PPP2CB
protein phosphatase 2 catalytic subunit beta, the group of STRIPAK complex|Protein phosphatase catalytic subunits
Basic information
Region (hg38): 8:30774457-30814314
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 PPP2CB 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 | 1 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 1 | 0 |
Variants in PPP2CB
This is a list of pathogenic ClinVar variants found in the PPP2CB region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-30786260-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
| 8-30786306-G-C | not specified | Uncertain significance (May 23, 2023) | ||
| 8-30791294-G-C | not specified | Uncertain significance (Feb 10, 2025) | ||
| 8-30797582-T-C | not specified | Uncertain significance (Jul 26, 2022) | ||
| 8-30797587-A-G | Likely benign (Apr 01, 2022) | |||
| 8-30797645-T-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 8-30797645-T-C | not specified | Uncertain significance (Dec 18, 2023) | ||
| 8-30797751-G-A | not specified | Uncertain significance (Nov 30, 2021) | ||
| 8-30799661-A-G | not specified | Uncertain significance (Feb 08, 2023) | ||
| 8-30799712-C-T | not specified | Uncertain significance (Feb 23, 2025) | ||
| 8-30799716-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 8-30799730-G-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 8-30799737-T-C | not specified | Uncertain significance (Jan 16, 2025) | ||
| 8-30799755-C-T | not specified | Uncertain significance (Jan 22, 2024) | ||
| 8-30812324-T-C | not specified | Uncertain significance (Sep 01, 2021) | ||
| 8-30812367-C-T | not specified | Uncertain significance (Feb 22, 2023) | ||
| 8-30812390-T-C | not specified | Uncertain significance (Nov 15, 2024) | ||
| 8-30812403-T-C | not specified | Uncertain significance (Aug 22, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP2CB | protein_coding | protein_coding | ENST00000221138 | 7 | 39858 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.344 | 0.655 | 125721 | 0 | 7 | 125728 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.11 | 61 | 178 | 0.343 | 0.00000977 | 2002 |
| Missense in Polyphen | 17 | 65.789 | 0.2584 | 752 | ||
| Synonymous | -0.0616 | 60 | 59.4 | 1.01 | 0.00000295 | 583 |
| Loss of Function | 2.99 | 4 | 17.5 | 0.229 | 9.09e-7 | 206 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: PP2A can modulate the activity of phosphorylase B kinase casein kinase 2, mitogen-stimulated S6 kinase, and MAP-2 kinase. {ECO:0000269|PubMed:2555176}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);TGF-beta signaling pathway - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Long-term depression - Homo sapiens (human);Tight junction - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);Autophagy - other - 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);Serotonin Transporter Activity;Dopamine metabolism;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Wnt Signaling Pathway and Pluripotency;Exercise-induced Circadian Regulation;PI3K-Akt Signaling Pathway;Glycogen Metabolism;Monoamine Transport;Signaling by GPCR;Negative regulation of FGFR2 signaling;Signaling by FGFR2;Degradation of beta-catenin by the destruction complex;RAF activation;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Negative regulation of FGFR3 signaling;Signaling by FGFR3;Signaling by WNT;Signal Transduction;Gene expression (Transcription);Inhibition of replication initiation of damaged DNA by RB1/E2F1;Signaling by Interleukins;Negative regulation of FGFR4 signaling;Signaling by FGFR4;Signaling by FGFR;Spry regulation of FGF signaling;Generic Transcription Pathway;Metabolism of carbohydrates;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;PP2A-mediated dephosphorylation of key metabolic factors;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;CTLA4 inhibitory signaling;Costimulation by the CD28 family;MASTL Facilitates Mitotic Progression;RNA Polymerase II Transcription;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Innate Immune System;Immune System;Metabolism;Cyclin D associated events in G1;G1 Phase;Adaptive Immune System;RHO GTPases Activate Formins;E2F mediated regulation of DNA replication;Mitotic G1-G1/S phases;Nuclear Events (kinase and transcription factor activation);Disassembly of the destruction complex and recruitment of AXIN to the membrane;Cyclin A/B1/B2 associated events during G2/M transition;DARPP-32 events;Glycolysis;RHO GTPase Effectors;Signaling by Rho GTPases;ERKs are inactivated;Signaling by NTRK1 (TRKA);Signaling by NTRKs;ERK/MAPK targets;MAPK targets/ Nuclear events mediated by MAP kinases;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;Hemostasis;MyD88 dependent cascade initiated on endosome;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;G2/M Transition;Mitotic G2-G2/M phases;PIP3 activates AKT signaling;G1/S Transition;Beta-catenin phosphorylation cascade;Mitotic Prophase;Regulation of TP53 Activity;Transcriptional Regulation by TP53;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;Opioid Signalling;G alpha (i) signalling events;M Phase;Glucose metabolism;Cell Cycle;Resolution of Sister Chromatid Cohesion;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases;Integration of energy metabolism;Platelet sensitization by LDL;Platelet homeostasis;Cell Cycle, Mitotic;GPCR downstream signalling;Intracellular signaling by second messengers;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;TCF dependent signaling in response to WNT;TGF-beta receptor signaling;Negative regulation of FGFR1 signaling;Signaling by FGFR1
(Consensus)
Recessive Scores
- pRec
- 0.171
Intolerance Scores
- loftool
- 0.472
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.717
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.694
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.945
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp2cb
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- protein dephosphorylation;apoptotic mitochondrial changes;response to lead ion;regulation of gene expression;response to endoplasmic reticulum stress;peptidyl-threonine dephosphorylation;response to hydrogen peroxide;proteasome-mediated ubiquitin-dependent protein catabolic process;negative regulation of Ras protein signal transduction;peptidyl-serine dephosphorylation;positive regulation of microtubule binding
- Cellular component
- protein phosphatase type 2A complex;chromosome, centromeric region;spindle pole;nucleus;cytosol
- Molecular function
- protein serine/threonine phosphatase activity;protein binding;protein C-terminus binding;metal ion binding;tau protein binding