PRKD1 (protein kinase D1)

Gene

• Entrez ID: 5587
• Gene name: Protein kinase D1
• Gene symbol: PRKD1
• Synonyms (NCBI Gene): CHDED, PKC-MU, PKCM, PKD, PRKCM
• Chromosome: 14
• Chromosome location: 14q12
• Summary: The protein encoded by this gene is a serine/threonine protein kinase involved in many cellular processes, including Golgi body membrane integrity and transport, cell migration and differentiation, MAPK8/JNK1 and Ras pathway signaling, MAPK1/3 (ERK1/2) pa

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1057519635	C>T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1057519636	A>C	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1439477100	C>T	Likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT052152	hsa-let-7b-5p	CLASH	23622248
MIRT572969	hsa-miR-4645-5p	PAR-CLIP	20371350
MIRT572968	hsa-miR-4673	PAR-CLIP	20371350
MIRT572967	hsa-miR-766-3p	PAR-CLIP	20371350
MIRT572966	hsa-miR-3925-3p	PAR-CLIP	20371350
MIRT572964	hsa-miR-6837-3p	PAR-CLIP	20371350
MIRT572965	hsa-miR-942-5p	PAR-CLIP	20371350
MIRT572963	hsa-miR-6740-3p	PAR-CLIP	20371350
MIRT572962	hsa-miR-515-5p	PAR-CLIP	20371350
MIRT572961	hsa-miR-519e-5p	PAR-CLIP	20371350
MIRT572969	hsa-miR-4645-5p	PAR-CLIP	20371350
MIRT572968	hsa-miR-4673	PAR-CLIP	20371350
MIRT572967	hsa-miR-766-3p	PAR-CLIP	20371350
MIRT572966	hsa-miR-3925-3p	PAR-CLIP	20371350
MIRT572964	hsa-miR-6837-3p	PAR-CLIP	20371350
MIRT572965	hsa-miR-942-5p	PAR-CLIP	20371350
MIRT572963	hsa-miR-6740-3p	PAR-CLIP	20371350
MIRT572962	hsa-miR-515-5p	PAR-CLIP	20371350
MIRT572961	hsa-miR-519e-5p	PAR-CLIP	20371350
MIRT1263463	hsa-miR-1206	CLIP-seq
MIRT1263464	hsa-miR-124	CLIP-seq
MIRT1263465	hsa-miR-128	CLIP-seq
MIRT1263466	hsa-miR-183	CLIP-seq
MIRT1263467	hsa-miR-323-3p	CLIP-seq
MIRT1263468	hsa-miR-34a	CLIP-seq
MIRT1263469	hsa-miR-34c-5p	CLIP-seq
MIRT1263470	hsa-miR-3714	CLIP-seq
MIRT1263471	hsa-miR-3910	CLIP-seq
MIRT1263472	hsa-miR-4263	CLIP-seq
MIRT1263473	hsa-miR-449a	CLIP-seq
MIRT1263474	hsa-miR-449b	CLIP-seq
MIRT1263475	hsa-miR-450b-5p	CLIP-seq
MIRT1263476	hsa-miR-4521	CLIP-seq
MIRT1263477	hsa-miR-506	CLIP-seq
MIRT1263478	hsa-miR-518a-5p	CLIP-seq
MIRT1263479	hsa-miR-527	CLIP-seq
MIRT1263480	hsa-miR-548a-3p	CLIP-seq
MIRT1263481	hsa-miR-548an	CLIP-seq
MIRT1263482	hsa-miR-548e	CLIP-seq
MIRT1263483	hsa-miR-548f	CLIP-seq
MIRT1263484	hsa-miR-576-5p	CLIP-seq
MIRT1263485	hsa-miR-586	CLIP-seq
MIRT2077571	hsa-miR-335	CLIP-seq
MIRT2077572	hsa-miR-587	CLIP-seq
MIRT2304089	hsa-miR-1827	CLIP-seq
MIRT1263468	hsa-miR-34a	CLIP-seq
MIRT1263469	hsa-miR-34c-5p	CLIP-seq
MIRT1263473	hsa-miR-449a	CLIP-seq
MIRT1263474	hsa-miR-449b	CLIP-seq
MIRT2304090	hsa-miR-4514	CLIP-seq
MIRT2304091	hsa-miR-4692	CLIP-seq
MIRT2304092	hsa-miR-4717-3p	CLIP-seq
MIRT2304093	hsa-miR-4733-3p	CLIP-seq
MIRT2304094	hsa-miR-4742-5p	CLIP-seq
MIRT2304095	hsa-miR-549	CLIP-seq
MIRT2304096	hsa-miR-940	CLIP-seq
MIRT1263463	hsa-miR-1206	CLIP-seq
MIRT2457181	hsa-miR-141	CLIP-seq
MIRT2457182	hsa-miR-200a	CLIP-seq
MIRT2457183	hsa-miR-376a	CLIP-seq
MIRT2457184	hsa-miR-376b	CLIP-seq
MIRT2457185	hsa-miR-4773	CLIP-seq
MIRT2457186	hsa-miR-875-3p	CLIP-seq
MIRT1263465	hsa-miR-128	CLIP-seq
MIRT2601019	hsa-miR-2052	CLIP-seq
MIRT2601020	hsa-miR-2276	CLIP-seq
MIRT1263468	hsa-miR-34a	CLIP-seq
MIRT1263469	hsa-miR-34c-5p	CLIP-seq
MIRT2601021	hsa-miR-3692	CLIP-seq
MIRT2601022	hsa-miR-3924	CLIP-seq
MIRT2601023	hsa-miR-4277	CLIP-seq
MIRT1263473	hsa-miR-449a	CLIP-seq
MIRT1263474	hsa-miR-449b	CLIP-seq
MIRT2601024	hsa-miR-4708-3p	CLIP-seq
MIRT2601025	hsa-miR-4772-3p	CLIP-seq
MIRT2601026	hsa-miR-514	CLIP-seq
MIRT2601027	hsa-miR-514b-3p	CLIP-seq
MIRT2601028	hsa-miR-544	CLIP-seq
