PKN2
protein kinase N2, the group of C2 domain containing protein kinases|AGC family kinases|Small nucleolar RNA protein coding host genes
Basic information
Region (hg38): 1:88684222-88836255
Previous symbols: [ "PRKCL2" ]
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 PKN2 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 | 32 | 33 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 32 | 1 | 0 |
Variants in PKN2
This is a list of pathogenic ClinVar variants found in the PKN2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-88684617-A-G | not specified | Uncertain significance (Nov 24, 2024) | ||
| 1-88684618-C-G | not specified | Uncertain significance (Dec 04, 2024) | ||
| 1-88740998-G-A | not specified | Uncertain significance (Nov 07, 2023) | ||
| 1-88741007-C-T | not specified | Uncertain significance (Jan 19, 2024) | ||
| 1-88741057-A-G | not specified | Likely benign (Feb 28, 2024) | ||
| 1-88760261-G-T | not specified | Uncertain significance (Mar 14, 2023) | ||
| 1-88760296-C-A | not specified | Uncertain significance (Aug 16, 2021) | ||
| 1-88771466-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 1-88771467-G-C | not specified | Uncertain significance (Sep 01, 2024) | ||
| 1-88771738-G-A | not specified | Uncertain significance (Mar 20, 2024) | ||
| 1-88771823-G-C | not specified | Uncertain significance (Jun 12, 2023) | ||
| 1-88771829-T-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 1-88771847-A-G | not specified | Uncertain significance (Jun 21, 2021) | ||
| 1-88784676-C-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 1-88784744-C-T | not specified | Uncertain significance (Apr 23, 2024) | ||
| 1-88784760-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
| 1-88784770-A-C | not specified | Uncertain significance (Aug 20, 2024) | ||
| 1-88784785-G-A | not specified | Uncertain significance (Dec 16, 2022) | ||
| 1-88784795-G-A | not specified | Uncertain significance (Jun 28, 2022) | ||
| 1-88786179-C-T | not specified | Uncertain significance (Jun 26, 2023) | ||
| 1-88804418-T-C | not specified | Uncertain significance (Mar 25, 2024) | ||
| 1-88804422-G-A | not specified | Uncertain significance (Apr 18, 2024) | ||
| 1-88804856-T-C | not specified | Uncertain significance (Aug 21, 2024) | ||
| 1-88805616-C-T | not specified | Uncertain significance (Nov 08, 2021) | ||
| 1-88805625-G-A | not specified | Uncertain significance (Aug 04, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PKN2 | protein_coding | protein_coding | ENST00000370521 | 22 | 152034 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000100 | 124774 | 0 | 9 | 124783 | 0.0000361 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.97 | 319 | 507 | 0.629 | 0.0000257 | 6482 |
| Missense in Polyphen | 57 | 172.56 | 0.33033 | 2283 | ||
| Synonymous | 0.512 | 161 | 169 | 0.950 | 0.00000838 | 1825 |
| Loss of Function | 6.28 | 3 | 51.7 | 0.0580 | 0.00000276 | 655 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000930 | 0.0000930 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000560 | 0.0000556 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000354 | 0.0000353 |
| Middle Eastern | 0.0000560 | 0.0000556 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000165 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: PKC-related serine/threonine-protein kinase and Rho/Rac effector protein that participates in specific signal transduction responses in the cell. Plays a role in the regulation of cell cycle progression, actin cytoskeleton assembly, cell migration, cell adhesion, tumor cell invasion and transcription activation signaling processes. Phosphorylates CTTN in hyaluronan-induced astrocytes and hence decreases CTTN ability to associate with filamentous actin. Phosphorylates HDAC5, therefore lead to impair HDAC5 import. Direct RhoA target required for the regulation of the maturation of primordial junctions into apical junction formation in bronchial epithelial cells. Required for G2/M phases of the cell cycle progression and abscission during cytokinesis in a ECT2-dependent manner. Stimulates FYN kinase activity that is required for establishment of skin cell-cell adhesion during keratinocytes differentiation. Regulates epithelial bladder cells speed and direction of movement during cell migration and tumor cell invasion. Inhibits Akt pro-survival-induced kinase activity. Mediates Rho protein-induced transcriptional activation via the c- fos serum response factor (SRF). Phosphorylates HCV NS5B leading to stimulation of HCV RNA replication. Involved in the negative regulation of ciliogenesis (PubMed:27104747). {ECO:0000269|PubMed:10226025, ECO:0000269|PubMed:10926925, ECO:0000269|PubMed:11777936, ECO:0000269|PubMed:11781095, ECO:0000269|PubMed:15364941, ECO:0000269|PubMed:17332740, ECO:0000269|PubMed:20188095, ECO:0000269|PubMed:20974804, ECO:0000269|PubMed:21754995, ECO:0000269|PubMed:27104747, ECO:0000269|PubMed:9121475}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Salmonella infection - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;PI3K-Akt Signaling Pathway;Signal Transduction;RHO GTPases activate PKNs;RHO GTPase Effectors;Signaling by Rho GTPases;EGFR1;RhoA signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.187
Intolerance Scores
- loftool
- 0.298
- rvis_EVS
- -1.07
- rvis_percentile_EVS
- 7.43
Haploinsufficiency Scores
- pHI
- 0.530
- hipred
- Y
- hipred_score
- 0.739
- ghis
- 0.656
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.842
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pkn2
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; respiratory system 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); normal 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); embryo phenotype;
Zebrafish Information Network
- Gene name
- pkn2
- Affected structure
- melanocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- protein phosphorylation;apoptotic process;cell cycle;cell adhesion;signal transduction;epithelial cell migration;peptidyl-serine phosphorylation;cell projection organization;positive regulation of cytokinesis;intracellular signal transduction;apical junction assembly;positive regulation of viral genome replication;positive regulation of mitotic cell cycle;cell division;regulation of cell motility
- Cellular component
- nucleus;nucleoplasm;cytoplasm;centrosome;cytosol;plasma membrane;nuclear body;lamellipodium;midbody;cleavage furrow;protein-containing complex;apical junction complex;intermediate filament cytoskeleton;perinuclear region of cytoplasm
- Molecular function
- RNA binding;protein kinase activity;protein serine/threonine kinase activity;protein kinase C activity;protein binding;ATP binding;kinase activity;GTP-Rho binding;histone deacetylase binding;cadherin binding;RNA polymerase binding