PIK3CA

protein-coding

phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha, the group of Phosphatidylinositol 3-kinase subunits

Gene summary

Phosphatidylinositol 3-kinase is composed of an 85 kDa regulatory subunit and a 110 kDa catalytic subunit. The protein encoded by this gene represents the catalytic subunit, which uses ATP to phosphorylate PtdIns, PtdIns4P and PtdIns(4,5)P2. This gene has been found to be oncogenic and has been implicated in cervical cancers. A pseudogene of this gene has been defined on chromosome 22. [provided by RefSeq, Apr 2016]

MANE transcript

NM_006218.4

Inheritance

AD

ClinVar variants

P:108U:671B:605

Top phenotype

Cowden syndrome 5

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr3:179,148,114-179,240,093

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~92.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

megalencephaly-capillary malformation-polymicrogyria syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011240

Submitter: Labcorp Genetics (formerly Invitae)

megalencephaly-capillary malformation-polymicrogyria syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011240

Submitter: Ambry Genetics

overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genesDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0100283

Submitter: G2P

hereditary breast carcinomaNO_KNOWN

Inheritance Pattern: AD

Disease ID:MONDO:0016419

Submitter: ClinGen

*PIK3CA* encodes the catalytic subunit of Phosphatidylinositol 3-kinase (PIK3), which phosphorylates PIP2 to PIP3 and activates the signaling pathway. Monoallelic *PIK3CA* activating mutations are associated with overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes (MONDO:0100283). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we only focus on hereditary breast cancer in this curation. Evidence curated in this gene-disease relationship includes case-control data. **Summary of Case-Control Data: 0 point** This gene-disease relationship has been studied in at least 1 case-control study at the aggregate variant level. In 2021, a large case-control study [BCAC (PMID: 33471991) with more than 48 thousand cases and controls] did not identify a significant association of aggregate loss of function (LOF) variants in *PI3KCA* and breast cancer. **Overall Summary:** In summary, given the lack of significant association in large breast cancer case-control studies to date, there is convincing evidence refuting the association between *PI3KCA* and autosomal dominant hereditary breast cancer. This gene-disease pair was originally evaluated as no known disease relationship by the Breast/Ovarian Cancer GCEP on 2/8//2017. This re-curation was approved by the ClinGen Hereditary Diseases GCEP on 6/9/2023 (SOP Version 9).

overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genesSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0100283

Submitter: PanelApp Australia

Cowden diseaseSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016063

Submitter: Orphanet

familial ovarian cancerNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0016248

Submitter: ClinGen

vascular malformationSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0024291

Submitter: Genomics England PanelApp

Cowden syndrome 5LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014047

Submitter: Labcorp Genetics (formerly Invitae)

megalencephaly-capillary malformation-polymicrogyria syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011240

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Cowden syndrome 5AD

Manifestation: Dermatologic; Endocrine; Oncologic

Intervention: Oncologic

Rationale: Individuals have been reported with a variety of types of cancer, including breast, thyroid, renal, and endometrial cancer, and surveillance and awareness may allow early detection and management of neoplastic disease

Comments: Somatic variants can cause Cerebral cavenous malformations 4 and Hemifacial myohyperplasia

Refs: 23246288; 34496175; 37712948Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PIK3CA variants in ClinVar

87 Conditions Cataloged
Inborn genetic diseasesTotal: 950
Cowden syndromeTotal: 597
not providedTotal: 203
PIK3CA related overgrowth syndromeTotal: 60
Megalencephaly-capillary malformation-polymicrogyria syndromeTotal: 60
Cowden syndrome 5Total: 48
PIK3CA-related disorderTotal: 46
CLOVES syndromeTotal: 34

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006218.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
5
clinvar
589
clinvar
594
missense
45
clinvar
54
clinvar
640
clinvar
13
clinvar
1
clinvar
753
nonsense
1
clinvar
9
clinvar
10
start loss
2
clinvar
2
frameshift
3
clinvar
4
clinvar
12
clinvar
19
splice donor/acceptor (+/-2bp)
1
clinvar
3
clinvar
2
clinvar
6
Total495967160411384