MIRT1263465	hsa-miR-128	CLIP-seq
MIRT2601019	hsa-miR-2052	CLIP-seq
MIRT2601020	hsa-miR-2276	CLIP-seq
MIRT1263468	hsa-miR-34a	CLIP-seq
MIRT1263469	hsa-miR-34c-5p	CLIP-seq
MIRT2601021	hsa-miR-3692	CLIP-seq
MIRT2601022	hsa-miR-3924	CLIP-seq
MIRT2601023	hsa-miR-4277	CLIP-seq
MIRT1263473	hsa-miR-449a	CLIP-seq
MIRT1263474	hsa-miR-449b	CLIP-seq
MIRT2601024	hsa-miR-4708-3p	CLIP-seq
MIRT2601025	hsa-miR-4772-3p	CLIP-seq
MIRT2601026	hsa-miR-514	CLIP-seq
MIRT2601027	hsa-miR-514b-3p	CLIP-seq
MIRT2601028	hsa-miR-544	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000421	Component	Autophagosome membrane	IDA	22095288
GO:0001525	Process	Angiogenesis	IEA
GO:0001938	Process	Positive regulation of endothelial cell proliferation	IGI	20497126
GO:0002376	Process	Immune system process	IEA
GO:0004672	Function	Protein kinase activity	IEA
GO:0004674	Function	Protein serine/threonine kinase activity	IBA
GO:0004674	Function	Protein serine/threonine kinase activity	IDA	18440775, 22095288
GO:0004674	Function	Protein serine/threonine kinase activity	IEA
GO:0004674	Function	Protein serine/threonine kinase activity	IMP	28428613
GO:0004674	Function	Protein serine/threonine kinase activity	TAS	8119958
GO:0004697	Function	Diacylglycerol-dependent serine/threonine kinase activity	IDA	12637538
GO:0004697	Function	Diacylglycerol-dependent serine/threonine kinase activity	IEA
GO:0004697	Function	Diacylglycerol-dependent serine/threonine kinase activity	TAS
GO:0005080	Function	Protein kinase C binding	IEA
GO:0005515	Function	Protein binding	IPI	10831594, 12893243, 14550308, 15695390, 18509061, 19135240, 22095288, 22939624, 22981988, 24623306
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005794	Component	Golgi apparatus	IDA	11239398
GO:0005794	Component	Golgi apparatus	IEA
GO:0005802	Component	Trans-Golgi network	IDA	19211839
GO:0005802	Component	Trans-Golgi network	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	ISS
GO:0005829	Component	Cytosol	TAS	10856238
GO:0005886	Component	Plasma membrane	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	10856238
GO:0005911	Component	Cell-cell junction	IEA
GO:0005938	Component	Cell cortex	IEA
GO:0006915	Process	Apoptotic process	IEA
GO:0006954	Process	Inflammatory response	IEA
GO:0007030	Process	Golgi organization	IMP	19211839
GO:0007165	Process	Signal transduction	TAS	8119958
GO:0007200	Process	Phospholipase C-activating G protein-coupled receptor signaling pathway	IBA
GO:0007229	Process	Integrin-mediated signaling pathway	TAS	21488147
GO:0007399	Process	Nervous system development	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0010508	Process	Positive regulation of autophagy	IMP	22095288
GO:0010595	Process	Positive regulation of endothelial cell migration	IMP	18332134
GO:0010628	Process	Positive regulation of gene expression	IEA
GO:0010837	Process	Regulation of keratinocyte proliferation	IEA
GO:0010837	Process	Regulation of keratinocyte proliferation	ISS
GO:0010976	Process	Positive regulation of neuron projection development	IMP	19211839
GO:0014723	Process	Regulation of skeletal muscle contraction by modulation of calcium ion sensitivity of myofibril	IEA
GO:0016020	Component	Membrane	IEA
GO:0016301	Function	Kinase activity	IDA	24623306
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0030018	Component	Z disc	IEA
GO:0030148	Process	Sphingolipid biosynthetic process	IEA
GO:0030148	Process	Sphingolipid biosynthetic process	TAS
GO:0030154	Process	Cell differentiation	IEA
GO:0031072	Function	Heat shock protein binding	IEA
GO:0034198	Process	Cellular response to amino acid starvation	IMP	22095288
