GAL3ST2
protein-codinggalactose-3-O-sulfotransferase 2, the group of Sulfotransferases, membrane bound
Gene summary
This gene encodes a member of the galactose-3-O-sulfotransferase protein family. The product of this gene catalyzes sulfonation by transferring a sulfate group to the hydroxyl at C-3 of nonreducing beta-galactosyl residues, and it can act on both type 1 and type 2 (Galbeta 1-3/1-4GlcNAc-R) oligosaccharides with similar efficiencies, and on core 1 glycans. This enzyme has been implicated in tumor metastasis processes. This gene is different from the GAL3ST3 gene located on chromosome 11, which has also been referred to as GAL3ST2 and encodes a related enzyme with distinct tissue distribution and substrate specificities, compared to galactose-3-O-sulfotransferase 2. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.5 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 GAL3ST2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022134.3. 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 | 1 | 86 | 6 | 93 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 1 | 88 | 7 | 0 | 96 |
Highest pathogenic variant AF is 0.000020458874
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071417.2 | 4 | MANE Select | |
| Ensembl | ENSP00000192314.6 | 4 | MANE Select | |
| Ensembl | ENSP00000801370.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metapathway biotransformation Phase I and II
Biological Process
- biological_process
- glycolipid biosynthetic process
Molecular Function
- galactosylceramide sulfotransferase activity
- protein binding
- sulfotransferase activity
Cellular Component
- membrane
- integral component of membrane
- Golgi cisterna membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000192314
- Coding exons
- 4
- Length
- 27384
- Individuals with no LoFs
- 124763
- Homozygous LoFs
- 7
- Heterozygous LoFs
- 825
- Defined
- 125595
- p
- 0.00332
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0524 | 219 | 217 | 1.01 | 0.0000127 | 2489 |
| Missense (PolyPhen) | 80 | 83.862 | 0.95395 | 1064 | ||
| Synonymous | 0.768 | 98 | 108 | 0.906 | 0.00000692 | 865 |
| Loss of Function | -1.07 | 14 | 10.3 | 1.36 | 5.40e-7 | 103 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00093 | 0.00074 | rare |
| Latino/Admixed American | 0.0036 | 0.0030 | notable |
| Ashkenazi Jewish | 0.0056 | 0.0047 | notable |
| East Asian | 0.00013 | 0.00011 | rare |
| Finnish | 0.00052 | 0.00051 | rare |
| European (Non-Finnish) | 0.0062 | 0.0054 | notable |
| South Asian | 0.00080 | 0.00072 | rare |
| Other | 0.0050 | 0.0039 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transfers a sulfate group to the hydroxyl group at C3 of non-reducing beta-galactosyl residues. Acts both on type 1 (Gal- beta-1,3-GlcNAc) and type 2 (Gal-beta-1,4-GlcNAc) chains with similar efficiency.;
Recessive Scores
- pRec
- 0.109
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.162
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |