PPP2CB
protein-codingprotein phosphatase 2 catalytic subunit beta, the group of STRIPAK complex|Protein phosphatase catalytic subunits
Gene summary
This gene encodes the phosphatase 2A catalytic subunit. Protein phosphatase 2A is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. This gene encodes a beta isoform of the catalytic subunit. [provided by RefSeq, Mar 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~39.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PPP2CB variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001009552.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 1 | 4 | |||
| missense | 29 | 1 | 30 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 35 | 2 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001009552.1 | 7 | MANE Select | |
| Ensembl | ENSP00000221138.4 | 7 | MANE Select | |
| Ensembl | ENSP00000428618.1 | 5 | Standard | |
| Ensembl | ENSP00000428142.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- protein dephosphorylation
- apoptotic mitochondrial changes
- response to lead ion
- regulation of gene expression
- response to endoplasmic reticulum stress
Molecular Function
- protein serine/threonine phosphatase activity
- protein binding
- protein C-terminus binding
- metal ion binding
- tau protein binding
Cellular Component
- protein phosphatase type 2A complex
- chromosome, centromeric region
- spindle pole
- nucleus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000221138
- Coding exons
- 7
- Length
- 39858
- Individuals with no LoFs
- 125721
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125728
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.11 | 61 | 178 | 0.343 | 0.00000977 | 2002 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.171
Intolerance Scores
- LoFtool
- 0.472
- RVIS EVS
- -0.19
- RVIS percentile EVS
- 39.68
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.945
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |