S100A6
Basic information
Region (hg38): 1:153534599-153536244
Previous symbols: [ "CACY" ]
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 S100A6 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 1 |
Variants in S100A6
This is a list of pathogenic ClinVar variants found in the S100A6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-153534700-C-T | Benign (Apr 24, 2018) | |||
| 1-153534779-T-C | not specified | Uncertain significance (Jul 12, 2023) | ||
| 1-153534787-TC-T | not specified | Uncertain significance (Jan 06, 2020) | ||
| 1-153534817-G-A | not specified | Uncertain significance (Jul 26, 2023) | ||
| 1-153535203-G-A | not specified | Uncertain significance (Aug 15, 2023) | ||
| 1-153535248-T-G | not specified | Uncertain significance (Jun 22, 2024) | ||
| 1-153535279-C-T | not specified | Uncertain significance (Feb 01, 2023) | ||
| 1-153535303-C-T | not specified | Uncertain significance (Apr 21, 2022) | ||
| 1-153535336-C-A | not specified | Uncertain significance (Apr 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| S100A6 | protein_coding | protein_coding | ENST00000368720 | 2 | 1646 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.176 | 0.656 | 125734 | 0 | 4 | 125738 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.246 | 43 | 47.8 | 0.900 | 0.00000244 | 587 |
| Missense in Polyphen | 9 | 9.6226 | 0.9353 | 136 | ||
| Synonymous | 0.915 | 16 | 21.4 | 0.748 | 0.00000108 | 173 |
| Loss of Function | 0.853 | 1 | 2.44 | 0.410 | 1.02e-7 | 34 |
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) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May function as calcium sensor and modulator, contributing to cellular calcium signaling. May function by interacting with other proteins, such as TPR-containing proteins, and indirectly play a role in many physiological processes such as the reorganization of the actin cytoskeleton and in cell motility. Binds 2 calcium ions. Calcium binding is cooperative. {ECO:0000269|PubMed:22399290}.;
- Pathway
- Gastric Cancer Network 2;Vitamin D Receptor Pathway;Prostaglandin Synthesis and Regulation
(Consensus)
Recessive Scores
- pRec
- 0.586
Intolerance Scores
- loftool
- 0.562
- rvis_EVS
- 0.41
- rvis_percentile_EVS
- 76.67
Haploinsufficiency Scores
- pHI
- 0.152
- hipred
- Y
- hipred_score
- 0.702
- ghis
- 0.443
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- S100a6
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; 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); reproductive system phenotype;
Gene ontology
- Biological process
- signal transduction;axonogenesis;ion transmembrane transport;positive regulation of fibroblast proliferation
- Cellular component
- ruffle;extracellular region;nucleus;nuclear envelope;cytoplasm;cytosol;plasma membrane;extrinsic component of cytoplasmic side of plasma membrane;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome
- Molecular function
- calcium ion binding;protein binding;tropomyosin binding;zinc ion binding;ion transmembrane transporter activity;protein homodimerization activity;S100 protein binding;calcium-dependent protein binding