S100A1
Basic information
Region (hg38): 1:153627926-153632039
Previous symbols: [ "S100A" ]
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 S100A1 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 | 1 | |||||
| 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 | 1 |
Variants in S100A1
This is a list of pathogenic ClinVar variants found in the S100A1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-153630541-C-T | not specified | Uncertain significance (May 20, 2024) | ||
| 1-153630581-G-A | Benign (Jun 12, 2018) | |||
| 1-153630594-G-C | not specified | Uncertain significance (May 12, 2024) | ||
| 1-153630640-C-T | not specified | Uncertain significance (Jun 12, 2023) | ||
| 1-153631727-G-T | not specified | Uncertain significance (Nov 22, 2022) | ||
| 1-153631775-G-C | not specified | Uncertain significance (May 02, 2024) | ||
| 1-153631798-C-T | not specified | Uncertain significance (Sep 17, 2021) | ||
| 1-153631835-C-G | not specified | Uncertain significance (Dec 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| S100A1 | protein_coding | protein_coding | ENST00000292169 | 2 | 4112 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00600 | 0.513 | 125739 | 0 | 8 | 125747 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.155 | 57 | 53.8 | 1.06 | 0.00000296 | 624 |
| Missense in Polyphen | 24 | 18.699 | 1.2835 | 231 | ||
| Synonymous | -0.133 | 27 | 26.1 | 1.03 | 0.00000185 | 174 |
| Loss of Function | -0.0615 | 3 | 2.89 | 1.04 | 1.20e-7 | 41 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Probably acts as a Ca(2+) signal transducer (PubMed:22399290). In response to an increase in intracellular Ca(2+) levels, binds calcium which triggers a conformational change (PubMed:23351007). This conformational change allows interaction of S1001A with specific target proteins, such as TPR- containing proteins, and the modulation of their activity (PubMed:22399290). {ECO:0000269|PubMed:22399290, ECO:0000269|PubMed:23351007}.;
- Pathway
- Toll-Like Receptors Cascades;Innate Immune System;Immune System;Regulation of TLR by endogenous ligand
(Consensus)
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- loftool
- 0.666
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.236
- hipred
- N
- hipred_score
- 0.439
- ghis
- 0.382
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- S100a1
- Phenotype
- normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;toll-like receptor signaling pathway;regulation of heart contraction;substantia nigra development;intracellular signal transduction;positive regulation of nitric-oxide synthase activity;positive regulation of voltage-gated calcium channel activity;positive regulation of sprouting angiogenesis
- Cellular component
- extracellular region;nucleus;sarcoplasmic reticulum;Z disc;M band;protein-containing complex;neuron projection
- Molecular function
- calcium ion binding;protein binding;identical protein binding;protein homodimerization activity;S100 protein binding;calcium-dependent protein binding;ATPase binding