S100A11
Basic information
Region (hg38): 1:152032506-152047907
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 S100A11 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 | 5 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 5 | 0 | 0 |
Variants in S100A11
This is a list of pathogenic ClinVar variants found in the S100A11 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-152032688-C-G | not specified | Uncertain significance (Jul 26, 2021) | ||
1-152032745-C-T | not specified | Uncertain significance (Apr 22, 2022) | ||
1-152032768-C-G | not specified | Uncertain significance (May 05, 2022) | ||
1-152033713-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
1-152033781-G-A | not specified | Uncertain significance (Dec 12, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
S100A11 | protein_coding | protein_coding | ENST00000271638 | 3 | 15402 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00847 | 0.586 | 125695 | 0 | 53 | 125748 | 0.000211 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.309 | 51 | 57.6 | 0.885 | 0.00000292 | 693 |
Missense in Polyphen | 7 | 11.605 | 0.60317 | 190 | ||
Synonymous | 0.580 | 18 | 21.4 | 0.841 | 9.87e-7 | 203 |
Loss of Function | 0.225 | 3 | 3.45 | 0.869 | 1.45e-7 | 45 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00223 | 0.00223 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000531 | 0.0000527 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.0000654 | 0.0000653 |
Other | 0.000327 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Facilitates the differentiation and the cornification of keratinocytes. {ECO:0000269|PubMed:18618420}.;
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System;EGFR1
(Consensus)
Recessive Scores
- pRec
- 0.198
Intolerance Scores
- loftool
- 0.575
- rvis_EVS
- 0.22
- rvis_percentile_EVS
- 67.92
Haploinsufficiency Scores
- pHI
- 0.143
- hipred
- Y
- hipred_score
- 0.506
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- 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
- S100a11
- Phenotype
- reproductive system phenotype;
Gene ontology
- Biological process
- signal transduction;negative regulation of DNA replication;negative regulation of cell population proliferation;neutrophil degranulation;cell-cell adhesion
- Cellular component
- ruffle;extracellular region;extracellular space;nucleus;cytoplasm;cell-cell adherens junction;secretory granule lumen;extracellular exosome
- Molecular function
- calcium ion binding;protein binding;protein homodimerization activity;S100 protein binding;calcium-dependent protein binding;cadherin binding involved in cell-cell adhesion