S100A6
S100 calcium binding protein A6, the group of S100 calcium binding proteins|EF-hand domain containing
Basic information
Region (hg38): 1:153534598-153536244
Previous symbols: [ "CACY" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not specified (1 variants)
- not provided (1 variants)
- Inborn genetic diseases (1 variants)
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 1 | 1 | 2 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 1 |
Variants in S100A6
This is a list of pathogenic ClinVar variants found in the S100A6 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-153534700-C-T | Benign (Apr 24, 2018) | |||
| 1-153534779-T-C | Inborn genetic diseases | Uncertain significance (Jul 12, 2023) | ||
| 1-153534787-TC-T | not specified | Uncertain significance (Jan 06, 2020) | ||
| 1-153534817-G-A | Inborn genetic diseases | Uncertain significance (Jul 26, 2023) | ||
| 1-153535203-G-A | Inborn genetic diseases | Uncertain significance (Aug 15, 2023) | ||
| 1-153535279-C-T | Inborn genetic diseases | Uncertain significance (Feb 01, 2023) | ||
| 1-153535303-C-T | Inborn genetic diseases | Uncertain significance (Apr 21, 2022) | ||
| 1-153535336-C-A | Inborn genetic diseases | 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