ST3GAL2
Basic information
Region (hg38): 16:70375977-70439237
Previous symbols: [ "SIAT4B" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST3GAL2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 19 | 20 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 19 | 1 | 0 |
Variants in ST3GAL2
This is a list of pathogenic ClinVar variants found in the ST3GAL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-70381732-A-G | not specified | Uncertain significance (Aug 17, 2021) | ||
16-70381798-C-G | not specified | Uncertain significance (Apr 15, 2024) | ||
16-70381798-C-T | not specified | Uncertain significance (Nov 21, 2024) | ||
16-70381799-G-A | not specified | Uncertain significance (Aug 14, 2024) | ||
16-70381856-C-G | not specified | Uncertain significance (Feb 27, 2023) | ||
16-70388499-C-T | not specified | Uncertain significance (Feb 22, 2025) | ||
16-70388502-C-T | not specified | Uncertain significance (Feb 06, 2024) | ||
16-70395030-C-T | not specified | Uncertain significance (Feb 25, 2025) | ||
16-70395071-C-G | not specified | Uncertain significance (Oct 25, 2022) | ||
16-70395109-G-A | not specified | Uncertain significance (Sep 08, 2024) | ||
16-70395157-T-C | not specified | Uncertain significance (Feb 27, 2024) | ||
16-70395174-A-G | Uncertain significance (-) | |||
16-70395175-T-A | not specified | Uncertain significance (Jan 16, 2024) | ||
16-70398226-A-G | not specified | Uncertain significance (Aug 10, 2021) | ||
16-70398227-T-C | not specified | Uncertain significance (Dec 28, 2024) | ||
16-70398260-C-T | not specified | Likely benign (Oct 06, 2022) | ||
16-70398310-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
16-70398337-A-C | not specified | Uncertain significance (Jan 24, 2025) | ||
16-70398341-T-A | not specified | Uncertain significance (Sep 26, 2023) | ||
16-70398382-A-G | not specified | Uncertain significance (Dec 14, 2023) | ||
16-70398397-G-A | not specified | Uncertain significance (May 03, 2023) | ||
16-70398412-C-T | not specified | Uncertain significance (Mar 31, 2024) | ||
16-70398413-C-G | not specified | Uncertain significance (Aug 01, 2022) | ||
16-70398428-G-C | not specified | Uncertain significance (Jun 10, 2024) | ||
16-70398433-G-A | not specified | Uncertain significance (Aug 01, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ST3GAL2 | protein_coding | protein_coding | ENST00000393640 | 6 | 59803 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.942 | 0.0583 | 125740 | 0 | 7 | 125747 | 0.0000278 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.70 | 160 | 233 | 0.686 | 0.0000149 | 2319 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000123 | 0.000123 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000575 | 0.0000544 |
Finnish | 0.0000490 | 0.0000462 |
European (Non-Finnish) | 0.0000177 | 0.0000176 |
Middle Eastern | 0.0000575 | 0.0000544 |
South Asian | 0.0000329 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- 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;Globo Sphingolipid Metabolism;Metabolism of carbohydrates;Keratan sulfate biosynthesis;Keratan sulfate/keratin metabolism;Glycosaminoglycan metabolism;Post-translational protein modification;Metabolism of proteins;Glycosphingolipid biosynthesis - ganglioseries;Glycosphingolipid biosynthesis - globoseries;Metabolism;mucin core 1 and core 2 <i>O</i>-glycosylation;O-Glycan biosynthesis;Sialic acid metabolism;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation;Termination of O-glycan biosynthesis;O-linked glycosylation of mucins;O-linked glycosylation
(Consensus)
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- loftool
- 0.237
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.93
Haploinsufficiency Scores
- pHI
- 0.224
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.658
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.886
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- St3gal2
- Phenotype
- immune system phenotype; normal phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- protein glycosylation;glycoprotein biosynthetic process;glycolipid biosynthetic process;oligosaccharide biosynthetic process;O-glycan processing;keratan sulfate biosynthetic process;lipid glycosylation;sialylation;protein sialylation
- Cellular component
- Golgi membrane;extracellular region;integral component of membrane;Golgi cisterna membrane
- Molecular function
- beta-galactoside (CMP) alpha-2,3-sialyltransferase activity;monosialoganglioside sialyltransferase activity