Highest pathogenic variant AF is 0.0000021059282

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006218.4RefSeqNP_006209.220MANE Select
ENST00000263967.4EnsemblENSP00000263967.320MANE Select
ENST00000468036.1EnsemblENSP00000417479.11Standard
ENST00000477735.1EnsemblENSP00000418145.11Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
pik3caDanio rerio

Structure: retinal ganglion cell

Quality: decreased branchiness

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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)

Biological Process

  • angiogenesis
  • liver development
  • vasculature development
  • glucose metabolic process
  • protein phosphorylation

Molecular Function

  • protein serine/threonine kinase activity
  • protein binding
  • ATP binding
  • kinase activity
  • 1-phosphatidylinositol-3-kinase activity

Cellular Component

  • cytoplasm
  • cytosol
  • plasma membrane
  • phosphatidylinositol 3-kinase complex
  • phosphatidylinositol 3-kinase complex, class IA

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000263967
Coding exons
20
Length
91980
Individuals with no LoFs
124789
Homozygous LoFs
0
Heterozygous LoFs
5
Defined
124794
p
0.0000200
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense5.601915660.3380.00002857098
Missense (PolyPhen)31200.840.154352490
Synonymous2.361441850.7790.000008791924
Loss of Function7.21366.40.04520.00000431710

