PKN3

protein-coding

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

Gene summary

Predicted to enable protein serine/threonine kinase activity. Involved in epithelial cell migration. Predicted to be located in Golgi apparatus; cytosol; and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_013355.5

Inheritance

—

ClinVar variants

U:200B:8

Top phenotype

See cases

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr9:128,702,503-128,720,916

External References & Databases

Ensembl (ENSG00000160447)

Transcript & Mutation Effects

hg38 • Region Span ~18.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PKN3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 196

See casesTotal: 2

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013355.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			191 clinvar	7 clinvar		198
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	200	8	0	208

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013355.5	RefSeq	NP_037487.2	22	MANE Select
ENST00000291906.5	Ensembl	ENSP00000291906.4	22	MANE Select
NM_001317926.2	RefSeq	NP_001304855.1	22	Standard
ENST00000855131.1	Ensembl	ENSP00000525190.1	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

PI3K-Akt signaling pathway - Homo sapiens (human)
Salmonella infection - Homo sapiens (human)
PI3K-Akt Signaling Pathway
Signal Transduction
RHO GTPases activate PKNs

Biological Process

protein phosphorylation
signal transduction
epithelial cell migration
peptidyl-serine phosphorylation
intracellular signal transduction

Molecular Function

protein kinase activity
protein serine/threonine kinase activity
protein kinase C activity
protein binding
ATP binding

Cellular Component

nucleus
Golgi apparatus
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000291906
Coding exons: 22
Length: 18396
Individuals with no LoFs: 125668
Homozygous LoFs: 0
Heterozygous LoFs: 80
Defined: 125748
p: 0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.30	475	562	0.845	0.0000378	5649
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00049	0.00049	rare
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.00029	0.00028	rare
South Asian	0.00030	0.00029	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Contributes to invasiveness in malignant prostate cancer. {ECO:0000269|PubMed:15282551}.;

Recessive Scores

pRec: 0.302

Intolerance Scores

RVIS EVS: -0.75
RVIS percentile EVS: 13.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.980

Gene Damage Prediction

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