PRKAB1
protein kinase AMP-activated non-catalytic subunit beta 1
Basic information
Region (hg38): 12:119667863-119681624
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 PRKAB1 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 1 |
Variants in PRKAB1
This is a list of pathogenic ClinVar variants found in the PRKAB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-119668361-C-G | not specified | Uncertain significance (Apr 21, 2022) | ||
| 12-119668380-C-T | not specified | Uncertain significance (Jul 20, 2021) | ||
| 12-119672364-G-T | not specified | Uncertain significance (Dec 21, 2022) | ||
| 12-119672374-G-A | not specified | Uncertain significance (Jan 04, 2024) | ||
| 12-119672380-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 12-119672396-G-A | Benign (Apr 26, 2018) | |||
| 12-119672400-G-A | not specified | Uncertain significance (Nov 21, 2023) | ||
| 12-119672403-G-A | not specified | Uncertain significance (Apr 08, 2024) | ||
| 12-119674041-C-T | not specified | Uncertain significance (May 13, 2024) | ||
| 12-119674341-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 12-119674395-C-G | not specified | Uncertain significance (Mar 27, 2023) | ||
| 12-119674424-G-C | not specified | Uncertain significance (Aug 02, 2021) | ||
| 12-119676581-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 12-119676606-G-C | not specified | Uncertain significance (Jan 03, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRKAB1 | protein_coding | protein_coding | ENST00000229328 | 7 | 13878 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00526 | 0.972 | 125735 | 0 | 13 | 125748 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.25 | 116 | 160 | 0.723 | 0.00000890 | 1778 |
| Missense in Polyphen | 40 | 63.752 | 0.62743 | 723 | ||
| Synonymous | 0.610 | 63 | 69.5 | 0.907 | 0.00000460 | 519 |
| Loss of Function | 1.99 | 6 | 14.1 | 0.427 | 7.63e-7 | 148 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000215 | 0.000214 |
| Ashkenazi Jewish | 0.0000994 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000468 | 0.0000462 |
| European (Non-Finnish) | 0.0000529 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Non-catalytic subunit of AMP-activated protein kinase (AMPK), an energy sensor protein kinase that plays a key role in regulating cellular energy metabolism. In response to reduction of intracellular ATP levels, AMPK activates energy-producing pathways and inhibits energy-consuming processes: inhibits protein, carbohydrate and lipid biosynthesis, as well as cell growth and proliferation. AMPK acts via direct phosphorylation of metabolic enzymes, and by longer-term effects via phosphorylation of transcription regulators. Also acts as a regulator of cellular polarity by remodeling the actin cytoskeleton; probably by indirectly activating myosin. Beta non-catalytic subunit acts as a scaffold on which the AMPK complex assembles, via its C-terminus that bridges alpha (PRKAA1 or PRKAA2) and gamma subunits (PRKAG1, PRKAG2 or PRKAG3).;
- Pathway
- Oxytocin signaling pathway - Homo sapiens (human);Adipocytokine signaling pathway - Homo sapiens (human);Circadian rhythm - Homo sapiens (human);Insulin resistance - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Longevity regulating pathway - multiple species - Homo sapiens (human);Tight junction - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Metformin Pathway, Pharmacodynamic;AMP-activated Protein Kinase (AMPK) Signaling;Target Of Rapamycin (TOR) Signaling;Energy Metabolism;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;fig-met-1-last-solution;Angiopoietin Like Protein 8 Regulatory Pathway;Leptin and adiponectin;Lipid Metabolism Pathway;Liver steatosis AOP;Hereditary Leiomyomatosis and Renal Cell Carcinoma Pathway;Signal Transduction;Gene expression (Transcription);Vesicle-mediated transport;reversal of insulin resistance by leptin;chrebp regulation by carbohydrates and camp;Membrane Trafficking;Generic Transcription Pathway;RNA Polymerase II Transcription;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;insulin Mam;TP53 Regulates Metabolic Genes;Macroautophagy;Cellular responses to external stimuli;IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Direct p53 effectors;Activation of PPARGC1A (PGC-1alpha) by phosphorylation;Mitochondrial biogenesis;Translocation of GLUT4 to the plasma membrane;VEGF;insulin;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.230
Intolerance Scores
- loftool
- 0.364
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.22
Haploinsufficiency Scores
- pHI
- 0.211
- hipred
- Y
- hipred_score
- 0.731
- ghis
- 0.542
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.984
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prkab1
- Phenotype
- growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; vision/eye 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); normal 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; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; 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);
Gene ontology
- Biological process
- protein phosphorylation;fatty acid biosynthetic process;cell cycle arrest;signal transduction;positive regulation of gene expression;macroautophagy;nail development;regulation of catalytic activity;protein heterooligomerization;positive regulation of cold-induced thermogenesis
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;nucleotide-activated protein kinase complex
- Molecular function
- protein kinase activity;AMP-activated protein kinase activity;protein binding;protein kinase binding