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GeneBe

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

ENSG00000160307NCBI:6285OMIM:176990HGNC:10500Uniprot:P04271AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100B gene.

  • Inborn genetic diseases (4 variants)

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
clinvar
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 Inborn genetic diseases Uncertain significance (Dec 16, 2022)2398383
21-46602282-A-G Inborn genetic diseases Uncertain significance (Oct 22, 2021)2217563
21-46602390-A-G Inborn genetic diseases Uncertain significance (Jan 26, 2022)2221247
21-46602405-A-G Inborn genetic diseases Uncertain significance (Jun 12, 2023)2559839

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
S100Bprotein_codingprotein_codingENST00000291700 26247
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.04390.682125738091257470.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4004351.00.8430.00000249627
Missense in Polyphen109.56381.0456136
Synonymous0.3771820.20.8930.00000121152
Loss of Function0.55023.030.6591.27e-744

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004630.0000462
European (Non-Finnish)0.00004400.0000439
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.0003260.000326

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerLowLowLow

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