PIK3C3 (phosphatidylinositol 3-kinase catalytic subunit type 3)

Gene

• Entrez ID: 5289
• Gene name: Phosphatidylinositol 3-kinase catalytic subunit type 3
• Gene symbol: PIK3C3
• Synonyms (NCBI Gene): VPS34, Vps34, hVps34
• Chromosome: 18
• Chromosome location: 18q12.3

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT027827	hsa-miR-98-5p	Microarray	19088304
MIRT045507	hsa-miR-149-5p	CLASH	23622248
MIRT497909	hsa-miR-5583-3p	PAR-CLIP	22291592
MIRT497908	hsa-miR-5579-5p	PAR-CLIP	22291592
MIRT497907	hsa-miR-4635	PAR-CLIP	22291592
MIRT497906	hsa-miR-4699-5p	PAR-CLIP	22291592
MIRT497905	hsa-miR-3148	PAR-CLIP	22291592
MIRT497904	hsa-miR-6124	PAR-CLIP	22291592
MIRT497903	hsa-miR-4709-3p	PAR-CLIP	22291592
MIRT497902	hsa-miR-3978	PAR-CLIP	22291592
MIRT737331	hsa-miR-340-5p	Luciferase reporter assay, Western blotting, Microarray, Immunohistochemistry (IHC), RNA-seq, qRT-PCR	32207410
MIRT497909	hsa-miR-5583-3p	PAR-CLIP	22291592
MIRT497908	hsa-miR-5579-5p	PAR-CLIP	22291592
MIRT497907	hsa-miR-4635	PAR-CLIP	22291592
MIRT497906	hsa-miR-4699-5p	PAR-CLIP	22291592
MIRT497905	hsa-miR-3148	PAR-CLIP	22291592
MIRT497904	hsa-miR-6124	PAR-CLIP	22291592
MIRT497903	hsa-miR-4709-3p	PAR-CLIP	22291592
MIRT497902	hsa-miR-3978	PAR-CLIP	22291592
MIRT2295965	hsa-miR-3682-5p	CLIP-seq
MIRT2295966	hsa-miR-421	CLIP-seq
MIRT2295967	hsa-miR-4680-5p	CLIP-seq
MIRT2295968	hsa-miR-4691-5p	CLIP-seq
MIRT2295969	hsa-miR-4775	CLIP-seq
MIRT2593936	hsa-miR-1236	CLIP-seq
MIRT2593937	hsa-miR-138	CLIP-seq
MIRT2593938	hsa-miR-2054	CLIP-seq
MIRT2593939	hsa-miR-300	CLIP-seq
MIRT2593940	hsa-miR-323b-3p	CLIP-seq
MIRT2593941	hsa-miR-3664-5p	CLIP-seq
MIRT2593942	hsa-miR-380	CLIP-seq
MIRT2593943	hsa-miR-381	CLIP-seq
MIRT2593944	hsa-miR-3913-3p	CLIP-seq
MIRT2593945	hsa-miR-409-5p	CLIP-seq
MIRT2593946	hsa-miR-4268	CLIP-seq
MIRT2593947	hsa-miR-4448	CLIP-seq
MIRT2593948	hsa-miR-4666-3p	CLIP-seq
MIRT2593949	hsa-miR-4714-5p	CLIP-seq
MIRT2593950	hsa-miR-4753-3p	CLIP-seq
MIRT2593951	hsa-miR-4768-5p	CLIP-seq
MIRT2593952	hsa-miR-489	CLIP-seq
MIRT2593953	hsa-miR-502-5p	CLIP-seq
MIRT2593954	hsa-miR-510	CLIP-seq
MIRT2593955	hsa-miR-515-5p	CLIP-seq
MIRT2593956	hsa-miR-520d-5p	CLIP-seq
MIRT2593957	hsa-miR-524-5p	CLIP-seq
MIRT2593936	hsa-miR-1236	CLIP-seq
MIRT2593937	hsa-miR-138	CLIP-seq
MIRT2593938	hsa-miR-2054	CLIP-seq
MIRT2593939	hsa-miR-300	CLIP-seq
MIRT2593940	hsa-miR-323b-3p	CLIP-seq
MIRT2593941	hsa-miR-3664-5p	CLIP-seq
MIRT2593942	hsa-miR-380	CLIP-seq
MIRT2593943	hsa-miR-381	CLIP-seq
MIRT2593944	hsa-miR-3913-3p	CLIP-seq
MIRT2593945	hsa-miR-409-5p	CLIP-seq
MIRT2593948	hsa-miR-4666-3p	CLIP-seq
MIRT2593949	hsa-miR-4714-5p	CLIP-seq
MIRT2593950	hsa-miR-4753-3p	CLIP-seq
MIRT2593951	hsa-miR-4768-5p	CLIP-seq
MIRT2593952	hsa-miR-489	CLIP-seq
MIRT2593953	hsa-miR-502-5p	CLIP-seq
MIRT2593954	hsa-miR-510	CLIP-seq
MIRT2593955	hsa-miR-515-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000045	Process	Autophagosome assembly	IBA
GO:0000045	Process	Autophagosome assembly	IDA	33637724
GO:0000045	Process	Autophagosome assembly	IEA
GO:0000045	Process	Autophagosome assembly	IEA
GO:0000166	Function	Nucleotide binding	IEA
GO:0000407	Component	Phagophore assembly site	IBA
GO:0000425	Process	Pexophagy	IBA
GO:0004672	Function	Protein kinase activity	IEA
GO:0005515	Function	Protein binding	IPI	7504174, 14617358, 16417406, 19050071, 19270696, 20142477, 20562859, 21062745, 22095288, 22493499, 23316280, 23332761, 23364696, 23878393, 23954414, 24034250, 24056303, 24472739, 24785657, 24849286, 25490155, 25594178, 26496610, 26783301, 28479384, 28514442, 28890335, 30767700, 3180
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005768	Component	Endosome	IBA
GO:0005768	Component	Endosome	IEA
GO:0005770	Component	Late endosome	IDA	14617358
GO:0005770	Component	Late endosome	IEA
GO:0005776	Component	Autophagosome	IEA
GO:0005777	Component	Peroxisome	IBA
