S100B
S100 calcium binding protein B, the group of S100 calcium binding proteins|EF-hand domain containing
Basic information
Region (hg38): 21:46598603-46605208
Links
Phenotypes
GenCC
Source:
No genCC data.
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 S100B 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in S100B
This is a list of pathogenic ClinVar variants found in the S100B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 21-46599370-T-C | not specified | Uncertain significance (Dec 16, 2022) | ||
| 21-46602282-A-G | not specified | Uncertain significance (Oct 22, 2021) | ||
| 21-46602390-A-G | not specified | Uncertain significance (Jan 26, 2022) | ||
| 21-46602405-A-G | not specified | Uncertain significance (Jun 12, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| S100B | protein_coding | protein_coding | ENST00000291700 | 2 | 6247 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0439 | 0.682 | 125738 | 0 | 9 | 125747 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.400 | 43 | 51.0 | 0.843 | 0.00000249 | 627 |
| Missense in Polyphen | 10 | 9.5638 | 1.0456 | 136 | ||
| Synonymous | 0.377 | 18 | 20.2 | 0.893 | 0.00000121 | 152 |
| Loss of Function | 0.550 | 2 | 3.03 | 0.659 | 1.27e-7 | 44 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000440 | 0.0000439 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Weakly binds calcium but binds zinc very tightly- distinct binding sites with different affinities exist for both ions on each monomer. Physiological concentrations of potassium ion antagonize the binding of both divalent cations, especially affecting high-affinity calcium-binding sites. Binds to and initiates the activation of STK38 by releasing autoinhibitory intramolecular interactions within the kinase. Interaction with AGER after myocardial infarction may play a role in myocyte apoptosis by activating ERK1/2 and p53/TP53 signaling. Could assist ATAD3A cytoplasmic processing, preventing aggregation and favoring mitochondrial localization. May mediate calcium-dependent regulation on many physiological processes by interacting with other proteins, such as TPR-containing proteins, and modulating their activity. {ECO:0000269|PubMed:20351179, ECO:0000269|PubMed:22399290}.;
- Pathway
- Signaling by ERBB4;Toll Like Receptor 7/8 (TLR7/8) Cascade;Signal Transduction;Signaling by Interleukins;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;ZBP1(DAI) mediated induction of type I IFNs;Toll-Like Receptors Cascades;TRAF6 mediated NF-kB activation;DDX58/IFIH1-mediated induction of interferon-alpha/beta;DEx/H-box helicases activate type I IFN and inflammatory cytokines production ;Interleukin-1 signaling;Innate Immune System;Immune System;RIP-mediated NFkB activation via ZBP1;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;Advanced glycosylation endproduct receptor signaling;Nuclear signaling by ERBB4;Signaling by ERBB4;Cytosolic sensors of pathogen-associated DNA ;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Interleukin-1 family signaling
(Consensus)
Intolerance Scores
- loftool
- 0.532
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.319
- hipred
- Y
- hipred_score
- 0.721
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.406
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- S100b
- Phenotype
- normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Gene ontology
- Biological process
- axonogenesis;central nervous system development;learning or memory;memory;cell population proliferation;positive regulation of cell population proliferation;regulation of cell shape;positive regulation of myelination;positive regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;innate immune response;regulation of neuronal synaptic plasticity;astrocyte differentiation;response to glucocorticoid;response to methylmercury;long-term synaptic potentiation;cellular response to hypoxia;negative regulation of skeletal muscle cell differentiation
- Cellular component
- ruffle;extracellular region;extracellular space;nucleus;cytoplasm;neuronal cell body;perinuclear region of cytoplasm
- Molecular function
- calcium ion binding;protein binding;zinc ion binding;identical protein binding;protein homodimerization activity;S100 protein binding;tau protein binding;calcium-dependent protein binding;RAGE receptor binding