PPP2R5A
protein-codingprotein 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
Gene summary
The product of this gene belongs to the phosphatase 2A regulatory subunit B family. 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. The B regulatory subunit might modulate substrate selectivity and catalytic activity. This gene encodes an alpha isoform of the regulatory subunit B56 subfamily. Alternative transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Dec 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~76.4 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 PPP2R5A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006243.4. 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 | 0 | |||||
| missense | 41 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 45 | 0 | 0 | 45 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006234.1 | 13 | MANE Select | |
| Ensembl | ENSP00000261461.2 | 13 | MANE Select | |
| RefSeq | NP_001186685.1 | 13 | Standard | |
| Ensembl | ENSP00000442866.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- protein dephosphorylation
- signal transduction
- regulation of protein autophosphorylation
- positive regulation of protein dephosphorylation
- regulation of phosphoprotein phosphatase activity
Molecular Function
- phosphoprotein phosphatase activity
- protein binding
- protein phosphatase regulator activity
- kinase binding
- protein phosphatase activator activity
Cellular Component
- protein phosphatase type 2A complex
- chromosome, centromeric region
- nucleus
- cytoplasm
- centrosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000261461
- Coding exons
- 13
- Length
- 76322
- Individuals with no LoFs
- 125667
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125680
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.41 | 128 | 231 | 0.554 | 0.0000111 | 3193 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00011 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000063 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000057 | 0.000053 | rare |
| South Asian | 0.00011 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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.;
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- LoFtool
- 0.176
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 33.97
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.976
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |