PPP1CC
protein phosphatase 1 catalytic subunit gamma, the group of Protein phosphatase catalytic subunits
Basic information
Region (hg38): 12:110719679-110742939
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (3 variants)
- not provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1CC 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 | 0 | |||||
| missense | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in PPP1CC
This is a list of pathogenic ClinVar variants found in the PPP1CC region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-110720185-C-T | not provided (-) | |||
| 12-110721128-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 12-110722665-T-A | not specified | Uncertain significance (May 27, 2022) | ||
| 12-110731817-A-C | not specified | Uncertain significance (Jan 23, 2023) | ||
| 12-110731881-T-C | not provided (-) | |||
| 12-110742689-G-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| 12-110742702-C-A | not provided (-) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP1CC | protein_coding | protein_coding | ENST00000340766 | 8 | 23260 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.958 | 0.0422 | 125732 | 0 | 12 | 125744 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.36 | 53 | 180 | 0.295 | 0.00000895 | 2211 |
| Missense in Polyphen | 10 | 59.979 | 0.16672 | 784 | ||
| Synonymous | -0.166 | 67 | 65.3 | 1.03 | 0.00000344 | 610 |
| Loss of Function | 3.58 | 2 | 18.7 | 0.107 | 0.00000104 | 226 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000964 | 0.0000964 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000720 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protein phosphatase that associates with over 200 regulatory proteins to form highly specific holoenzymes which dephosphorylate hundreds of biological targets. Protein phosphatase 1 (PP1) is essential for cell division, and participates in the regulation of glycogen metabolism, muscle contractility and protein synthesis. Dephosphorylates RPS6KB1. Involved in regulation of ionic conductances and long-term synaptic plasticity. May play an important role in dephosphorylating substrates such as the postsynaptic density- associated Ca(2+)/calmodulin dependent protein kinase II. Component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. In balance with CSNK1D and CSNK1E, determines the circadian period length, through the regulation of the speed and rhythmicity of PER1 and PER2 phosphorylation. May dephosphorylate CSNK1D and CSNK1E. Dephosphorylates the 'Ser-418' residue of FOXP3 in regulatory T- cells (Treg) from patients with rheumatoid arthritis, thereby inactivating FOXP3 and rendering Treg cells functionally defective (PubMed:23396208). {ECO:0000269|PubMed:17936702, ECO:0000269|PubMed:20516061, ECO:0000269|PubMed:21712997, ECO:0000269|PubMed:23396208}.;
- Pathway
- Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Platelet activation - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Long-term potentiation - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Insulin resistance - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Alcoholism - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);TGF-Ncore;Common Pathways Underlying Drug Addiction;Focal Adhesion;Signal Transduction;Circadian Clock;Metabolism of lipids;GPCR Dopamine D1like receptor;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Metabolism;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Triglyceride catabolism;Triglyceride metabolism;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Cell Cycle, Mitotic;Downregulation of TGF-beta receptor signaling;TGF-beta receptor signaling activates SMADs;Aurora B signaling;Insulin-mediated glucose transport
(Consensus)
Recessive Scores
- pRec
- 0.292
Intolerance Scores
- loftool
- 0.518
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.999
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.673
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp1cc
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- ppp1cc
- Affected structure
- intersegmental vessel
- Phenotype tag
- abnormal
- Phenotype quality
- decreased functionality
Gene ontology
- Biological process
- glycogen metabolic process;protein dephosphorylation;cell cycle;neuron differentiation;circadian regulation of gene expression;regulation of circadian rhythm;entrainment of circadian clock by photoperiod;regulation of nucleocytoplasmic transport;cell division;positive regulation of glial cell proliferation
- Cellular component
- protein phosphatase type 1 complex;condensed chromosome kinetochore;nuclear chromosome, telomeric region;nucleus;nucleolus;cytoplasm;mitochondrion;mitochondrial outer membrane;cytosol;focal adhesion;nuclear speck;midbody;cleavage furrow;protein-containing complex;dendritic spine;PTW/PP1 phosphatase complex;presynapse;glutamatergic synapse
- Molecular function
- RNA binding;phosphoprotein phosphatase activity;protein serine/threonine phosphatase activity;protein binding;lamin binding;protein C-terminus binding;protein phosphatase 1 binding;phosphatase activity;protein kinase binding;protein domain specific binding;protein-containing complex binding;metal ion binding;protein N-terminus binding