GO:0034599	Process	Cellular response to oxidative stress	IDA	12505989
GO:0035556	Process	Intracellular signal transduction	IBA
GO:0035556	Process	Intracellular signal transduction	IEA
GO:0035556	Process	Intracellular signal transduction	IMP	18059339, 18440775
GO:0035924	Process	Cellular response to vascular endothelial growth factor stimulus	IGI	20497126
GO:0035924	Process	Cellular response to vascular endothelial growth factor stimulus	IMP	18059339, 18332134, 18440775
GO:0042307	Process	Positive regulation of protein import into nucleus	IEA
GO:0042802	Function	Identical protein binding	IPI	10831594
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IMP	12505989
GO:0043536	Process	Positive regulation of blood vessel endothelial cell migration	IGI	20497126
GO:0043536	Process	Positive regulation of blood vessel endothelial cell migration	IMP	18440775
GO:0044331	Process	Cell-cell adhesion mediated by cadherin	IDA	18593713
GO:0045087	Process	Innate immune response	IEA
GO:0045669	Process	Positive regulation of osteoblast differentiation	IEA
GO:0045669	Process	Positive regulation of osteoblast differentiation	ISS
GO:0045766	Process	Positive regulation of angiogenesis	IGI	20497126
GO:0045766	Process	Positive regulation of angiogenesis	IMP	18332134, 18440775
GO:0045793	Process	Positive regulation of cell size	IEA
GO:0045806	Process	Negative regulation of endocytosis	TAS	21488147
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IGI	20497126
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	18059339
GO:0046777	Process	Protein autophosphorylation	IDA	24623306
GO:0046827	Process	Positive regulation of protein export from nucleus	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048010	Process	Vascular endothelial growth factor receptor signaling pathway	IGI	20497126
GO:0048010	Process	Vascular endothelial growth factor receptor signaling pathway	IMP	18059339, 18440775
GO:0048193	Process	Golgi vesicle transport	IEA
GO:0048193	Process	Golgi vesicle transport	ISS
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0050829	Process	Defense response to Gram-negative bacterium	IEA
GO:0051092	Process	Positive regulation of NF-kappaB transcription factor activity	IMP	12505989
GO:0051279	Process	Regulation of release of sequestered calcium ion into cytosol	IEA
GO:0051897	Process	Positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IDA	22095288
GO:0060298	Process	Positive regulation of sarcomere organization	IEA
GO:0070633	Process	Transepithelial transport	IDA	34969853
GO:0070633	Process	Transepithelial transport	IDA	34969853
GO:0071447	Process	Cellular response to hydroperoxide	IMP	22095288
GO:0071873	Process	Response to norepinephrine	IEA
GO:0071874	Process	Cellular response to norepinephrine stimulus	IEA
GO:0090277	Process	Positive regulation of peptide hormone secretion	IEA
GO:0106310	Function	Protein serine kinase activity	IEA
GO:0106310	Function	Protein serine kinase activity	IGI	20497126
GO:0141038	Function	Phosphatidylinositol 3-kinase activator activity	IDA	22095288
GO:1900227	Process	Positive regulation of NLRP3 inflammasome complex assembly	IEA
GO:1900227	Process	Positive regulation of NLRP3 inflammasome complex assembly	ISS
GO:1904385	Process	Cellular response to angiotensin	IEA
GO:1904628	Process	Cellular response to phorbol 13-acetate 12-myristate	IEA
GO:1990859	Process	Cellular response to endothelin	IEA
GO:2001028	Process	Positive regulation of endothelial cell chemotaxis	IGI	20497126
GO:2001028	Process	Positive regulation of endothelial cell chemotaxis	IMP	18440775
GO:2001044	Process	Regulation of integrin-mediated signaling pathway	TAS	21488147

