PRKAR2A
protein kinase cAMP-dependent type II regulatory subunit alpha, the group of Protein kinase A subunits
Basic information
Region (hg38): 3:48744597-48847874
Previous symbols: [ "PRKAR2" ]
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 PRKAR2A 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 | 17 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 2 | 0 |
Variants in PRKAR2A
This is a list of pathogenic ClinVar variants found in the PRKAR2A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-48751593-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 3-48751624-C-T | not specified | Uncertain significance (Mar 26, 2024) | ||
| 3-48752283-A-G | not specified | Uncertain significance (Jul 25, 2023) | ||
| 3-48752311-A-G | not specified | Uncertain significance (Mar 29, 2024) | ||
| 3-48756381-T-C | not specified | Uncertain significance (Aug 02, 2023) | ||
| 3-48765258-T-G | not specified | Uncertain significance (Feb 07, 2023) | ||
| 3-48765325-T-C | not specified | Uncertain significance (May 04, 2023) | ||
| 3-48773052-T-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 3-48773059-C-T | not specified | Uncertain significance (Oct 12, 2022) | ||
| 3-48773080-C-G | not specified | Uncertain significance (Nov 17, 2023) | ||
| 3-48783035-G-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| 3-48783082-G-C | not specified | Uncertain significance (Jan 23, 2023) | ||
| 3-48794004-T-C | not specified | Uncertain significance (May 30, 2024) | ||
| 3-48794026-C-T | not specified | Uncertain significance (Feb 14, 2023) | ||
| 3-48794029-G-A | not specified | Uncertain significance (May 06, 2022) | ||
| 3-48807673-T-C | not specified | Uncertain significance (Jan 24, 2023) | ||
| 3-48847365-T-C | not specified | Uncertain significance (Mar 24, 2023) | ||
| 3-48847391-T-G | not specified | Uncertain significance (Mar 06, 2023) | ||
| 3-48847421-A-G | not specified | Likely benign (Jul 14, 2021) | ||
| 3-48847437-T-G | not specified | Likely benign (Nov 30, 2021) | ||
| 3-48847457-G-A | not specified | Uncertain significance (Jul 19, 2022) | ||
| 3-48847527-G-C | not specified | Uncertain significance (Feb 16, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRKAR2A | protein_coding | protein_coding | ENST00000265563 | 11 | 103250 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.119 | 0.881 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.26 | 167 | 220 | 0.760 | 0.0000112 | 2625 |
| Missense in Polyphen | 45 | 85.1 | 0.52879 | 1078 | ||
| Synonymous | 0.323 | 77 | 80.7 | 0.954 | 0.00000406 | 761 |
| Loss of Function | 3.24 | 6 | 22.6 | 0.265 | 0.00000116 | 272 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000682 | 0.0000615 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000334 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulatory subunit of the cAMP-dependent protein kinases involved in cAMP signaling in cells. Type II regulatory chains mediate membrane association by binding to anchoring proteins, including the MAP2 kinase.;
- Pathway
- Insulin signaling pathway - Homo sapiens (human);miRs in Muscle Cell Differentiation;Myometrial Relaxation and Contraction Pathways;G Protein Signaling Pathways;TGF-beta Signaling Pathway;Lipid Metabolism Pathway;Liver steatosis AOP;Calcium Regulation in the Cardiac Cell;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Developmental Biology;Signaling by GPCR;Signal Transduction;mechanism of gene regulation by peroxisome proliferators via ppara;phospholipase c-epsilon pathway;gata3 participate in activating the th2 cytokine genes expression;repression of pain sensation by the transcriptional regulator dream;transcription factor creb and its extracellular signals;regulation of ck1/cdk5 by type 1 glutamate receptors;nitric oxide signaling pathway;stathmin and breast cancer resistance to antimicrotubule agents;cystic fibrosis transmembrane conductance regulator (cftr) and beta 2 adrenergic receptor (b2ar) pathway;regulation of bad phosphorylation;transcription regulation by methyltransferase of carm1;activation of csk by camp-dependent protein kinase inhibits signaling through the t cell receptor;mcalpain and friends in cell motility;rho-selective guanine exchange factor akap13 mediates stress fiber formation;chrebp regulation by carbohydrates and camp;signaling pathway from g-protein families;how progesterone initiates the oocyte maturation;protein kinase a at the centrosome;attenuation of gpcr signaling;activation of camp-dependent protein kinase pka;Glucagon signaling in metabolic regulation;GPCR Dopamine D1like receptor;Factors involved in megakaryocyte development and platelet production;GPCR Adenosine A2A receptor;GPCR signaling-cholera toxin;Hedgehog;Metabolism;PKA activation;PKA-mediated phosphorylation of CREB;Calmodulin induced events;CaM pathway;Transport of small molecules;Glucagon-like Peptide-1 (GLP1) regulates insulin secretion;Regulation of insulin secretion;actions of nitric oxide in the heart;akap95 role in mitosis and chromosome dynamics;Hedgehog ,off, state;DARPP-32 events;IL-7 signaling;GPCR signaling-G alpha s PKA and ERK;Signaling by Hedgehog;TGF_beta_Receptor;ROBO receptors bind AKAP5;Hemostasis;DAG and IP3 signaling;JAK STAT pathway and regulation;EPO signaling;Signaling by ROBO receptors;Ca-dependent events;PLC beta mediated events;G-protein mediated events;Opioid Signalling;G alpha (i) signalling events;Axon guidance;PKA activation in glucagon signalling;Vasopressin regulates renal water homeostasis via Aquaporins;Aquaporin-mediated transport;Integration of energy metabolism;VEGF;GPCR downstream signalling;Intracellular signaling by second messengers
(Consensus)
Recessive Scores
- pRec
- 0.321
Intolerance Scores
- loftool
- 0.231
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- 0.798
- hipred
- Y
- hipred_score
- 0.729
- ghis
- 0.573
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.544
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prkar2a
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- renal water homeostasis;blood coagulation;cGMP-mediated signaling;activation of protein kinase A activity;intracellular signal transduction;cellular response to glucagon stimulus;negative regulation of cAMP-dependent protein kinase activity
- Cellular component
- cytoplasm;centrosome;cytosol;plasma membrane;focal adhesion;axoneme;cAMP-dependent protein kinase complex;membrane;nucleotide-activated protein kinase complex;protein-containing complex;plasma membrane raft;extracellular exosome;ciliary base
- Molecular function
- cAMP-dependent protein kinase inhibitor activity;protein binding;cAMP-dependent protein kinase regulator activity;protein domain specific binding;cAMP binding;ubiquitin protein ligase binding;protein kinase A catalytic subunit binding;3',5'-cyclic-GMP phosphodiesterase activity