PPP3CC
protein phosphatase 3 catalytic subunit gamma, the group of Protein phosphatase catalytic subunits
Basic information
Region (hg38): 8:22440819-22541142
Links
Phenotypes
GenCC
Source:
- schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (51 variants)
- not_provided (2 variants)
- Keratoconus (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP3CC gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005605.5. 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 | 0 | |||||
| missense | 51 | 53 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 51 | 2 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP3CC | protein_coding | protein_coding | ENST00000397775 | 15 | 100321 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.264 | 0.736 | 125721 | 0 | 26 | 125747 | 0.000103 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.32 | 222 | 284 | 0.780 | 0.0000148 | 3404 |
| Missense in Polyphen | 76 | 108.41 | 0.70107 | 1305 | ||
| Synonymous | 1.31 | 86 | 103 | 0.836 | 0.00000549 | 971 |
| Loss of Function | 3.86 | 7 | 29.7 | 0.236 | 0.00000157 | 359 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000909 | 0.0000908 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000177 | 0.000176 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000391 | 0.0000327 |
| Other | 0.000327 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-dependent, calmodulin-stimulated protein phosphatase which plays an essential role in the transduction of intracellular Ca(2+)-mediated signals. Dephosphorylates and activates transcription factor NFATC1. Dephosphorylates and inactivates transcription factor ELK1. Dephosphorylates DARPP32. {ECO:0000269|PubMed:19154138}.;
- Pathway
- Oxytocin signaling pathway - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);B cell receptor signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Long-term potentiation - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Axon guidance - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Renin secretion - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Tacrolimus/Cyclosporine Pathway, Pharmacodynamics;Energy Metabolism;Alzheimers Disease;Amyotrophic lateral sclerosis (ALS);Initiation of transcription and translation elongation at the HIV-1 LTR;G Protein Signaling Pathways;MAPK Signaling Pathway;Wnt Signaling Pathway;Signaling by GPCR;Signal Transduction;regulation of pgc-1a;nitric oxide signaling pathway;endocytotic role of ndk phosphins and dynamin;role of mef2d in t-cell apoptosis;effects of calcineurin in keratinocyte differentiation;nfat and hypertrophy of the heart ;signaling pathway from g-protein families;t cell receptor signaling pathway;bcr signaling pathway;Activation of BAD and translocation to mitochondria ;Activation of BH3-only proteins;Intrinsic Pathway for Apoptosis;Apoptosis;Programmed Cell Death;DARPP-32 events;fmlp induced chemokine gene expression in hmc-1 cells;BCR signaling pathway;Opioid Signalling;G alpha (i) signalling events;GPCR downstream signalling;CD4 T cell receptor signaling-JNK cascade;CD4 T cell receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.161
Intolerance Scores
- loftool
- 0.612
- rvis_EVS
- 0.53
- rvis_percentile_EVS
- 80.82
Haploinsufficiency Scores
- pHI
- 0.165
- hipred
- Y
- hipred_score
- 0.704
- ghis
- 0.488
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.900
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp3cc
- Phenotype
- reproductive system phenotype; cellular phenotype;
Gene ontology
- Biological process
- protein dephosphorylation;brain development;calcineurin-NFAT signaling cascade;calcineurin-mediated signaling;positive regulation of synaptic vesicle endocytosis
- Cellular component
- cytoplasm;cytosol;calcineurin complex;glutamatergic synapse;presynaptic cytosol
- Molecular function
- protein binding;calmodulin binding;calmodulin-dependent protein phosphatase activity;metal ion binding