S100A10
Basic information
Region (hg38): 1:151982915-151993859
Previous symbols: [ "ANX2LG", "CAL1L" ]
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 S100A10 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 | 1 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 1 | 0 | 0 |
Variants in S100A10
This is a list of pathogenic ClinVar variants found in the S100A10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-151986166-T-G | not specified | Uncertain significance (May 24, 2024) | ||
1-151986178-T-G | not specified | Uncertain significance (Mar 25, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
S100A10 | protein_coding | protein_coding | ENST00000368811 | 2 | 11476 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.168 | 0.654 | 116709 | 0 | 1 | 116710 | 0.00000428 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.683 | 35 | 48.4 | 0.724 | 0.00000221 | 657 |
Missense in Polyphen | 0 | 4.125 | 0 | 78 | ||
Synonymous | -0.126 | 18 | 17.3 | 1.04 | 9.87e-7 | 157 |
Loss of Function | 0.808 | 1 | 2.33 | 0.429 | 9.59e-8 | 39 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000651 | 0.0000651 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Because S100A10 induces the dimerization of ANXA2/p36, it may function as a regulator of protein phosphorylation in that the ANXA2 monomer is the preferred target (in vitro) of tyrosine- specific kinase.;
- Pathway
- Prostaglandin Synthesis and Regulation;Dissolution of Fibrin Clot;EGFR1;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.292
Intolerance Scores
- loftool
- 0.385
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 62.74
Haploinsufficiency Scores
- pHI
- 0.552
- hipred
- Y
- hipred_score
- 0.506
- ghis
- 0.478
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.991
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Low | Low |
Primary Immunodeficiency | Medium | Low | Medium |
Cancer | Medium | Low | Medium |
Mouse Genome Informatics
- Gene name
- S100a10
- 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); 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
- membrane raft assembly;vesicle budding from membrane;positive regulation of GTPase activity;positive regulation of binding;protein heterotetramerization;positive regulation of stress fiber assembly;positive regulation of focal adhesion assembly;protein localization to plasma membrane;positive regulation of substrate adhesion-dependent cell spreading
- Cellular component
- extracellular region;extrinsic component of plasma membrane;membrane raft;collagen-containing extracellular matrix;extracellular exosome
- Molecular function
- calcium ion binding;protein binding;lipid binding;protein homodimerization activity;ion channel binding