PPP3R1
protein phosphatase 3 regulatory subunit B, alpha, the group of EF-hand domain containing|Protein phosphatase 3 regulatory subunits
Basic information
Region (hg38): 2:68178856-68256237
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 PPP3R1 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 | 1 | |||||
| missense | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 1 | 0 | 2 |
Variants in PPP3R1
This is a list of pathogenic ClinVar variants found in the PPP3R1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-68180794-A-G | Benign (Feb 18, 2020) | |||
| 2-68188635-G-A | Benign (Jun 15, 2021) | |||
| 2-68188684-G-A | not specified | Uncertain significance (Feb 17, 2024) | ||
| 2-68218181-ATTAAT-A | not provided (-) | |||
| 2-68252586-G-GGGCGGAGGCGGGGGCGCGCGCGGGCCGGC | not provided (-) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP3R1 | protein_coding | protein_coding | ENST00000234310 | 6 | 77381 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.415 | 0.578 | 124538 | 0 | 6 | 124544 | 0.0000241 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.89 | 10 | 84.8 | 0.118 | 0.00000380 | 1147 |
| Missense in Polyphen | 1 | 27.524 | 0.036332 | 385 | ||
| Synonymous | 1.02 | 23 | 30.1 | 0.764 | 0.00000151 | 283 |
| Loss of Function | 2.25 | 2 | 9.48 | 0.211 | 4.83e-7 | 123 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000105 | 0.000105 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000291 | 0.0000266 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulatory subunit of calcineurin, a calcium-dependent, calmodulin stimulated protein phosphatase. Confers calcium sensitivity. {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);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;TFs Regulate miRNAs related to cardiac hypertrophy;miR-targeted genes in lymphocytes - TarBase;Alzheimers Disease;Initiation of transcription and translation elongation at the HIV-1 LTR;MAPK Signaling Pathway;Wnt Signaling Pathway;Signaling by GPCR;Signaling by WNT;Signal Transduction;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);Activation of BAD and translocation to mitochondria ;Activation of BH3-only proteins;FCERI mediated Ca+2 mobilization;Fc epsilon receptor (FCERI) signaling;Intrinsic Pathway for Apoptosis;Innate Immune System;Immune System;Apoptosis;Programmed Cell Death;Adaptive Immune System;Downstream signaling events of B Cell Receptor (BCR);DARPP-32 events;Ca2+ pathway;Beta-catenin independent WNT signaling;Opioid Signalling;G alpha (i) signalling events;GPCR downstream signalling;CD4 T cell receptor signaling-JNK cascade;CD4 T cell receptor signaling
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.43
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.594
- ghis
- 0.641
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.486
Mouse Genome Informatics
- Gene name
- Ppp3r1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo 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); hematopoietic system 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- protein dephosphorylation;Wnt signaling pathway, calcium modulating pathway;calcineurin-NFAT signaling cascade;Fc-epsilon receptor signaling pathway;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleoplasm;cytosol;calcineurin complex;sarcolemma
- Molecular function
- calcium-dependent protein serine/threonine phosphatase activity;calcium ion binding;protein binding;calmodulin binding;cyclosporin A binding;phosphatase binding;protein domain specific binding