PKN3

protein kinase N3, the group of AGC family kinases|Minor histocompatibility antigens|C2 domain containing protein kinases

Basic information

Region (hg38): 9:128702502-128720916

Links

ENSG00000160447 ∙ NCBI:29941 ∙ OMIM:610714 ∙ HGNC:17999 ∙ Uniprot:Q6P5Z2 ∙ 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 PKN3 gene.

• Inborn genetic diseases (61 variants)
• See cases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKN3 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			59	3		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	60	3	0

Variants in PKN3

This is a list of pathogenic ClinVar variants found in the PKN3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-128705302-G-T		See cases	Uncertain significance (Jan 07, 2020)
9-128705321-C-A		not specified	Uncertain significance (Nov 18, 2022)
9-128705335-G-C		not specified	Uncertain significance (Jan 03, 2024)
9-128705348-C-T		not specified	Uncertain significance (Dec 21, 2022)
9-128705352-G-A		not specified	Uncertain significance (Dec 27, 2023)
9-128705405-G-A		not specified	Uncertain significance (Aug 16, 2022)
9-128705460-A-C		not specified	Uncertain significance (Jan 19, 2024)
9-128705465-C-T		not specified	Uncertain significance (Nov 08, 2022)
9-128705466-G-A		not specified	Uncertain significance (Jan 29, 2024)
9-128705480-C-T		not specified	Uncertain significance (Oct 17, 2023)
9-128705490-T-G		not specified	Uncertain significance (Jan 24, 2024)
9-128705522-G-A		not specified	Uncertain significance (Jan 30, 2024)
9-128705525-C-T		not specified	Uncertain significance (Oct 05, 2023)
9-128705755-G-A		not specified	Likely benign (Dec 22, 2023)
9-128705758-C-T		not specified	Uncertain significance (May 05, 2023)
9-128705799-C-T		not specified	Uncertain significance (Dec 06, 2023)
9-128705827-T-C		not specified	Uncertain significance (Aug 08, 2023)
9-128706816-C-T		not specified	Uncertain significance (Oct 17, 2023)
9-128706822-C-A		not specified	Uncertain significance (Nov 07, 2023)
9-128706998-C-T		not specified	Uncertain significance (May 04, 2022)
9-128707006-C-T		not specified	Uncertain significance (Oct 06, 2021)
9-128707249-C-A		not specified	Uncertain significance (Nov 13, 2023)
9-128707288-C-A		not specified	Uncertain significance (Oct 13, 2023)
9-128707318-C-T		not specified	Uncertain significance (Dec 16, 2022)
9-128707319-G-A		not specified	Uncertain significance (Jun 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKN3	protein_coding	protein_coding	ENST00000291906	22	18396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.11e-19	0.493	125668	0	80	125748	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	475	562	0.845	0.0000378	5649
Missense in Polyphen		171	219.1	0.78047		2344
Synonymous	0.737	217	231	0.938	0.0000148	1892
Loss of Function	1.84	36	50.0	0.719	0.00000269	511

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000783	0.000782
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000491	0.000489
Finnish	0.000333	0.000323
European (Non-Finnish)	0.000286	0.000281
Middle Eastern	0.000491	0.000489
South Asian	0.000300	0.000294
Other	0.000501	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contributes to invasiveness in malignant prostate cancer. {ECO:0000269|PubMed:15282551}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Salmonella infection - Homo sapiens (human);PI3K-Akt Signaling Pathway;Signal Transduction;RHO GTPases activate PKNs;RHO GTPase Effectors;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.302

Intolerance Scores

• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.77

Haploinsufficiency Scores

• pHI: 0.0800
• hipred: Y
• hipred_score: 0.603
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pkn3
• Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; immune system phenotype; neoplasm; hematopoietic system 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

Gene ontology

• Biological process: protein phosphorylation;signal transduction;epithelial cell migration;peptidyl-serine phosphorylation;intracellular signal transduction
• Cellular component: nucleus;Golgi apparatus;perinuclear region of cytoplasm
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein kinase C activity;protein binding;ATP binding;GTP-Rho binding