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IDA	17307798
GO:0005930	Component	Axoneme	ISS
GO:0006622	Process	Protein targeting to lysosome	NAS	16467569
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006897	Process	Endocytosis	IBA
GO:0006914	Process	Autophagy	IEA
GO:0006914	Process	Autophagy	IMP	25327288
GO:0007032	Process	Endosome organization	IEA
GO:0009267	Process	Cellular response to starvation	IEA
GO:0010506	Process	Regulation of autophagy	IDA	16799551
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IBA
GO:0016236	Process	Macroautophagy	IEA
GO:0016236	Process	Macroautophagy	ISS
GO:0016236	Process	Macroautophagy	TAS
GO:0016241	Process	Regulation of macroautophagy	IDA	10625637
GO:0016301	Function	Kinase activity	IEA
GO:0016303	Function	1-phosphatidylinositol-3-kinase activity	IBA
GO:0016303	Function	1-phosphatidylinositol-3-kinase activity	IDA	7628435, 25327288
GO:0016303	Function	1-phosphatidylinositol-3-kinase activity	IEA
GO:0016303	Function	1-phosphatidylinositol-3-kinase activity	IMP	20208530
GO:0016303	Function	1-phosphatidylinositol-3-kinase activity	TAS	7628435
GO:0016485	Process	Protein processing	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016773	Function	Phosphotransferase activity, alcohol group as acceptor	IEA
GO:0030496	Component	Midbody	IDA	20208530
GO:0030496	Component	Midbody	IEA
GO:0030670	Component	Phagocytic vesicle membrane	TAS
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0032465	Process	Regulation of cytokinesis	IMP	20208530, 20643123
GO:0034271	Component	Phosphatidylinositol 3-kinase complex, class III, type I	IBA
GO:0034272	Component	Phosphatidylinositol 3-kinase complex, class III, type II	IBA
GO:0034497	Process	Protein localization to phagophore assembly site	IEA
GO:0035032	Component	Phosphatidylinositol 3-kinase complex, class III	IEA
GO:0035032	Component	Phosphatidylinositol 3-kinase complex, class III	IPI	25490155
GO:0035032	Component	Phosphatidylinositol 3-kinase complex, class III	ISS
GO:0036092	Process	Phosphatidylinositol-3-phosphate biosynthetic process	IBA
GO:0036092	Process	Phosphatidylinositol-3-phosphate biosynthetic process	IDA	8999962
GO:0036092	Process	Phosphatidylinositol-3-phosphate biosynthetic process	IEA
GO:0036092	Process	Phosphatidylinositol-3-phosphate biosynthetic process	IEA
GO:0042149	Process	Cellular response to glucose starvation	IEA
GO:0042149	Process	Cellular response to glucose starvation	ISS
GO:0043201	Process	Response to L-leucine	IEA
GO:0043491	Process	Phosphatidylinositol 3-kinase/protein kinase B signal transduction	IEA
GO:0044754	Component	Autolysosome	IDA	25327288
GO:0044829	Process	Host-mediated activation of viral genome replication	IDA	34320401
GO:0045022	Process	Early endosome to late endosome transport	IDA	14617358
GO:0045022	Process	Early endosome to late endosome transport	IMP	14617358
GO:0045335	Component	Phagocytic vesicle	IEA
GO:0045954	Process	Positive regulation of natural killer cell mediated cytotoxicity	IMP	17307798
GO:0046854	Process	Phosphatidylinositol phosphate biosynthetic process	IDA	7628435
GO:0046854	Process	Phosphatidylinositol phosphate biosynthetic process	IEA
GO:0048015	Process	Phosphatidylinositol-mediated signaling	IBA
GO:0048488	Process	Synaptic vesicle endocytosis	IEA
GO:0051301	Process	Cell division	IEA
GO:0052742	Function	Phosphatidylinositol kinase activity	IDA	7628435
GO:0060333	Process	Type II interferon-mediated signaling pathway	IDA	16914093
GO:0070102	Process	Interleukin-6-mediated signaling pathway	IDA	12829785
GO:0097352	Process	Autophagosome maturation	IDA	10625637
GO:0098794	Component	Postsynapse	IEA
GO:0098830	Component	Presynaptic endosome	IEA
GO:0098845	Component	Postsynaptic endosome	IEA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0098982	Component	GABA-ergic synapse	IEA
GO:1903061	Process	Positive regulation of protein lipidation	IMP	25327288

