PPP2R5C
protein phosphatase 2 regulatory subunit B'gamma, the group of Protein phosphatase 2 regulatory subunits|Armadillo like helical domain containing
Basic information
Region (hg38): 14:101761709-101927989
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Moderate), mode of inheritance: AD
- neurodevelopmental disorder (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (65 variants)
- not_specified (32 variants)
- PPP2R5C-related_disorder (6 variants)
- Prostate_cancer (1 variants)
- Neurodevelopmental_disorder (1 variants)
- Macrocephaly-developmental_delay_syndrome (1 variants)
- HOUGE-JANSSENS_SYNDROME_4 (1 variants)
- Global_developmental_delay (1 variants)
- Intellectual_disability (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R5C gene is commonly pathogenic or not. These statistics are base on transcript: NM_001352913.2. 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 | 12 | 14 | ||||
| missense | 43 | 50 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 4 | 44 | 14 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP2R5C | protein_coding | protein_coding | ENST00000422945 | 16 | 166192 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.971 | 0.0293 | 125729 | 0 | 18 | 125747 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.08 | 150 | 300 | 0.499 | 0.0000161 | 3669 |
| Missense in Polyphen | 32 | 101.99 | 0.31376 | 1324 | ||
| Synonymous | 0.687 | 98 | 107 | 0.915 | 0.00000609 | 980 |
| Loss of Function | 4.51 | 5 | 33.0 | 0.152 | 0.00000162 | 428 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000185 | 0.000185 |
| 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 | 0.000392 | 0.000392 |
| 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. The PP2A-PPP2R5C holoenzyme may specifically dephosphorylate and activate TP53 and play a role in DNA damage- induced inhibition of cell proliferation. PP2A-PPP2R5C may also regulate the ERK signaling pathway through ERK dephosphorylation. {ECO:0000269|PubMed:16456541, ECO:0000269|PubMed:17245430}.;
- 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);miR-targeted genes in lymphocytes - TarBase;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Glycogen Metabolism;DNA Damage Response (only ATM dependent);Degradation of beta-catenin by the destruction complex;RAF activation;Signaling by WNT;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;GPCR Dopamine D1like receptor;CTLA4 inhibitory signaling;Costimulation by the CD28 family;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;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;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;PIP3 activates AKT signaling;Beta-catenin phosphorylation cascade;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;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Platelet sensitization by LDL;Platelet homeostasis;Cell Cycle, Mitotic;Intracellular signaling by second messengers;TCF dependent signaling in response to WNT;insulin
(Consensus)
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- 0.0814
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.45
Haploinsufficiency Scores
- pHI
- 0.160
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.616
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.981
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp2r5c
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; muscle phenotype;
Gene ontology
- Biological process
- protein dephosphorylation;signal transduction;negative regulation of cell population proliferation;regulation of phosphatidylinositol 3-kinase signaling;regulation of protein autophosphorylation;proteasome-mediated ubiquitin-dependent protein catabolic process;regulation of phosphoprotein phosphatase activity
- Cellular component
- protein phosphatase type 2A complex;chromosome, centromeric region;nucleus;nucleoplasm;Golgi apparatus;cytosol
- Molecular function
- protein binding;protein phosphatase regulator activity;protein phosphatase activator activity