Other IDs

• MIM: 605435
• HGNC: 9407
• e!Ensembl: ENSG00000184304

Protein

• UniProt ID: Q15139
• Protein name: Serine/threonine-protein kinase D1 (EC 2.7.11.13) (Protein kinase C mu type) (Protein kinase D) (nPKC-D1) (nPKC-mu)
• Protein function: Serine/threonine-protein kinase that converts transient diacylglycerol (DAG) signals into prolonged physiological effects downstream of PKC, and is involved in the regulation of MAPK8/JNK1 and Ras signaling, Golgi membrane integrity and traffick
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00130	C1_1	147 → 198	Phorbol esters/diacylglycerol binding domain (C1 domain)	Domain
  PF00130	C1_1	271 → 323	Phorbol esters/diacylglycerol binding domain (C1 domain)	Domain
  PF00169	PH	423 → 541	PH domain	Domain
  PF00069	Pkinase	584 → 839	Protein kinase domain	Domain

• Sequence:

  MSAPPVLRPPSPLLPVAAAAAAAAAALVPGSGPGPAPFLAPVAAPVGGISFHLQIGLSRE
  PVLLLQDSSGDYSLAHVREMACSIVDQKFPECGFYGMYDKILLFRHDPTSENILQLVKAA
  SDIQEGDLIEVVLSASATFEDFQIRPHALFVHSYRAPAFCDHCGEMLWGLVRQGLKCEGC
  GLNYHKRCAFKIPNNCSGVRRRRLSNVSLTGVSTIRTSSAELSTSAPDEPLLQKSPSESF
  IGREKRSNSQSYIGRPIHLDKILMSKVKVPHTFVIHSYTRPTVCQYCKKLLKGLFRQGLQ
  CKDCRFNCHKRCAPKVPNNCLGEVTINGDLLSPGAESDVVMEEGSDDNDSERNSGLMDDM
  EEAMVQDAEMAMAECQNDSGEMQDPDPDHEDANRTISPSTSNNIPLMRVVQSVKHTKRKS
  STVMKEGWMVHYTSKDTLRKRHYWRLDSKCITLFQNDTGSRYYKEIPLSEILSLEPVKTS
  ALIPNGANPHCFEITTANVVYYVGENVVNPSSPSPNNSVLTSGVGADVARMWEIAIQHAL
  MPVIPKGSSVGTGTNLHRDISVSISVSNCQIQENVDISTVYQIFPDEVLGSGQFGIVYGG
  KHRKTGRDVAIKIIDKLRFPTKQESQLRNEVAILQNLHHPGVVNLECMFETPERVFVVME
  KLHGDMLEMILSSEKGRLPEHITKFLITQILVALRHLHFKNIVHCDLKPENVLLASADPF
  PQVKLCDFGFARIIGEKSFRRSVVGTPAYLAPEVLRNKGYNRSLDMWSVGVIIYVSLSGT
  FPFNEDEDIHDQIQNAAFMYPPNPWKEISHEAIDLINNLLQVKMRKRYSVDKTLSHPWLQ
  DYQTWLDLRELECKIGERYITHESDDLRWEKYAGEQGLQYPTHLINPSASHSDTPETEET
  EMKALGERVSIL

• Sequence length: 912

Pathways

KEGG:

Rap1 signaling pathway
Aldosterone synthesis and secretion
Chemical carcinogenesis - reactive oxygen species

Reactome:

Sphingolipid de novo biosynthesis

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Congenital heart defects and ectodermal dysplasia	Likely pathogenic; Pathogenic	rs2139090218, rs2502849610, rs1057519635, rs1057519636, rs1439477100	RCV002254370 RCV003988983 RCV000417214 RCV000417210 RCV000989200

