PPP3CB
protein phosphatase 3 catalytic subunit beta, the group of Protein phosphatase catalytic subunits
Basic information
Region (hg38): 10:73436433-73496024
Previous symbols: [ "CALNB" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP3CB 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in PPP3CB
This is a list of pathogenic ClinVar variants found in the PPP3CB region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-73438264-G-A | not specified | Uncertain significance (Mar 20, 2024) | ||
| 10-73438267-C-T | not specified | Uncertain significance (Dec 03, 2024) | ||
| 10-73438292-T-C | not specified | Uncertain significance (Jan 30, 2024) | ||
| 10-73438325-C-A | not specified | Uncertain significance (Jul 12, 2023) | ||
| 10-73439887-T-C | not specified | Uncertain significance (Dec 07, 2021) | ||
| 10-73471488-T-C | not specified | Uncertain significance (Aug 19, 2024) | ||
| 10-73479342-C-T | not specified | Uncertain significance (Jun 11, 2021) | ||
| 10-73479358-C-T | not specified | Uncertain significance (Oct 16, 2024) | ||
| 10-73479449-C-T | not specified | Uncertain significance (Mar 22, 2023) | ||
| 10-73479463-T-A | not specified | Uncertain significance (Aug 14, 2023) | ||
| 10-73495826-C-T | not specified | Uncertain significance (May 10, 2023) | ||
| 10-73495874-G-C | not specified | Uncertain significance (Nov 10, 2024) | ||
| 10-73495883-C-A | not specified | Uncertain significance (Dec 04, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP3CB | protein_coding | protein_coding | ENST00000394829 | 14 | 59597 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000202 | 125540 | 0 | 1 | 125541 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.79 | 100 | 278 | 0.360 | 0.0000138 | 3431 |
| Missense in Polyphen | 10 | 89.336 | 0.11194 | 1115 | ||
| Synonymous | 0.271 | 95 | 98.4 | 0.965 | 0.00000509 | 984 |
| Loss of Function | 5.11 | 0 | 30.4 | 0.00 | 0.00000174 | 367 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000881 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-dependent, calmodulin-stimulated protein phosphatase which plays an essential role in the transduction of intracellular Ca(2+)-mediated signals (PubMed:19154138, PubMed:26794871). Dephosphorylates and activates transcription factor NFATC1 (PubMed:19154138). Dephosphorylates and inactivates transcription factor ELK1 (PubMed:19154138). Dephosphorylates DARPP32 (PubMed:19154138). {ECO:0000269|PubMed:19154138, ECO:0000269|PubMed:26794871}.;
- 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;Physiological and Pathological Hypertrophy of the Heart;Energy Metabolism;MicroRNAs in cardiomyocyte hypertrophy;Alzheimers Disease;Amyotrophic lateral sclerosis (ALS);Initiation of transcription and translation elongation at the HIV-1 LTR;MAPK Signaling Pathway;Wnt Signaling Pathway;Developmental Biology;Signaling by GPCR;Signaling by WNT;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;Calcineurin activates NFAT;Signaling by the B Cell Receptor (BCR);CLEC7A (Dectin-1) induces NFAT activation;CLEC7A (Dectin-1) signaling;C-type lectin receptors (CLRs);FCERI mediated Ca+2 mobilization;Fc epsilon receptor (FCERI) signaling;TCR;Innate Immune System;Immune System;Adaptive Immune System;Downstream signaling events of B Cell Receptor (BCR);DARPP-32 events;ROBO receptors bind AKAP5;Ca2+ pathway;Beta-catenin independent WNT signaling;fmlp induced chemokine gene expression in hmc-1 cells;BCR signaling pathway;Signaling by ROBO receptors;Opioid Signalling;G alpha (i) signalling events;Axon guidance;GPCR downstream signalling;ErbB2/ErbB3 signaling events;CD4 T cell receptor signaling-JNK cascade;CD4 T cell receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.185
Intolerance Scores
- loftool
- 0.156
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.760
- hipred
- Y
- hipred_score
- 0.794
- ghis
- 0.634
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp3cb
- Phenotype
- muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; hematopoietic system 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); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- negative regulation of T cell mediated cytotoxicity;lymphangiogenesis;protein phosphorylation;protein dephosphorylation;signal transduction;Wnt signaling pathway, calcium modulating pathway;heart development;learning;memory;dephosphorylation;calcium ion regulated exocytosis;T cell differentiation;locomotion involved in locomotory behavior;calcineurin-NFAT signaling cascade;response to cytokine;social behavior;cellular response to drug;positive regulation of insulin secretion involved in cellular response to glucose stimulus;Fc-epsilon receptor signaling pathway;T cell proliferation;T cell activation;T cell homeostasis;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;regulation of synaptic plasticity;axon extension;regulation of insulin secretion;calcineurin-mediated signaling;regulation of synaptic vesicle endocytosis
- Cellular component
- nucleoplasm;cytoplasm;cytosol;plasma membrane;calcineurin complex;Z disc;T-tubule;glutamatergic synapse
- Molecular function
- protein serine/threonine phosphatase activity;calcium ion binding;protein binding;calmodulin binding;drug binding;enzyme binding;protein phosphatase 2B binding;calmodulin-dependent protein phosphatase activity;protein dimerization activity