ST8SIA2
ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2, the group of Sialyltransferases
Basic information
Region (hg38): 15:92393881-92468728
Previous symbols: [ "SIAT8B" ]
Links
Phenotypes
GenCC
Source:
- schizophrenia (Limited), mode of inheritance: AD
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 ST8SIA2 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 | 4 | |||||
| missense | 13 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 4 | 1 |
Variants in ST8SIA2
This is a list of pathogenic ClinVar variants found in the ST8SIA2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-92394141-C-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 15-92394149-G-A | not specified | Uncertain significance (May 10, 2024) | ||
| 15-92438417-C-G | not specified | Uncertain significance (Oct 26, 2022) | ||
| 15-92438444-G-A | not specified | Uncertain significance (Oct 06, 2021) | ||
| 15-92438519-C-T | not specified | Uncertain significance (Jun 23, 2023) | ||
| 15-92438551-G-A | ST8SIA2-related disorder | Likely benign (Sep 25, 2020) | ||
| 15-92438570-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 15-92438591-G-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 15-92438603-G-A | not specified | Uncertain significance (Sep 27, 2022) | ||
| 15-92444668-G-A | not specified | Uncertain significance (Mar 21, 2022) | ||
| 15-92444842-T-C | not specified | Uncertain significance (Jul 20, 2022) | ||
| 15-92444856-G-A | not specified | Uncertain significance (May 05, 2023) | ||
| 15-92444926-G-A | not specified | Uncertain significance (May 25, 2022) | ||
| 15-92464096-C-A | Likely benign (Jul 02, 2018) | |||
| 15-92464139-C-G | ST8SIA2-related disorder | Likely benign (Apr 29, 2020) | ||
| 15-92464216-T-C | not specified | Uncertain significance (Mar 20, 2023) | ||
| 15-92464265-G-T | not specified | Uncertain significance (Oct 05, 2022) | ||
| 15-92464286-C-T | Benign (Jul 31, 2018) | |||
| 15-92464292-G-A | Likely benign (Jul 02, 2018) | |||
| 15-92464367-G-T | ST8SIA2-related disorder | Likely benign (Dec 27, 2022) | ||
| 15-92464377-G-A | not specified | Uncertain significance (Feb 21, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ST8SIA2 | protein_coding | protein_coding | ENST00000268164 | 6 | 74901 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0581 | 0.939 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.50 | 160 | 223 | 0.717 | 0.0000140 | 2437 |
| Missense in Polyphen | 35 | 84.637 | 0.41353 | 913 | ||
| Synonymous | -1.28 | 114 | 97.9 | 1.16 | 0.00000672 | 741 |
| Loss of Function | 2.57 | 5 | 16.2 | 0.309 | 7.63e-7 | 188 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May transfer sialic acid through alpha-2,8-linkages to the alpha-2,3-linked and alpha-2,6-linked sialic acid of N-linked oligosaccharides of glycoproteins and may be involved in PSA (polysialic acid) expression.;
- Pathway
- Developmental Biology;Post-translational protein modification;N-Glycan antennae elongation;N-glycan antennae elongation in the medial/trans-Golgi;Metabolism of proteins;terminal <i>O</i>-glycans residues modification;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;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;NCAM signaling for neurite out-growth;NCAM1 interactions;Axon guidance
(Consensus)
Recessive Scores
- pRec
- 0.268
Intolerance Scores
- loftool
- 0.155
- rvis_EVS
- -0.42
- rvis_percentile_EVS
- 25.56
Haploinsufficiency Scores
- pHI
- 0.392
- hipred
- Y
- hipred_score
- 0.851
- ghis
- 0.439
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.802
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- St8sia2
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- st8sia2
- Affected structure
- diencephalic white matter
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- ganglioside biosynthetic process;carbohydrate metabolic process;cellular protein modification process;protein glycosylation;N-glycan processing;nervous system development;oligosaccharide metabolic process;sialylation
- Cellular component
- Golgi membrane;early endosome;integral component of membrane;recycling endosome
- Molecular function
- alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity;sialic acid binding