PPP1R15A
protein phosphatase 1 regulatory subunit 15A, the group of Protein phosphatase 1 regulatory subunits
Basic information
Region (hg38): 19:48872212-48876059
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (103 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R15A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014330.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 90 | 13 | 103 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 90 | 14 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP1R15A | protein_coding | protein_coding | ENST00000200453 | 2 | 3666 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.21e-12 | 0.125 | 122881 | 0 | 4 | 122885 | 0.0000163 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.158 | 391 | 382 | 1.02 | 0.0000203 | 4296 |
| Missense in Polyphen | 178 | 166.51 | 1.069 | 1840 | ||
| Synonymous | -0.875 | 164 | 150 | 1.09 | 0.00000800 | 1428 |
| Loss of Function | 0.674 | 20 | 23.5 | 0.850 | 0.00000125 | 271 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000595 | 0.0000595 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000914 | 0.00000903 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000328 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Recruits the serine/threonine-protein phosphatase PP1 to dephosphorylate the translation initiation factor eIF-2A/EIF2S1, thereby reversing the shut-off of protein synthesis initiated by stress-inducible kinases and facilitating recovery of cells from stress. Down-regulates the TGF-beta signaling pathway by promoting dephosphorylation of TGFB1 by PP1. May promote apoptosis by inducing TP53 phosphorylation on 'Ser-15'. {ECO:0000269|PubMed:11564868, ECO:0000269|PubMed:12556489, ECO:0000269|PubMed:14635196, ECO:0000269|PubMed:14718519, ECO:0000269|PubMed:8139541}.;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human);TGF-Ncore;Photodynamic therapy-induced unfolded protein response;Signal Transduction;TGF_beta_Receptor;BMP receptor signaling;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Downregulation of TGF-beta receptor signaling;TGF-beta receptor signaling activates SMADs;TGF-beta receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.195
Intolerance Scores
- loftool
- 0.946
- rvis_EVS
- 2.56
- rvis_percentile_EVS
- 98.74
Haploinsufficiency Scores
- pHI
- 0.0292
- hipred
- N
- hipred_score
- 0.352
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Ppp1r15a
- Phenotype
- cellular phenotype; hematopoietic system phenotype; normal 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); immune system phenotype;
Gene ontology
- Biological process
- apoptotic process;cellular response to DNA damage stimulus;cell cycle arrest;positive regulation of translational initiation in response to stress;negative regulation of phosphoprotein phosphatase activity;positive regulation of phosphoprotein phosphatase activity;response to endoplasmic reticulum stress;negative regulation of protein dephosphorylation;regulation of translational initiation by eIF2 alpha dephosphorylation;intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress;protein localization to endoplasmic reticulum;positive regulation of peptidyl-serine dephosphorylation;negative regulation of PERK-mediated unfolded protein response;positive regulation of endoplasmic reticulum stress-induced eIF2 alpha dephosphorylation
- Cellular component
- protein phosphatase type 1 complex;cytoplasm;mitochondrion;mitochondrial outer membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;cytosol;membrane
- Molecular function
- protein binding;protein phosphatase 1 binding;protein phosphatase regulator activity;protein kinase binding;protein phosphatase activator activity