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): 1:88684221-88836255

Previous symbols: [ "PRKCL2" ]

Links

ENSG00000065243 ∙ NCBI:5586 ∙ OMIM:602549 ∙ HGNC:9406 ∙ Uniprot:Q16513 ∙ 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 PKN2 gene.

• Inborn genetic diseases (21 variants)

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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	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
1-88740998-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)
1-88771823-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)
1-88784760-G-A		not specified	Uncertain significance (Feb 27, 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)
1-88805616-C-T		not specified	Uncertain significance (Nov 08, 2021)
1-88805625-G-A		not specified	Uncertain significance (Jan 10, 2022)
1-88805644-G-A		not specified	Uncertain significance (Jun 29, 2022)
1-88805937-C-A		not specified	Uncertain significance (Nov 19, 2022)
1-88805953-G-A		not specified	Uncertain significance (Nov 18, 2023)
1-88805958-T-G		not specified	Uncertain significance (Nov 10, 2021)
1-88807329-T-C		not specified	Uncertain significance (Feb 17, 2024)
1-88807564-T-G		not specified	Uncertain significance (Apr 20, 2023)
1-88807574-T-G		not specified	Uncertain significance (Oct 26, 2021)
1-88807706-A-G		not specified	Uncertain significance (Apr 12, 2023)
1-88807718-T-C		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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