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000270.000026rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Phosphoinositide-3-kinase (PI3K) that phosphorylates PtdIns (Phosphatidylinositol), PtdIns4P (Phosphatidylinositol 4- phosphate) and PtdIns(4,5)P2 (Phosphatidylinositol 4,5- bisphosphate) to generate phosphatidylinositol 3,4,5-trisphosphate (PIP3). PIP3 plays a key role by recruiting PH domain-containing proteins to the membrane, including AKT1 and PDPK1, activating signaling cascades involved in cell growth, survival, proliferation, motility and morphology. Participates in cellular signaling in response to various growth factors. Involved in the activation of AKT1 upon stimulation by receptor tyrosine kinases ligands such as EGF, insulin, IGF1, VEGFA and PDGF. Involved in signaling via insulin-receptor substrate (IRS) proteins. Essential in endothelial cell migration during vascular development through VEGFA signaling, possibly by regulating RhoA activity. Required for lymphatic vasculature development, possibly by binding to RAS and by activation by EGF and FGF2, but not by PDGF. Regulates invadopodia formation through the PDPK1-AKT1 pathway. Participates in cardiomyogenesis in embryonic stem cells through a AKT1 pathway. Participates in vasculogenesis in embryonic stem cells through PDK1 and protein kinase C pathway. Also has serine-protein kinase activity: phosphorylates PIK3R1 (p85alpha regulatory subunit), EIF4EBP1 and HRAS. Plays a role in the positive regulation of phagocytosis and pinocytosis (By similarity). {ECO:0000250|UniProtKB:P42337, ECO:0000269|PubMed:21708979, ECO:0000269|PubMed:26593112}.;
Disease
DISEASE: Note=PIK3CA mutations are involved in various type of cancer. Most of the cancer-associated mutations are missense mutations and map to one of the three hotspots: Glu-542; Glu-545 and His-1047. Mutated isoforms participate in cellular transformation and tumorigenesis induced by oncogenic receptor tyrosine kinases (RTKs) and HRAS/KRAS. Interaction with HRAS/KRAS is required for Ras-driven tumor formation. Mutations increasing the lipid kinase activity are required for oncogenic signaling. The protein kinase activity may not be required for tumorigenesis. {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15930273, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16432179, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:19805105, ECO:0000269|PubMed:21708979, ECO:0000269|PubMed:22658544, ECO:0000269|PubMed:22729224}.; DISEASE: Colorectal cancer (CRC) [MIM:114500]: A complex disease characterized by malignant lesions arising from the inner wall of the large intestine (the colon) and the rectum. Genetic alterations are often associated with progression from premalignant lesion (adenoma) to invasive adenocarcinoma. Risk factors for cancer of the colon and rectum include colon polyps, long-standing ulcerative colitis, and genetic family history. {ECO:0000269|PubMed:15930273, ECO:0000269|PubMed:15994075}. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Breast cancer (BC) [MIM:114480]: A common malignancy originating from breast epithelial tissue. Breast neoplasms can be distinguished by their histologic pattern. Invasive ductal carcinoma is by far the most common type. Breast cancer is etiologically and genetically heterogeneous. Important genetic factors have been indicated by familial occurrence and bilateral involvement. Mutations at more than one locus can be involved in different families or even in the same case. {ECO:0000269|PubMed:16353168}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Ovarian cancer (OC) [MIM:167000]: The term ovarian cancer defines malignancies originating from ovarian tissue. Although many histologic types of ovarian tumors have been described, epithelial ovarian carcinoma is the most common form. Ovarian cancers are often asymptomatic and the recognized signs and symptoms, even of late-stage disease, are vague. Consequently, most patients are diagnosed with advanced disease. {ECO:0000269|PubMed:15520168}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Hepatocellular carcinoma (HCC) [MIM:114550]: A primary malignant neoplasm of epithelial liver cells. The major risk factors for HCC are chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, prolonged dietary aflatoxin exposure, alcoholic cirrhosis, and cirrhosis due to other causes. {ECO:0000269|PubMed:15608678}. Note=The gene represented in this entry may be involved in disease pathogenesis.; DISEASE: Keratosis, seborrheic (KERSEB) [MIM:182000]: A common benign skin tumor. Seborrheic keratoses usually begin with the appearance of one or more sharply defined, light brown, flat macules. The lesions may be sparse or numerous. As they initially grow, they develop a velvety to finely verrucous surface, followed by an uneven warty surface with multiple plugged follicles and a dull or lackluster appearance. {ECO:0000269|PubMed:17673550}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Megalencephaly-capillary malformation-polymicrogyria syndrome (MCAP) [MIM:602501]: A syndrome characterized by a spectrum of anomalies including primary megalencephaly, prenatal overgrowth, brain and body asymmetry, cutaneous vascular malformations, digital anomalies consisting of syndactyly with or without postaxial polydactyly, connective tissue dysplasia involving the skin, subcutaneous tissue, and joints, and cortical brain malformations, most distinctively polymicrogyria. {ECO:0000269|PubMed:22729224, ECO:0000269|PubMed:26593112}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi (CLOVE) [MIM:612918]: A sporadically occurring, non-hereditary disorder characterized by asymmetric somatic hypertrophy and anomalies in multiple organs. It is defined by four main clinical findings: congenital lipomatous overgrowth, vascular malformations, epidermal nevi, and skeletal/spinal abnormalities. The presence of truncal overgrowth and characteristic patterned macrodactyly at birth differentiates CLOVE from other syndromic forms of overgrowth. {ECO:0000269|PubMed:22658544}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Cowden syndrome 5 (CWS5) [MIM:615108]: A form of Cowden syndrome, a hamartomatous polyposis syndrome with age-related penetrance. Cowden syndrome is characterized by hamartomatous lesions affecting derivatives of ectodermal, mesodermal and endodermal layers, macrocephaly, facial trichilemmomas (benign tumors of the hair follicle infundibulum), acral keratoses, papillomatous papules, and elevated risk for development of several types of malignancy, particularly breast carcinoma in women and thyroid carcinoma in both men and women. Colon cancer and renal cell carcinoma have also been reported. Hamartomas can be found in virtually every organ, but most commonly in the skin, gastrointestinal tract, breast and thyroid. {ECO:0000269|PubMed:23246288}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.851

Intolerance Scores

LoFtool
0.268
RVIS EVS
-0.45
RVIS percentile EVS
24.19

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
H
Indispensability pred.
E
Indispensability score
0.997

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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