PPP2R2A
protein phosphatase 2 regulatory subunit Balpha, the group of Protein phosphatase 2 regulatory subunits|WD repeat domain containing
Basic information
Region (hg38): 8:26291508-26372680
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
- Hereditary_breast_ovarian_cancer_syndrome (11 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002717.4. 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 | 20 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 1 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP2R2A | protein_coding | protein_coding | ENST00000315985 | 10 | 81190 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.995 | 0.00505 | 125733 | 0 | 4 | 125737 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.36 | 95 | 242 | 0.392 | 0.0000118 | 3072 |
| Missense in Polyphen | 13 | 78.299 | 0.16603 | 1052 | ||
| Synonymous | 0.794 | 72 | 81.1 | 0.888 | 0.00000388 | 793 |
| Loss of Function | 4.21 | 2 | 24.5 | 0.0817 | 0.00000146 | 288 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000554 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.0000554 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| 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);Tight junction - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);EGF-Ncore;Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Glycogen Metabolism;Cyclin D associated events in G1;G1 Phase;Mitotic G1-G1/S phases;Cyclin A/B1/B2 associated events during G2/M transition;TGF_beta_Receptor;ErbB1 downstream signaling;G2/M Transition;Mitotic G2-G2/M phases;Initiation of Nuclear Envelope Reformation;Nuclear Envelope Reassembly;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;TGF-beta receptor signaling
(Consensus)
Intolerance Scores
- loftool
- 0.402
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.627
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.944
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp2r2a
- Phenotype
- renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- G2/M transition of mitotic cell cycle;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;mitotic cell cycle;protein dephosphorylation;response to morphine;regulation of phosphoprotein phosphatase activity;peptidyl-serine dephosphorylation
- Cellular component
- protein phosphatase type 2A complex;nucleoplasm;cytosol;glutamatergic synapse
- Molecular function
- protein serine/threonine phosphatase activity;protein binding;protein phosphatase regulator activity;protein-containing complex binding;tau protein binding;protein phosphatase 2A binding