ST3GAL2
protein-codingST3 beta-galactoside alpha-2,3-sialyltransferase 2, the group of Sialyltransferases
Gene summary
The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi but can be proteolytically processed to a soluble form. This protein, which is a member of glycosyltransferase family 29, can use the same acceptor substrates as does sialyltransferase 4A. [provided by RefSeq, Jul 2008]
- SIAT4B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~63.3 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 ST3GAL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006927.4. 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 | 2 | 1 | 3 | |||
| missense | 46 | 1 | 47 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 50 | 2 | 0 | 52 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_008858.1 | 6 | MANE Select | |
| Ensembl | ENSP00000345477.2 | 6 | MANE Select | |
| Ensembl | ENSP00000377257.4 | 6 | Standard | |
| Ensembl | ENSP00000377257.4 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycosphingolipid biosynthesis - ganglio series - Homo sapiens (human)
- Mucin type O-glycan biosynthesis - Homo sapiens (human)
- Glycosphingolipid biosynthesis - globo and isoglobo series - Homo sapiens (human)
- Glycosaminoglycan biosynthesis - keratan sulfate - Homo sapiens (human)
- Ganglio Sphingolipid Metabolism
Biological Process
- protein glycosylation
- glycoprotein biosynthetic process
- glycolipid biosynthetic process
- oligosaccharide biosynthetic process
- O-glycan processing
Molecular Function
- beta-galactoside (CMP) alpha-2,3-sialyltransferase activity
- monosialoganglioside sialyltransferase activity
Cellular Component
- Golgi membrane
- extracellular region
- integral component of membrane
- Golgi cisterna membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000393640
- Coding exons
- 6
- Length
- 59803
- Individuals with no LoFs
- 125740
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125747
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.70 | 160 | 233 | 0.686 | 0.0000149 | 2319 |
| Missense (PolyPhen) | 39 | 92.033 | 0.42376 | 955 | ||
| Synonymous | -0.583 | 110 | 102 | 1.07 | 0.00000718 | 687 |
| Loss of Function | 3.47 | 2 | 17.8 | 0.112 | 0.00000109 | 155 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000057 | 0.000054 | rare |
| Finnish | 0.000049 | 0.000046 | rare |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Responsible for the synthesis of the sequence NeuAc- alpha-2,3-Gal-beta-1,3-GalNAc- found in terminal carbohydrate groups of certain glycoproteins, oligosaccharides and glycolipids. SIAT4A and SIAT4B sialylate the same acceptor substrates but exhibit different Km values. {ECO:0000250|UniProtKB:Q11204}.;
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- LoFtool
- 0.237
- RVIS EVS
- -0.36
- RVIS percentile EVS
- 28.93
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.886
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |