PRKCI
protein kinase C iota, the group of AGC family kinases
Basic information
Region (hg38): 3:170222424-170305977
Previous symbols: [ "DXS1179E" ]
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 PRKCI 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 | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 1 | 0 |
Variants in PRKCI
This is a list of pathogenic ClinVar variants found in the PRKCI region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-170222699-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
| 3-170235322-T-G | not specified | Uncertain significance (Nov 30, 2022) | ||
| 3-170235354-G-A | PRKCI-related disorder | Likely benign (Oct 21, 2020) | ||
| 3-170260011-C-G | not specified | Uncertain significance (Feb 15, 2023) | ||
| 3-170260038-A-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 3-170267922-C-G | not specified | Uncertain significance (Mar 02, 2023) | ||
| 3-170267966-A-G | not specified | Uncertain significance (Dec 13, 2023) | ||
| 3-170270533-T-C | not specified | Uncertain significance (Nov 30, 2022) | ||
| 3-170275238-A-G | not specified | Uncertain significance (Jun 09, 2022) | ||
| 3-170280230-A-G | not specified | Uncertain significance (May 13, 2024) | ||
| 3-170280249-G-A | not specified | Uncertain significance (Aug 09, 2021) | ||
| 3-170280336-G-A | not specified | Uncertain significance (Dec 20, 2023) | ||
| 3-170281180-A-C | PRKCI-related disorder | Likely benign (Jun 10, 2019) | ||
| 3-170284483-C-G | not specified | Uncertain significance (Mar 15, 2024) | ||
| 3-170284487-C-G | not specified | Uncertain significance (Jul 16, 2021) | ||
| 3-170284492-A-G | not specified | Uncertain significance (Mar 14, 2023) | ||
| 3-170293378-T-G | PRKCI-related disorder | Likely benign (Jan 05, 2023) | ||
| 3-170293418-A-G | not specified | Uncertain significance (Apr 12, 2022) | ||
| 3-170297365-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 3-170299013-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 3-170299022-T-C | not specified | Uncertain significance (Mar 16, 2022) | ||
| 3-170299108-C-A | not specified | Uncertain significance (Apr 23, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRKCI | protein_coding | protein_coding | ENST00000295797 | 18 | 83617 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0680 | 0.932 | 125722 | 0 | 26 | 125748 | 0.000103 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.79 | 190 | 333 | 0.570 | 0.0000176 | 3978 |
| Missense in Polyphen | 76 | 174 | 0.43678 | 2073 | ||
| Synonymous | -0.717 | 115 | 106 | 1.09 | 0.00000514 | 1058 |
| Loss of Function | 4.27 | 10 | 38.6 | 0.259 | 0.00000222 | 428 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000281 | 0.000278 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000219 | 0.000217 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000794 | 0.0000791 |
| Middle Eastern | 0.000219 | 0.000217 |
| South Asian | 0.0000981 | 0.0000980 |
| Other | 0.000340 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium- and diacylglycerol-independent serine/ threonine-protein kinase that plays a general protective role against apoptotic stimuli, is involved in NF-kappa-B activation, cell survival, differentiation and polarity, and contributes to the regulation of microtubule dynamics in the early secretory pathway. Is necessary for BCR-ABL oncogene-mediated resistance to apoptotic drug in leukemia cells, protecting leukemia cells against drug-induced apoptosis. In cultured neurons, prevents amyloid beta protein-induced apoptosis by interrupting cell death process at a very early step. In glioblastoma cells, may function downstream of phosphatidylinositol 3-kinase (PI(3)K) and PDPK1 in the promotion of cell survival by phosphorylating and inhibiting the pro-apoptotic factor BAD. Can form a protein complex in non- small cell lung cancer (NSCLC) cells with PARD6A and ECT2 and regulate ECT2 oncogenic activity by phosphorylation, which in turn promotes transformed growth and invasion. In response to nerve growth factor (NGF), acts downstream of SRC to phosphorylate and activate IRAK1, allowing the subsequent activation of NF-kappa-B and neuronal cell survival. Functions in the organization of the apical domain in epithelial cells by phosphorylating EZR. This step is crucial for activation and normal distribution of EZR at the early stages of intestinal epithelial cell differentiation. Forms a protein complex with LLGL1 and PARD6B independently of PARD3 to regulate