PIK3R3
phosphoinositide-3-kinase regulatory subunit 3, the group of SH2 domain containing
Basic information
Region (hg38): 1:46040139-46133036
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (10 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIK3R3 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in PIK3R3
This is a list of pathogenic ClinVar variants found in the PIK3R3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-46043740-T-C | not specified | Uncertain significance (Aug 30, 2022) | ||
| 1-46043827-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 1-46043867-C-T | not specified | Uncertain significance (Jun 05, 2023) | ||
| 1-46045945-T-C | not specified | Uncertain significance (Sep 06, 2022) | ||
| 1-46045975-T-A | not specified | Uncertain significance (Mar 14, 2023) | ||
| 1-46046014-T-C | not specified | Uncertain significance (Sep 22, 2023) | ||
| 1-46055904-C-G | not specified | Uncertain significance (Nov 09, 2022) | ||
| 1-46055939-C-T | Familial cancer of breast | Uncertain significance (Feb 01, 2014) | ||
| 1-46061926-T-TA | Likely benign (-) | |||
| 1-46066127-T-C | not specified | Uncertain significance (Aug 22, 2023) | ||
| 1-46066981-T-C | not specified | Uncertain significance (May 27, 2022) | ||
| 1-46066985-G-C | not specified | Uncertain significance (Jun 13, 2022) | ||
| 1-46077554-G-C | not specified | Uncertain significance (Dec 26, 2023) | ||
| 1-46077560-C-T | not specified | Uncertain significance (Nov 15, 2021) | ||
| 1-46077579-C-T | not specified | Uncertain significance (Jun 24, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PIK3R3 | protein_coding | protein_coding | ENST00000262741 | 10 | 136349 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.36e-10 | 0.751 | 125675 | 0 | 73 | 125748 | 0.000290 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0444 | 248 | 250 | 0.992 | 0.0000126 | 3073 |
| Missense in Polyphen | 88 | 87.886 | 1.0013 | 1058 | ||
| Synonymous | 1.59 | 67 | 85.8 | 0.781 | 0.00000409 | 784 |
| Loss of Function | 1.54 | 19 | 27.8 | 0.684 | 0.00000159 | 315 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000391 | 0.000391 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000383 | 0.000381 |
| Finnish | 0.0000491 | 0.0000462 |
| European (Non-Finnish) | 0.000362 | 0.000360 |
| Middle Eastern | 0.000383 | 0.000381 |
| South Asian | 0.000362 | 0.000359 |
| Other | 0.000509 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to activated (phosphorylated) protein-tyrosine kinases through its SH2 domain and regulates their kinase activity. During insulin stimulation, it also binds to IRS-1.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Non-small cell lung cancer - Homo sapiens (human);Platelet activation - Homo sapiens (human);Chronic myeloid leukemia - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Focal adhesion - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);Relaxin signaling pathway - Homo sapiens (human);Regulation of lipolysis in adipocytes - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);B cell receptor signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Fc gamma R-mediated phagocytosis - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Renal cell carcinoma - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Neurotrophin signaling pathway - Homo sapiens (human);Central carbon metabolism in cancer - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Melanoma - Homo sapiens (human);Type II diabetes mellitus - Homo sapiens (human);Insulin resistance - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Longevity regulating pathway - multiple species - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Influenza A - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);Breast cancer - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Carbohydrate digestion and absorption - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Axon guidance - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Aldosterone-regulated sodium reabsorption - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Prolactin signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Measles - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Apoptosis - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Cholinergic synapse - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);EGFR Inhibitor Pathway, Pharmacodynamics;Human papillomavirus infection - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Anti-diabetic Drug Potassium Channel Inhibitors Pathway, Pharmacodynamics;Sorafenib Pharmacodynamics;AMP-activated Protein Kinase (AMPK) Signaling;Regulation of toll-like receptor signaling pathway;MicroRNAs in cardiomyocyte hypertrophy;Focal Adhesion;PI3K-AKT-mTOR signaling pathway and therapeutic opportunities;Angiopoietin Like Protein 8 Regulatory Pathway;Chemokine signaling pathway;Leptin Insulin Overlap;Microglia Pathogen Phagocytosis Pathway;Endometrial cancer;PI3K-Akt Signaling Pathway;MET in type 1 papillary renal cell carcinoma;Ras Signaling;EMT transition in Colorectal Cancer;Insulin Signaling;Regulation of Actin Cytoskeleton;DNA Damage Response (only ATM dependent);Toll-like Receptor Signaling Pathway;Signaling by GPCR;Interleukin-7 signaling;Disease;Signal Transduction;Signaling by Interleukins;Metabolism of lipids;Cytokine Signaling in Immune system;Alpha6Beta4Integrin;CD28 dependent PI3K/Akt signaling;CD28 co-stimulation;Costimulation by the CD28 family;Immune System;Metabolism;3-phosphoinositide biosynthesis;Interleukin receptor SHC signaling;Interleukin-2 family signaling;Adaptive Immune System;superpathway of inositol phosphate compounds;GPVI-mediated activation cascade;Platelet activation, signaling and aggregation;EGFR1;Hemostasis;PIP3 activates AKT signaling;IL2;Gastrin;Synthesis of PIPs at the plasma membrane;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;PI Metabolism;Phospholipid metabolism;G alpha (12/13) signalling events;Signaling by SCF-KIT;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;Signaling by Receptor Tyrosine Kinases;G alpha (q) signalling events;G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;Intracellular signaling by second messengers;Diseases of signal transduction;Regulation of signaling by CBL;Interleukin-3, 5 and GM-CSF signaling
(Consensus)
Recessive Scores
- pRec
- 0.342
Intolerance Scores
- loftool
- 0.485
- rvis_EVS
- -0.09
- rvis_percentile_EVS
- 46.74
Haploinsufficiency Scores
- pHI
- 0.440
- hipred
- Y
- hipred_score
- 0.715
- ghis
- 0.524
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pik3r3
- Phenotype
Gene ontology
- Biological process
- positive regulation of protein phosphorylation;cell migration involved in sprouting angiogenesis;insulin receptor signaling pathway;positive regulation of gene expression;positive regulation of cell migration;phosphatidylinositol-3-phosphate biosynthetic process;protein kinase B signaling;regulation of phosphatidylinositol 3-kinase activity;phosphatidylinositol phosphorylation
- Cellular component
- cytosol;phosphatidylinositol 3-kinase complex
- Molecular function
- phosphotyrosine residue binding;protein binding;1-phosphatidylinositol-3-kinase activity;1-phosphatidylinositol-3-kinase regulator activity