A3GALT2
protein-codingalpha 1,3-galactosyltransferase 2, the group of Glycosyltransferase family 6
Gene summary
Predicted to enable N-acetyllactosaminide 3-alpha-galactosyltransferase activity and alpha-1,3-galactosyltransferase activity. Predicted to be involved in glycosphingolipid biosynthetic process. Predicted to be located in Golgi cisterna membrane. Predicted to be active in Golgi apparatus and vesicle. [provided by Alliance of Genome Resources, Jun 2026]
- A3GALT2P
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.3 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 A3GALT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080438.1. 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 | 1 | 1 | 2 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 1 | 1 | 1 | 3 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073907.1 | 5 | MANE Select | |
| Ensembl | ENSP00000475261.1 | 5 | MANE Select |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human)
- Ganglio Sphingolipid Metabolism
- Globo Sphingolipid Metabolism
Biological Process
- carbohydrate metabolic process
- glycosphingolipid biosynthetic process
- lipid glycosylation
Molecular Function
- alpha-1,3-galactosyltransferase activity
- transferase activity, transferring glycosyl groups
- metal ion binding
- N-acetyllactosaminide 3-alpha-galactosyltransferase activity
Cellular Component
- Golgi apparatus
- integral component of membrane
- vesicle
- Golgi cisterna membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000442999
- Coding exons
- 5
- Length
- 14333
- Individuals with no LoFs
- 119682
- Homozygous LoFs
- 51
- Heterozygous LoFs
- 3633
- Defined
- 123366
- p
- 0.0150
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0464 | 170 | 172 | 0.990 | 0.0000110 | 2110 |
| Missense (PolyPhen) | 41 | 38.657 | 1.0606 | 523 | ||
| Synonymous | 0.126 | 77 | 78.4 | 0.982 | 0.00000555 | 697 |
| Loss of Function | -0.553 | 14 | 11.9 | 1.17 | 5.14e-7 | 134 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0045 | 0.0044 | notable |
| Latino/Admixed American | 0.0089 | 0.0089 | notable |
| Ashkenazi Jewish | 0.0090 | 0.0090 | notable |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.011 | 0.011 | notable |
| European (Non-Finnish) | 0.025 | 0.024 | notable |
| South Asian | 0.0080 | 0.0079 | notable |
| Other | 0.015 | 0.015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Synthesizes the galactose-alpha(1,3)-galactose group on the glycosphingolipid isoglobotrihexosylceramide or isogloboside 3 (iGb3) by catalyzing the transfer of galactose from UDP-Galactose to its acceptor molecule Gal-beta-1,4-Glc-ceramide. Can also catalyze the addition of galactose to iGb3 itself to form polygalactose structures. {ECO:0000305|PubMed:23378701}.;
Recessive Scores
- pRec
- 0.0960
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |