S100A5
S100 calcium binding protein A5, the group of EF-hand domain containing|S100 calcium binding proteins
Basic information
Region (hg38): 1:153537146-153541765
Previous symbols: [ "S100D" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A5 gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 6 | 6 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 6 | 0 | 0 |
Variants in S100A5
This is a list of pathogenic ClinVar variants found in the S100A5 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-153537324-T-C | Inborn genetic diseases | Uncertain significance (Sep 30, 2021) | ||
1-153537384-T-A | Inborn genetic diseases | Uncertain significance (Mar 16, 2022) | ||
1-153537385-C-T | Inborn genetic diseases | Uncertain significance (Mar 23, 2022) | ||
1-153537419-G-C | Inborn genetic diseases | Uncertain significance (Jan 05, 2022) | ||
1-153540119-T-C | Inborn genetic diseases | Uncertain significance (May 13, 2022) | ||
1-153540157-A-G | Inborn genetic diseases | Uncertain significance (Sep 28, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
S100A5 | protein_coding | protein_coding | ENST00000368718 | 2 | 4619 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000551 | 0.151 | 125738 | 0 | 9 | 125747 | 0.0000358 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.132 | 54 | 51.3 | 1.05 | 0.00000266 | 620 |
Missense in Polyphen | 16 | 17.641 | 0.90698 | 211 | ||
Synonymous | -0.646 | 27 | 23.1 | 1.17 | 0.00000152 | 157 |
Loss of Function | -1.53 | 5 | 2.43 | 2.06 | 9.96e-8 | 40 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000148 | 0.000148 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000264 | 0.0000264 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds calcium, zinc and copper. One subunit can simultaneously bind 2 calcium ions or 2 copper ions plus 1 zinc ion. Calcium and copper ions compete for the same binding sites. {ECO:0000269|PubMed:10882717}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- loftool
- 0.662
- rvis_EVS
- 0.39
- rvis_percentile_EVS
- 75.87
Haploinsufficiency Scores
- pHI
- 0.0650
- hipred
- N
- hipred_score
- 0.170
- ghis
- 0.398
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.150
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- S100a5
- Phenotype
- taste/olfaction phenotype; normal 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);
Gene ontology
- Biological process
- Cellular component
- nucleus;neuronal cell body
- Molecular function
- copper ion binding;calcium ion binding;zinc ion binding;protein homodimerization activity