PRKD3

protein kinase D3, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 2:37250501-37324833

Previous symbols: [ "PRKCN" ]

Links

ENSG00000115825 ∙ NCBI:23683 ∙ OMIM:607077 ∙ HGNC:9408 ∙ Uniprot:O94806 ∙ 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 PRKD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRKD3 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			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in PRKD3

This is a list of pathogenic ClinVar variants found in the PRKD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-37253204-A-T		not specified	Uncertain significance (Mar 24, 2023)
2-37253206-T-G		not specified	Uncertain significance (Jan 23, 2024)
2-37253233-A-G		not specified	Uncertain significance (Apr 08, 2024)
2-37253308-T-C		not specified	Uncertain significance (May 11, 2022)
2-37253310-C-T		not specified	Uncertain significance (Jun 21, 2022)
2-37253350-C-G		not specified	Uncertain significance (Oct 25, 2022)
2-37256830-G-A		not specified	Uncertain significance (Apr 01, 2022)
2-37256902-G-A		not specified	Uncertain significance (Oct 14, 2023)
2-37260248-C-T		not specified	Uncertain significance (May 04, 2023)
2-37260374-T-A		not specified	Uncertain significance (Nov 13, 2023)
2-37274422-G-C		not specified	Uncertain significance (Mar 18, 2024)
2-37274490-G-A		not specified	Uncertain significance (May 27, 2022)
2-37274540-G-C		not specified	Uncertain significance (Aug 16, 2022)
2-37274583-C-A		not specified	Uncertain significance (May 03, 2023)
2-37274619-A-T		not specified	Uncertain significance (Mar 18, 2024)
2-37274627-T-C		not specified	Uncertain significance (Dec 20, 2021)
2-37274670-T-C		not specified	Likely benign (Oct 20, 2021)
2-37277883-T-C		not specified	Uncertain significance (Aug 30, 2022)
2-37277929-C-G		not specified	Uncertain significance (Jan 06, 2023)
2-37279783-C-T		not specified	Uncertain significance (Dec 08, 2023)
2-37279881-T-C		not specified	Likely benign (Oct 26, 2021)
2-37279899-A-G		not specified	Uncertain significance (Feb 13, 2024)
2-37282547-T-C		not specified	Uncertain significance (Feb 06, 2023)
2-37282549-G-C		not specified	Uncertain significance (Nov 01, 2022)
2-37286198-G-A		not specified	Uncertain significance (Oct 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRKD3	protein_coding	protein_coding	ENST00000379066	18	74307

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00529	0.995	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	397	491	0.808	0.0000258	5870
Missense in Polyphen		100	185.76	0.53834		2157
Synonymous	-1.00	176	160	1.10	0.00000754	1676
Loss of Function	4.41	13	44.9	0.290	0.00000238	547

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000245	0.000242
Ashkenazi Jewish	0.000298	0.000198
East Asian	0.000113	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000887	0.0000879
Middle Eastern	0.000113	0.000109
South Asian	0.0000981	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts transient diacylglycerol (DAG) signals into prolonged physiological effects, downstream of PKC. Involved in resistance to oxidative stress (By similarity). {ECO:0000250}.
• Pathway: Aldosterone synthesis and secretion - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);miRs in Muscle Cell Differentiation;G Protein Signaling Pathways;Metabolism of lipids;Metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.305

Intolerance Scores

• loftool: 0.342
• rvis_EVS: 0.14
• rvis_percentile_EVS: 63.62

Haploinsufficiency Scores

• pHI: 0.195
• hipred: Y
• hipred_score: 0.554
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.549

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prkd3
• Phenotype: endocrine/exocrine gland phenotype; immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: protein phosphorylation;protein kinase C-activating G protein-coupled receptor signaling pathway;sphingolipid biosynthetic process;protein kinase D signaling
• Cellular component: nucleoplasm;cytosol;membrane
• Molecular function: protein serine/threonine kinase activity;protein kinase C activity;protein binding;ATP binding;kinase activity;metal ion binding