Other IDs

• MIM: 602609
• HGNC: 8974
• e!Ensembl: ENSG00000078142

Protein

• UniProt ID: Q8NEB9
• Protein name: Phosphatidylinositol 3-kinase catalytic subunit type 3 (PI3-kinase type 3) (PI3K type 3) (PtdIns-3-kinase type 3) (EC 2.7.1.137) (Phosphatidylinositol 3-kinase p100 subunit) (Phosphoinositide-3-kinase class 3) (hVps34)
• Protein function: Catalytic subunit of the PI3K complex that mediates formation of phosphatidylinositol 3-phosphate; different complex forms are believed to play a role in multiple membrane trafficking pathways: PI3KC3-C1 is involved in initiation of autophagosom
• PDB: 3IHY, 3LS8, 4OYS, 4PH4, 4UWF, 4UWG, 4UWH, 4UWK, 4UWL, 5ANL, 5ENN, 6HOG, 6HOH, 6I3U, 6YKG, 7BL1, 7RSJ, 7RSP, 7RSV, 8RXR, 8SOR, 9C82, 9E4V, 9MHF, 9MHG, 9MHH
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00792	PI3K_C2	53 → 198	Phosphoinositide 3-kinase C2	Domain
  PF00613	PI3Ka	284 → 530	Phosphoinositide 3-kinase family, accessory domain (PIK domain)	Family
  PF00454	PI3_PI4_kinase	630 → 702	Phosphatidylinositol 3- and 4-kinase	Family
  PF00454	PI3_PI4_kinase	689 → 833	Phosphatidylinositol 3- and 4-kinase	Family

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitously expressed, with a highest expression in skeletal muscle. {ECO:0000269|PubMed:7628435}.
• Sequence:

  MGEAEKFHYIYSCDLDINVQLKIGSLEGKREQKSYKAVLEDPMLKFSGLYQETCSDLYVT
  CQVFAEGKPLALPVRTSYKAFSTRWNWNEWLKLPVKYPDLPRNAQVALTIWDVYGPGKAV
  PVGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTPGRTSSTLSEDQMSRLAKLTK
  AHRQGHMVKVDWLDRLTFREIEMINESEKRSSNFMYLMVEFRCVKCDDKEYGIVYYEKDG
  DESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGPSDHDLKPNAATRDQLNIIV
  SYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQALELLGKWKPMDV
  EDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYENFDDIKNGLEPTKK
  DSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKEVPDGENLEQDLCTFLI
  SRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMRRFSQALLKGDKSVRVMRS
  LLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDNEKMNLSDVELIPLPLEPQVK
  IRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHGDDLRQDQLILQIISLMDKLLRK
  ENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDTEGSIQNFFRKYAPSENGPNGISAE
  VMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKTGKLFHIDFGYILGRDPKPLPPPMKLN
  KEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRYSNLILNLFSLMVDANIPDIALEPDKTVK
  KVQDKFRLDLSDEEAVHYMQSLIDESVHALFAAVVEQIHKFAQYWRK

