SLA2
Basic information
Region (hg38): 20:36612318-36646196
Previous symbols: [ "C20orf156" ]
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 SLA2 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 | 20 | 22 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 20 | 0 | 2 |
Variants in SLA2
This is a list of pathogenic ClinVar variants found in the SLA2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
20-36613907-T-C | not specified | Uncertain significance (Dec 19, 2023) | ||
20-36614342-C-T | Benign (Jun 27, 2018) | |||
20-36614359-A-G | not specified | Uncertain significance (Jun 17, 2024) | ||
20-36614396-C-T | not specified | Uncertain significance (Aug 30, 2021) | ||
20-36615252-G-A | not specified | Uncertain significance (Jun 07, 2023) | ||
20-36615326-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
20-36615327-G-C | not specified | Uncertain significance (Jan 10, 2022) | ||
20-36615353-C-T | not specified | Uncertain significance (Nov 30, 2022) | ||
20-36615354-G-A | not specified | Uncertain significance (Mar 11, 2024) | ||
20-36615365-G-C | not specified | Uncertain significance (Nov 15, 2024) | ||
20-36632603-G-A | not specified | Uncertain significance (Jul 20, 2021) | ||
20-36632637-G-C | not specified | Uncertain significance (Dec 20, 2022) | ||
20-36632646-G-A | not specified | Uncertain significance (Jun 11, 2024) | ||
20-36633606-A-G | not specified | Uncertain significance (Oct 05, 2023) | ||
20-36633612-G-A | not specified | Uncertain significance (Nov 13, 2024) | ||
20-36633612-G-C | not specified | Uncertain significance (Nov 14, 2023) | ||
20-36634526-G-A | not specified | Uncertain significance (Jun 28, 2024) | ||
20-36634550-G-A | Benign (Jul 21, 2018) | |||
20-36634577-G-A | not specified | Uncertain significance (Mar 10, 2025) | ||
20-36641268-T-G | not specified | Uncertain significance (Oct 29, 2024) | ||
20-36641283-G-A | not specified | Uncertain significance (Feb 28, 2023) | ||
20-36641307-G-T | not specified | Uncertain significance (Aug 09, 2021) | ||
20-36641316-C-A | not specified | Uncertain significance (Aug 28, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLA2 | protein_coding | protein_coding | ENST00000262866 | 7 | 33899 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0763 | 0.913 | 125726 | 1 | 20 | 125747 | 0.0000835 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.102 | 147 | 151 | 0.977 | 0.00000847 | 1663 |
Missense in Polyphen | 47 | 59.724 | 0.78696 | 628 | ||
Synonymous | -0.0930 | 68 | 67.0 | 1.01 | 0.00000407 | 555 |
Loss of Function | 2.24 | 4 | 12.6 | 0.319 | 5.30e-7 | 154 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000203 | 0.000203 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.000274 | 0.000272 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000352 | 0.0000352 |
Middle Eastern | 0.000274 | 0.000272 |
South Asian | 0.000131 | 0.0000980 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Adapter protein, which negatively regulates T-cell receptor (TCR) signaling. Inhibits T-cell antigen-receptor induced activation of nuclear factor of activated T-cells. May act by linking signaling proteins such as ZAP70 with CBL, leading to a CBL dependent degradation of signaling proteins. {ECO:0000269|PubMed:11696592}.;
- Pathway
- TCR;BCR;TCR signaling in naïve CD4+ T cells
(Consensus)
Recessive Scores
- pRec
- 0.234
Intolerance Scores
- loftool
- 0.260
- rvis_EVS
- 0.26
- rvis_percentile_EVS
- 70.26
Haploinsufficiency Scores
- pHI
- 0.0979
- hipred
- Y
- hipred_score
- 0.681
- ghis
- 0.429
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.685
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sla2
- Phenotype
- cellular phenotype; immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;positive regulation of signal transduction;B cell mediated immunity;intracellular receptor signaling pathway;T cell activation;regulation of phosphatidylinositol 3-kinase activity;negative regulation of insulin receptor signaling pathway;phosphatidylinositol phosphorylation;regulation of immune response;negative regulation of calcium-mediated signaling;antigen receptor-mediated signaling pathway;negative regulation of B cell activation
- Cellular component
- nucleoplasm;cytoplasm;late endosome;Golgi apparatus;plasma membrane;phosphatidylinositol 3-kinase complex;endosome membrane;intracellular membrane-bounded organelle
- Molecular function
- SH3/SH2 adaptor activity;protein binding;1-phosphatidylinositol-3-kinase regulator activity;protein N-terminus binding