PRKAR2A

protein kinase cAMP-dependent type II regulatory subunit alpha, the group of Protein kinase A subunits

Basic information

Region (hg38): 3:48744596-48847874

Previous symbols: [ "PRKAR2" ]

Links

ENSG00000114302 ∙ NCBI:5576 ∙ OMIM:176910 ∙ HGNC:9391 ∙ Uniprot:P13861 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PRKAR2A gene.

• Inborn genetic diseases (16 variants)

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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	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)
3-48752283-A-G		not specified	Uncertain significance (Jul 25, 2023)
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)
3-48794026-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: gnomAD

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: dbNSFP

• 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