11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022087.4. 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 | 84 | 5 | 2 | 91 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 89 | 5 | 2 | 96 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071370.2 | 11 | MANE Select | |
| Ensembl | ENSP00000395122.2 | 11 | MANE Select | |
| RefSeq | NP_001291443.1 | 11 | Standard | |
| RefSeq | NP_001358387.1 | 11 | 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
- Notch receptor processing
- determination of left/right symmetry
- regulation of Notch signaling pathway
- O-glycan processing
- protein O-linked glycosylation via threonine
Molecular Function
- polypeptide N-acetylgalactosaminyltransferase activity
- Notch binding
- carbohydrate binding
- metal ion binding
Cellular Component
- Golgi membrane
- Golgi apparatus
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000434507
- Coding exons
- 11
- Length
- 96667
- Individuals with no LoFs
- 125709
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 39
- Defined
- 125748
- p
- 0.000155
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.896 | 322 | 371 | 0.869 | 0.0000221 | 3976 |
| Missense (PolyPhen) | 112 | 146.24 | 0.76585 | 1600 | ||
| Synonymous | 0.0630 | 140 | 141 | 0.993 | 0.00000870 | 1167 |
| Loss of Function | 3.16 | 14 | 33.9 | 0.413 | 0.00000210 | 360 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00028 | 0.00027 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00020 | 0.00020 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Polypeptide N-acetylgalactosaminyltransferase that catalyzes the initiation of protein O-linked glycosylation and is involved in left/right asymmetry by mediating O-glycosylation of NOTCH1. O-glycosylation of NOTCH1 promotes activation of NOTCH1, modulating the balance between motile and immotile (sensory) cilia at the left-right organiser (LRO). Polypeptide N- acetylgalactosaminyltransferases catalyze the transfer of an N- acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Displays the same enzyme activity toward MUC1, MUC4, and EA2 than GALNT1. Not involved in glycosylation of erythropoietin (EPO). {ECO:0000269|PubMed:11925450, ECO:0000269|PubMed:24226769}.;
- Disease
- DISEASE: Note=Defects in GALNT11 may be a cause of heterotaxy, a congenital heart disease resulting from abnormalities in left- right (LR) body patterning. {ECO:0000269|PubMed:21282601}.;
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- LoFtool
- 0.412
- RVIS EVS
- -0.44
- RVIS percentile EVS
- 24.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.160
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |