PEA15
Basic information
Region (hg38): 1:160205380-160215376
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 PEA15 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 PEA15
This is a list of pathogenic ClinVar variants found in the PEA15 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-160211557-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 1-160211675-C-G | not specified | Uncertain significance (Jul 30, 2024) | ||
| 1-160213151-C-T | Uncertain significance (Jul 15, 2024) | |||
| 1-160213167-C-T | not specified | Uncertain significance (Jul 31, 2024) | ||
| 1-160213431-G-A | not specified | Uncertain significance (Nov 10, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PEA15 | protein_coding | protein_coding | ENST00000360472 | 3 | 10040 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.792 | 0.202 | 125743 | 0 | 3 | 125746 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.24 | 21 | 75.9 | 0.277 | 0.00000445 | 861 |
| Missense in Polyphen | 6 | 25.177 | 0.23832 | 317 | ||
| Synonymous | -0.502 | 33 | 29.5 | 1.12 | 0.00000162 | 248 |
| Loss of Function | 2.11 | 0 | 5.20 | 0.00 | 2.20e-7 | 66 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Blocks Ras-mediated inhibition of integrin activation and modulates the ERK MAP kinase cascade. Inhibits RPS6KA3 activities by retaining it in the cytoplasm (By similarity). Inhibits both TNFRSF6- and TNFRSF1A-mediated CASP8 activity and apoptosis. Regulates glucose transport by controlling both the content of SLC2A1 glucose transporters on the plasma membrane and the insulin-dependent trafficking of SLC2A4 from the cell interior to the surface. {ECO:0000250, ECO:0000269|PubMed:10442631, ECO:0000269|PubMed:9670003}.;
- Pathway
- EGF-Ncore;Apoptosis Modulation and Signaling;Signal Transduction;p73 transcription factor network;RAF-independent MAPK1/3 activation;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades
(Consensus)
Recessive Scores
- pRec
- 0.250
Intolerance Scores
- loftool
- 0.444
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.317
- hipred
- Y
- hipred_score
- 0.723
- ghis
- 0.626
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Pea15a
- Phenotype
- cellular phenotype; growth/size/body region 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); reproductive system phenotype;
Gene ontology
- Biological process
- DNA damage checkpoint;MAPK cascade;activation of MAPK activity;apoptotic process;carbohydrate transport;response to morphine;negative regulation of glucose import;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;positive regulation of extrinsic apoptotic signaling pathway via death domain receptors
- Cellular component
- nucleus;cytosol;microtubule associated complex
- Molecular function
- protein binding