PIK3C3
phosphatidylinositol 3-kinase catalytic subunit type 3, the group of Phosphatidylinositol 3-kinase subunits|PIK3C3 complex subunits
Basic information
Region (hg38): 18:41955234-42087830
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (57 variants)
- not_provided (9 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIK3C3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002647.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 58 | 59 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 60 | 2 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PIK3C3 | protein_coding | protein_coding | ENST00000262039 | 25 | 132624 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.42e-11 | 1.00 | 125684 | 0 | 64 | 125748 | 0.000255 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.44 | 325 | 475 | 0.685 | 0.0000248 | 5846 |
| Missense in Polyphen | 95 | 178.03 | 0.53361 | 2162 | ||
| Synonymous | -0.517 | 174 | 166 | 1.05 | 0.00000877 | 1597 |
| Loss of Function | 3.55 | 26 | 54.2 | 0.480 | 0.00000268 | 692 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000600 | 0.000584 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000389 | 0.000381 |
| Finnish | 0.0000929 | 0.0000924 |
| European (Non-Finnish) | 0.000295 | 0.000290 |
| Middle Eastern | 0.000389 | 0.000381 |
| South Asian | 0.000304 | 0.000294 |
| Other | 0.000511 | 0.000489 |
dbNSFP
Source:
- Function
- 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 autophagosomes and PI3KC3-C2 in maturation of autophagosomes and endocytosis. Involved in regulation of degradative endocytic trafficking and required for the abcission step in cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123, PubMed:20208530). Involved in the transport of lysosomal enzyme precursors to lysosomes. Required for transport from early to late endosomes (By similarity). {ECO:0000250|UniProtKB:O88763, ECO:0000269|PubMed:14617358, ECO:0000269|PubMed:20208530, ECO:0000269|PubMed:20643123, ECO:0000269|PubMed:7628435, ECO:0000305}.;
- Pathway
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Inositol phosphate metabolism - Homo sapiens (human);Phagosome - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Phosphatidylinositol Phosphate Metabolism;Joubert syndrome;Inositol Metabolism;AMP-activated Protein Kinase (AMPK) Signaling;Angiopoietin Like Protein 8 Regulatory Pathway;Microglia Pathogen Phagocytosis Pathway;Insulin Signaling;Regulation of Actin Cytoskeleton;Senescence and Autophagy in Cancer;DNA Damage Response (only ATM dependent);Signal Transduction;Metabolism of lipids;Toll Like Receptor 9 (TLR9) Cascade;Toll-Like Receptors Cascades;PI3K Cascade;IRS-mediated signalling;Insulin receptor signalling cascade;Signaling by Insulin receptor;Inositol phosphate metabolism;Innate Immune System;Immune System;Metabolism;3-phosphoinositide biosynthesis;superpathway of inositol phosphate compounds;Macroautophagy;Cellular responses to external stimuli;RHO GTPases Activate NADPH Oxidases;RHO GTPase Effectors;Phosphatidylinositol phosphate metabolism;Signaling by Rho GTPases;Synthesis of PIPs at the Golgi membrane;Synthesis of PIPs at the early endosome membrane;Synthesis of PIPs at the late endosome membrane;PI Metabolism;Phospholipid metabolism;IRS-related events triggered by IGF1R;IGF1R signaling cascade;Signaling by Receptor Tyrosine Kinases;Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)
(Consensus)
Recessive Scores
- pRec
- 0.487
Intolerance Scores
- loftool
- 0.481
- rvis_EVS
- -1.35
- rvis_percentile_EVS
- 4.56
Haploinsufficiency Scores
- pHI
- 0.682
- hipred
- Y
- hipred_score
- 0.611
- ghis
- 0.666
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pik3c3
- Phenotype
- growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); muscle 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; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; immune system phenotype; vision/eye phenotype;
Gene ontology
- Biological process
- autophagosome assembly;protein phosphorylation;protein lipidation;endocytosis;autophagy;endosome organization;cell cycle;macroautophagy;protein processing;autophagy of peroxisome;regulation of cytokinesis;toll-like receptor 9 signaling pathway;protein localization to phagophore assembly site;phosphatidylinositol-3-phosphate biosynthetic process;cellular response to glucose starvation;response to leucine;early endosome to late endosome transport;phosphatidylinositol phosphorylation;phosphatidylinositol-mediated signaling;regulation of protein secretion;cell division
- Cellular component
- phagophore assembly site;cytoplasm;endosome;late endosome;peroxisome;cytosol;axoneme;membrane;midbody;phagocytic vesicle membrane;phosphatidylinositol 3-kinase complex, class III, type I;phosphatidylinositol 3-kinase complex, class III, type II;phosphatidylinositol 3-kinase complex, class III;autolysosome
- Molecular function
- protein kinase activity;protein binding;ATP binding;kinase activity;1-phosphatidylinositol-3-kinase activity