GAL3ST3
protein-codinggalactose-3-O-sulfotransferase 3, 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 3' position of galactose in N-acetyllactosamine in both type 2 (Gal-beta-1-4GlcNAc-R) oligosaccharides and core-2-branched O-glycans, but not on type 1 or core-1-branched structures. This gene, which has also been referred to as GAL3ST2, is different from the GAL3ST2 gene located on chromosome 2 that encodes a related enzyme with distinct tissue distribution and substrate specificities, compared to galactose-3-O-sulfotransferase 3. [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 ~8.4 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 GAL3ST3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033036.3. 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 | 2 | 2 | ||||
| missense | 90 | 90 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 90 | 0 | 2 | 92 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_149025.1 | 2 | MANE Select | |
| Ensembl | ENSP00000308591.3 | 2 | MANE Select | |
| Ensembl | ENSP00000434829.1 | 2 | Standard | |
| Ensembl | ENSP00000434829.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metapathway biotransformation Phase I and II
Biological Process
- monosaccharide metabolic process
- sulfur compound metabolic process
- glycolipid biosynthetic process
- oligosaccharide metabolic process
- proteoglycan biosynthetic process
Molecular Function
- galactosylceramide sulfotransferase activity
- carbohydrate binding
- 3'-phosphoadenosine 5'-phosphosulfate binding
- galactose 3-O-sulfotransferase activity
- proteoglycan sulfotransferase activity
Cellular Component
- integral component of membrane
- Golgi cisterna membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000312006
- Coding exons
- 2
- Length
- 7229
- Individuals with no LoFs
- 125474
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 23
- Defined
- 125497
- p
- 0.0000916
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.774 | 262 | 300 | 0.874 | 0.0000242 | 2698 |
| Missense (PolyPhen) | 115 | 126.64 | 0.90811 | 1180 | ||
| Synonymous | 0.858 | 132 | 145 | 0.909 | 0.0000127 | 943 |
| Loss of Function | -0.442 | 11 | 9.53 | 1.15 | 4.09e-7 | 114 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00019 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00015 | 0.00014 | rare |
| European (Non-Finnish) | 0.000092 | 0.000088 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transfers a sulfate to position 3 of non-reducing beta- galactosyl residues in N-glycans and core2-branched O-glycans. Has high activity towards Gal-beta-1,4-GlcNAc, Gal-beta-1,4(Fuc-alpha- 1,3)GlcNAc and lower activity towards Gal-beta-1,3(Fuc-alpha- 1,4)GlcNAc. {ECO:0000269|PubMed:11323440, ECO:0000269|PubMed:11356829}.;
Recessive Scores
- pRec
- 0.110
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.201
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |