PPP2R5A
protein phosphatase 2 regulatory subunit B'alpha, the group of Protein phosphatase 2 regulatory subunits|Armadillo like helical domain containing|Small nucleolar RNA protein coding host genes
Basic information
Region (hg38): 1:212285410-212361853
Links
Phenotypes
GenCC
Source:
No genCC data.
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 PPP2R5A 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 0 |
Variants in PPP2R5A
This is a list of pathogenic ClinVar variants found in the PPP2R5A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-212286144-A-G | not specified | Uncertain significance (Mar 11, 2022) | ||
| 1-212286204-G-A | not specified | Uncertain significance (May 05, 2023) | ||
| 1-212286244-G-T | not specified | Uncertain significance (Apr 26, 2024) | ||
| 1-212286252-G-A | not specified | Uncertain significance (Jan 26, 2023) | ||
| 1-212329135-A-G | not specified | Uncertain significance (Nov 30, 2022) | ||
| 1-212329216-T-C | not specified | Uncertain significance (Sep 01, 2021) | ||
| 1-212342260-G-C | not specified | Uncertain significance (Nov 21, 2022) | ||
| 1-212342272-G-A | not specified | Uncertain significance (Mar 21, 2023) | ||
| 1-212348405-G-A | not specified | Uncertain significance (Apr 18, 2024) | ||
| 1-212357049-G-A | not specified | Uncertain significance (Apr 16, 2024) | ||
| 1-212360661-G-T | not specified | Uncertain significance (Feb 13, 2023) | ||
| 1-212360739-A-C | not specified | Uncertain significance (Feb 15, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP2R5A | protein_coding | protein_coding | ENST00000261461 | 13 | 76322 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.816 | 0.184 | 125667 | 0 | 13 | 125680 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.41 | 128 | 231 | 0.554 | 0.0000111 | 3193 |
| Missense in Polyphen | 30 | 86.893 | 0.34525 | 1270 | ||
| Synonymous | 0.842 | 72 | 81.7 | 0.882 | 0.00000395 | 842 |
| Loss of Function | 3.98 | 5 | 27.6 | 0.181 | 0.00000144 | 353 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000112 | 0.000112 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000631 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000570 | 0.0000528 |
| Middle Eastern | 0.0000631 | 0.0000544 |
| South Asian | 0.000109 | 0.0000981 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: The B regulatory subunit might modulate substrate selectivity and catalytic activity, and also might direct the localization of the catalytic enzyme to a particular subcellular compartment.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Glycogen Metabolism;Degradation of beta-catenin by the destruction complex;RAF activation;Signaling by WNT;Signal Transduction;GPCR Dopamine D1like receptor;CTLA4 inhibitory signaling;Costimulation by the CD28 family;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Immune System;Adaptive Immune System;insulin Mam;RHO GTPases Activate Formins;Disassembly of the destruction complex and recruitment of AXIN to the membrane;RHO GTPase Effectors;Signaling by Rho GTPases;Hemostasis;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;PIP3 activates AKT signaling;Beta-catenin phosphorylation cascade;C-MYC pathway;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Platelet sensitization by LDL;Platelet homeostasis;Cell Cycle, Mitotic;Intracellular signaling by second messengers;Validated transcriptional targets of deltaNp63 isoforms;TCF dependent signaling in response to WNT;Canonical Wnt signaling pathway;insulin
(Consensus)
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- loftool
- 0.176
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.722
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.575
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.976
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp2r5a
- Phenotype
- neoplasm; hematopoietic system phenotype; liver/biliary system phenotype; immune system phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- protein dephosphorylation;signal transduction;regulation of protein autophosphorylation;positive regulation of protein dephosphorylation;regulation of phosphoprotein phosphatase activity;negative regulation of lipid kinase activity;negative regulation of protein localization to plasma membrane
- Cellular component
- protein phosphatase type 2A complex;chromosome, centromeric region;nucleus;cytoplasm;centrosome;cytosol;membrane;Z disc;M band
- Molecular function
- phosphoprotein phosphatase activity;protein binding;protein phosphatase regulator activity;kinase binding;protein phosphatase activator activity