GeneBe

PIK3R4

phosphoinositide-3-kinase regulatory subunit 4, the group of WD repeat domain containing|PIK3C3 complex subunits|Armadillo like helical domain containing

Basic information

Region (hg38): 3:130678934-130746829

Links

ENSG00000196455 ∙ NCBI:30849 ∙ OMIM:602610 ∙ HGNC:8982 ∙ Uniprot:Q99570 ∙ 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 PIK3R4 gene.

  • not_specified (131 variants)
  • not_provided (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIK3R4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014602.3. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
 3
missense
133
clinvar
3
clinvar
3
clinvar
 139
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 134 5 4
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PIK3R4protein_codingprotein_codingENST00000356763 1967895
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.02450.9751257110371257480.000147
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.485487370.7430.00003918953
Missense in Polyphen149258.040.577433052
Synonymous0.1722542580.9860.00001342624
Loss of Function5.431662.30.2570.00000344729

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003340.000272
Ashkenazi Jewish0.00009930.0000992
East Asian0.0001090.000109
Finnish0.0001390.000139
European (Non-Finnish)0.0001870.000185
Middle Eastern0.0001090.000109
South Asian0.0001350.000131
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Regulatory 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 cytokinesis, probably in the context of PI3KC3-C2 (PubMed:20643123). {ECO:0000269|PubMed:20643123}.;
Pathway
Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Phosphatidylinositol Phosphate Metabolism;Joubert syndrome;Inositol Metabolism;Angiopoietin Like Protein 8 Regulatory Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Insulin Signaling;Regulation of Actin Cytoskeleton;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;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;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)

Intolerance Scores

loftool
0.548
rvis_EVS
-1.13
rvis_percentile_EVS
6.56

Haploinsufficiency Scores

pHI
0.861
hipred
Y
hipred_score
0.624
ghis
0.636

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.964

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pik3r4
Phenotype
immune system phenotype; normal 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); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype;

Zebrafish Information Network

Gene name
pik3r4
Affected structure
whole organism
Phenotype tag
abnormal
Phenotype quality
curved

Gene ontology

Biological process
protein phosphorylation;protein targeting to vacuole;macroautophagy;autophagy of peroxisome;regulation of cytokinesis;receptor catabolic process;toll-like receptor 9 signaling pathway;phosphatidylinositol-3-phosphate biosynthetic process;cellular response to glucose starvation;positive regulation of phosphatidylinositol 3-kinase activity;late endosome to vacuole transport
Cellular component
late endosome;autophagosome;cytosol;axoneme;microtubule cytoskeleton;membrane;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;intracellular membrane-bounded organelle;nucleus-vacuole junction
Molecular function
protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;1-phosphatidylinositol-3-kinase activity