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Neurodevelopmental delay	Conflicting classifications of pathogenicity	rs2139012188	RCV002274399
Premature ovarian failure	Conflicting classifications of pathogenicity	rs145651161	RCV001002742
PRKD1-related disorder	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	rs2502316171, rs2502557348, rs201154013, rs750955192, rs55654917, rs149055040, rs2273807, rs570805784, rs200522575, rs569529923, rs150018148, rs45589232, rs375056616, rs776034417, rs139355024, rs45585836, rs147948478, rs55831426, rs45460991, rs45458201, rs74503963, rs200000096, rs201539683, rs1005293562	RCV003400418 RCV003420732 RCV003397493 RCV003408800 RCV003906881 RCV003934001 RCV003941927 RCV003959544 RCV003941379 RCV003924572 RCV003914749 RCV003961844 RCV003969012 RCV003981333 RCV003942679 RCV003916200 RCV003936117 RCV003902836 RCV003950666 RCV003932970 RCV003916080 RCV003943211 RCV003943171 RCV003928608
Prostate cancer	Uncertain significance	rs193921103	RCV000149135

Associations from Text Mining
Disease Name	Relationship Type	References
Adenocarcinoma	Associate	29266837, 31917707, 33878706
Asthma	Associate	27504716
Breast Neoplasms	Inhibit	19243594
Breast Neoplasms	Associate	23944680, 25287328
Bruton type agammaglobulinemia	Associate	10561498
Burnett Schwartz Berberian syndrome	Associate	25000413
Carcinogenesis	Stimulate	31819177
Carcinoid Tumor	Associate	16899224
Carcinoma Adenoid Cystic	Associate	29266837
Carcinoma Non Small Cell Lung	Associate	32985371
Carcinoma Pancreatic Ductal	Associate	27649783, 28360038, 31819177
Carcinoma Renal Cell	Associate	20459627
Cardiomegaly	Associate	37972803
Cholangiocarcinoma	Associate	36231050
Colorectal Neoplasms	Associate	24475022, 30451989, 37225445
Congenital Hereditary and Neonatal Diseases and Abnormalities	Associate	27479907
Cysts	Associate	34962918
Ductus Arteriosus Patent	Associate	27649783
Fahr's disease	Associate	39740729
Failed Back Surgery Syndrome	Associate	20443916
Glioma	Associate	15842253
Graves Ophthalmopathy	Associate	24086448
Heart Defects Congenital	Associate	27479907, 33919081
Heart Septal Defects Atrial	Associate	33919081
Hyperimmunoglobulin G1(A1) Syndrome	Stimulate	30958903
Hypoxia	Inhibit	30896865
Idiopathic Pulmonary Fibrosis	Associate	25000413
Inflammation	Associate	21292998
Intervertebral Disc Degeneration	Associate	34858418
Ischemia	Associate	31167779
Leukemia Lymphocytic Chronic B Cell	Associate	27127886
Leukemia Prolymphocytic T Cell	Associate	27127886
Lymphatic Diseases	Associate	27127886
Lymphatic Metastasis	Associate	37225445
Lymphoma Non Hodgkin	Associate	26426580
Melanoma	Associate	21993564, 35969127
Multiple Myeloma	Associate	12786795, 14504085
Multiple Myeloma	Stimulate	32799769
Nasopharyngeal Carcinoma	Associate	17494074
Neoplasm Metastasis	Associate	24336522, 30451989
Neoplasm Metastasis	Inhibit	25287328, 30958903
Neoplasms	Associate	16083495, 22791710, 24086585, 24336522, 25287328, 29266837, 30018032, 30045871, 30451989, 30843621, 30896865, 31167779, 35908410, 36497140
Neoplasms	Inhibit	20160036, 30958903
Neoplasms	Stimulate	32985371
Neoplasms Adipose Tissue	Associate	33491310
Obesity	Associate	25893265, 33491310
Pancreatic Neoplasms	Associate	20082306, 24336522, 24847910, 27649783, 28360038, 31819177
Polycystic Kidney Autosomal Dominant	Associate	26632257
Prostatic Neoplasms	Associate	17979146, 18602367, 20160036, 22797919, 24086585, 28077787, 31167779, 35595103, 37611675
Prostatic Neoplasms	Inhibit	18602367, 26764245
Pulmonary Valve Stenosis	Associate	33919081
Salivary Gland Neoplasms	Associate	26426580, 31917707, 33878706
Seizures	Associate	39740729
Squamous Cell Carcinoma of Head and Neck	Associate	32319563
Syndrome	Associate	27479907
Truncus Arteriosus Persistent	Associate	33919081
Uterine Cervical Dysplasia	Associate	31819177