epithelial cell polarity. Plays a role in microtubule dynamics in the early secretory pathway through interaction with RAB2A and GAPDH and recruitment to vesicular tubular clusters (VTCs). In human coronary artery endothelial cells (HCAEC), is activated by saturated fatty acids and mediates lipid-induced apoptosis. {ECO:0000269|PubMed:10356400, ECO:0000269|PubMed:10467349, ECO:0000269|PubMed:10906326, ECO:0000269|PubMed:11042363, ECO:0000269|PubMed:11724794, ECO:0000269|PubMed:12871960, ECO:0000269|PubMed:14684752, ECO:0000269|PubMed:15994303, ECO:0000269|PubMed:18270268, ECO:0000269|PubMed:19327373, ECO:0000269|PubMed:21189248, ECO:0000269|PubMed:21419810, ECO:0000269|PubMed:8226978, ECO:0000269|PubMed:9346882}.;
- Pathway
- Platelet activation - Homo sapiens (human);Endocytosis - Homo sapiens (human);Tight junction - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Proton Pump Inhibitor Pathway, Pharmacodynamics;VEGF Signaling Pathway;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miRs in Muscle Cell Differentiation;Signaling Pathways in Glioblastoma;Corticotropin-releasing hormone signaling pathway;G Protein Signaling Pathways;VEGFA-VEGFR2 Signaling Pathway;Wnt Signaling Pathway and Pluripotency;Steatosis AOP;EGF-EGFR Signaling Pathway;Insulin Signaling;Signal Transduction;p75NTR signals via NF-kB;GPCR GroupI metabotropic glutamate receptor;GPCR signaling-G alpha q;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;Signaling by NOTCH;IL-7 signaling;EGFR1;JAK STAT pathway and regulation;p75NTR recruits signalling complexes;EPO signaling;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Tight junction interactions;Cell-cell junction organization;Cell junction organization;VEGF;Cell-Cell communication;Insulin Pathway;Neurotrophic factor-mediated Trk receptor signaling;TNF receptor signaling pathway ;Insulin-mediated glucose transport;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);p75(NTR)-mediated signaling;IL1-mediated signaling events;Nephrin/Neph1 signaling in the kidney podocyte
(Consensus)
Intolerance Scores
- loftool
- 0.499
- rvis_EVS
- -0.89
- rvis_percentile_EVS
- 10.3
Haploinsufficiency Scores
- pHI
- 0.749
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.656
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.993
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prkci
- Phenotype
- renal/urinary system phenotype; immune system phenotype; vision/eye 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); pigmentation 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); 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); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- prkci
- Affected structure
- neuroepithelial cell
- Phenotype tag
- abnormal
- Phenotype quality
- broken
Gene ontology
- Biological process
- protein phosphorylation;protein targeting to membrane;cytoskeleton organization;actin filament organization;positive regulation of neuron projection development;vesicle-mediated transport;cell migration;peptidyl-serine phosphorylation;cellular response to insulin stimulus;negative regulation of glial cell apoptotic process;establishment of apical/basal cell polarity;intracellular signal transduction;eye photoreceptor cell development;negative regulation of apoptotic process;negative regulation of neuron apoptotic process;establishment or maintenance of epithelial cell apical/basal polarity;cell-cell junction organization;positive regulation of Notch signaling pathway;positive regulation of glucose import;secretion;Golgi vesicle budding;positive regulation of NF-kappaB transcription factor activity;positive regulation of glial cell proliferation;membrane organization;response to interleukin-1;bicellular tight junction assembly;regulation of postsynaptic membrane neurotransmitter receptor levels;positive regulation of protein localization to plasma membrane;positive regulation of endothelial cell apoptotic process
- Cellular component
- Golgi membrane;nucleus;nucleoplasm;endosome;cytosol;plasma membrane;bicellular tight junction;microtubule cytoskeleton;apical plasma membrane;cell leading edge;protein-containing complex;Schmidt-Lanterman incisure;intercellular bridge;extracellular exosome;Schaffer collateral - CA1 synapse;glutamatergic synapse
- Molecular function
- protein kinase activity;protein serine/threonine kinase activity;protein kinase C activity;protein binding;ATP binding;phospholipid binding;protein domain specific binding;metal ion binding