• Sequence length: 887

Pathways

KEGG:

Inositol phosphate metabolism
Metabolic pathways
Phosphatidylinositol signaling system
Autophagy - other
Autophagy - animal
Phagosome
Apelin signaling pathway
Alzheimer disease
Amyotrophic lateral sclerosis
Huntington disease
Spinocerebellar ataxia
Pathways of neurodegeneration - multiple diseases
Shigellosis
Salmonella infection
Tuberculosis
Kaposi sarcoma-associated herpesvirus infection

Reactome:

PI3K Cascade
Macroautophagy
Synthesis of PIPs at the Golgi membrane
Synthesis of PIPs at the early endosome membrane
Synthesis of PIPs at the late endosome membrane
Toll Like Receptor 9 (TLR9) Cascade
RHO GTPases Activate NADPH Oxidases

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIODONTAL DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIODONTITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	20559548	Associate	★☆☆☆☆ Found in Text Mining only
Anaplasia	Anaplasia	BEFREE	30703554		★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	20671926	Associate	★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar Disorder	BEFREE	15121481		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bipolar Disorder	Bipolar Disorder	PSYGENET_DG	15121481		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bladder Neoplasm	Bladder Neoplasm	BEFREE	29222162		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	30055290		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	24818135, 34870550	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	25070394		★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	29222162		★☆☆☆☆ Found in Text Mining only
Central Nervous System Neoplasms	Central Nervous System Neoplasms	BEFREE	31515514		★☆☆☆☆ Found in Text Mining only
Chronic Kidney Diseases	Kidney Disease	BEFREE	30607007		★☆☆☆☆ Found in Text Mining only
Colon Carcinoma	Colon Carcinoma	BEFREE	31092562		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	30982765		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	31092562, 33846805	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	29180704		★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	18649358, 32207410, 35333349	Associate	★☆☆☆☆ Found in Text Mining only
Giant Cell Arteritis	Giant Cell Arteritis	BEFREE	30900102		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	16522686		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	16522686		★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	Pubtator	25042561	Associate	★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	BEFREE	28097232		★☆☆☆☆ Found in Text Mining only
Hypertrophic obstructive cardiomyopathy	Hypertrophic cardiomyopathy	BEFREE	28097232		★☆☆☆☆ Found in Text Mining only
Hypothyroidism	Hypothyroidism	BEFREE	31650902		★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	32833964, 35626732	Associate	★☆☆☆☆ Found in Text Mining only
Idiopathic pulmonary arterial hypertension	Pulmonary arterial hypertension	BEFREE	30703554		★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	29980668		★☆☆☆☆ Found in Text Mining only
Kidney Failure	Kidney Failure	BEFREE	30237523		★☆☆☆☆ Found in Text Mining only
Kidney Failure, Acute	Kidney Failure	BEFREE	26686095		★☆☆☆☆ Found in Text Mining only
Leukemia	Leukemia	Pubtator	30381299	Associate	★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung Neoplasms	BEFREE	26686095		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	20671926	Associate	★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development, Group II	Malformation of cortical development	BEFREE	27607605		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	30055290		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	BEFREE	29222162		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	31514441		★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	BEFREE	31092562		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	LHGDN	16874027		★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	30339727		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	26686095, 28846113, 30242175		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	20513426	Associate	★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	27607605		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	30231667		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	20508647	Associate	★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	20406981	Associate	★☆☆☆☆ Found in Text Mining only
Pulmonary arterial hypertension	Pulmonary arterial hypertension	BEFREE	30703554		★☆☆☆☆ Found in Text Mining only
Renal Insufficiency	Renal Insufficiency	BEFREE	30237523		★☆☆☆☆ Found in Text Mining only
Rhinitis Allergic	Rhinitis	Pubtator	39528529	Associate	★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	15121481, 15814194, 18077426, 18420347, 19451863		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	PSYGENET_DG	15121481, 15814194, 18420347		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sepsis	Sepsis	Pubtator	28296904	Associate	★☆☆☆☆ Found in Text Mining only
Spastic paraplegia 11 autosomal recessive	Spastic paraplegia	Pubtator	30081747	Associate	★☆☆☆☆ Found in Text Mining only
Spastic paraplegia 15 autosomal recessive	Spastic paraplegia	Pubtator	30081747	Associate	★☆☆☆☆ Found in Text Mining only
Tuberous Sclerosis	Tuberous Sclerosis	BEFREE	30242175		★☆☆☆☆ Found in Text Mining only