PIK3CA-related overgrowth spectrum

disease
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Also known as overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes

Summary

PIK3CA-related overgrowth spectrum (MONDO:1040002) is a disease (an umbrella term covering 5 Mondo subtypes) with 1 cohort gene and 14 clinical trials. Top therapeutic interventions include alpelisib, sirolimus, and miransertib.

At a glance

  • Umbrella term: 5 Mondo subtypes
  • Cohort genes: 1
  • ClinVar variants: 60
  • Clinical trials: 14

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namePIK3CA-related overgrowth spectrum
Mondo IDMONDO:1040002
UMLSC4728213
MedGen1790024
GARD0027113
Is cancer (heuristic)no

Also known as: overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes

Data availability: 60 ClinVar variants.

Disease family

An umbrella term covering 5 Mondo subtypes.

Classification path: disease › human disease › disease by developmental or physiological process › disorder of development or morphogenesisovergrowth syndromePIK3CA-related overgrowth spectrum

Related subtypes (30): Beckwith-Wiedemann syndrome, hemifacial hypertrophy, angioosteohypertrophic syndrome, Bannayan-Riley-Ruvalcaba syndrome, Proteus syndrome, isolated hemihyperplasia, hypoinsulinemic hypoglycemia and body hemihypertrophy, Perlman syndrome, Weaver syndrome, Simpson-Golabi-Behmel syndrome, tetrasomy 12p, Marshall-Smith syndrome, hemifacial myohyperplasia, CLAPO syndrome, Maffucci syndrome, Malan overgrowth syndrome, segmental outgrowth-lipomatosis-arteriovenous malformation-epidermal nevus syndrome, trisomy 5p, hemihyperplasia-multiple lipomatosis syndrome, 11p15.4 microduplication syndrome, 15q overgrowth syndrome, global developmental delay - lung cysts - overgrowth - Wilms tumor syndrome, megalencephaly-severe kyphoscoliosis-overgrowth syndrome, congenital isolated hyperinsulinism, 4p16.3 microduplication syndrome, overgrowth syndrome with 2q37 translocation, MTOR-related overgrowth spectrum, AKT3-related overgrowth spectrum, PRC-2 complex-related overgrowth spectrum, PIK3R2-related overgrowth spectrum

Subtypes (5): megalencephaly-capillary malformation-polymicrogyria syndrome, CLOVES syndrome, Cowden syndrome 5, segmental progressive overgrowth syndrome with fibroadipose hyperplasia, megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

60 retrieved; paginated sample, class counts are floors:

27 pathogenic, 14 likely pathogenic, 13 pathogenic/likely pathogenic, 4 conflicting classifications of pathogenicity, 2 uncertain significance

ClinVarVariant (HGVS)GeneClassificationReview
1172582NM_006218.4(PIK3CA):c.344G>C (p.Arg115Pro)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1172583NM_006218.4(PIK3CA):c.3104C>T (p.Ala1035Val)PIK3CAPathogeniccriteria provided, single submitter
1198826NM_006218.4(PIK3CA):c.277C>T (p.Arg93Trp)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1209066NM_006218.4(PIK3CA):c.3012G>A (p.Met1004Ile)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
13652NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg)PIK3CAPathogenicreviewed by expert panel
13653NM_006218.4(PIK3CA):c.3140A>T (p.His1047Leu)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
13655NM_006218.4(PIK3CA):c.1633G>A (p.Glu545Lys)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
13656NM_006218.4(PIK3CA):c.1634A>G (p.Glu545Gly)PIK3CAPathogeniccriteria provided, single submitter
13657NM_006218.4(PIK3CA):c.1636C>A (p.Gln546Lys)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
13659NM_006218.4(PIK3CA):c.1634A>C (p.Glu545Ala)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
156446NM_006218.4(PIK3CA):c.353G>A (p.Gly118Asp)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
1691391NM_006218.4(PIK3CA):c.3061T>C (p.Tyr1021His)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
179173NM_006218.4(PIK3CA):c.3129G>A (p.Met1043Ile)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1804026NM_006218.4(PIK3CA):c.1346C>T (p.Pro449Leu)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
217291NM_006218.4(PIK3CA):c.311C>T (p.Pro104Leu)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
217292NM_006218.4(PIK3CA):c.3129G>T (p.Met1043Ile)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
217293NM_006218.4(PIK3CA):c.1635G>T (p.Glu545Asp)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
2571196NM_006218.4(PIK3CA):c.1340_1366del (p.Pro447_Leu455del)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2672088NM_006218.4(PIK3CA):c.1632_1633delinsAA (p.Glu545Lys)PIK3CAPathogeniccriteria provided, single submitter
31944NM_006218.4(PIK3CA):c.1624G>A (p.Glu542Lys)PIK3CAPathogenicreviewed by expert panel
31945NM_006218.4(PIK3CA):c.1258T>C (p.Cys420Arg)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
375898NM_006218.4(PIK3CA):c.1637A>C (p.Gln546Pro)PIK3CAPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
376049NM_006218.4(PIK3CA):c.263G>A (p.Arg88Gln)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
376050NM_006218.4(PIK3CA):c.1035T>A (p.Asn345Lys)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
376470NM_006218.4(PIK3CA):c.1357G>A (p.Glu453Lys)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
376476NM_006218.4(PIK3CA):c.2176G>A (p.Glu726Lys)PIK3CAPathogenicreviewed by expert panel
376478NM_006218.4(PIK3CA):c.241G>A (p.Glu81Lys)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
376498NM_006218.4(PIK3CA):c.1030G>A (p.Val344Met)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts
39703NM_006218.4(PIK3CA):c.2740G>A (p.Gly914Arg)PIK3CAPathogenicreviewed by expert panel
39704NM_006218.4(PIK3CA):c.1133G>A (p.Cys378Tyr)PIK3CAPathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 15 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
PIK3CAOrphanet:140944CLOVES syndrome
PIK3CAOrphanet:144Lynch syndrome
PIK3CAOrphanet:168984CLAPO syndrome
PIK3CAOrphanet:201Cowden syndrome
PIK3CAOrphanet:210159Adult hepatocellular carcinoma
PIK3CAOrphanet:221061Familial cerebral cavernous malformation
PIK3CAOrphanet:2495Meningioma
PIK3CAOrphanet:276280Hemihyperplasia-multiple lipomatosis syndrome
PIK3CAOrphanet:295239Macrodactyly of fingers, unilateral
PIK3CAOrphanet:295243Macrodactyly of toes, unilateral
PIK3CAOrphanet:314662Segmental progressive overgrowth syndrome with fibroadipose hyperplasia
PIK3CAOrphanet:60040Megalencephaly-capillary malformation-polymicrogyria syndrome
PIK3CAOrphanet:714737Diffuse capillary malformation with overgrowth
PIK3CAOrphanet:90308Capillary-lymphatic-venous malformation with segmental distribution
PIK3CAOrphanet:99802Hemimegalencephaly

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence1

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
PIK3CAHGNC:8975ENSG00000121879P42336Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoformclinvar,civic_evidence

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
PIK3CAPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoformPhosphoinositide-3-kinase (PI3K) phosphorylates phosphatidylinositol (PI) and its phosphorylated derivatives at position 3 of the inositol ring to produce 3-phosphoinositides.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Kinase127.7×0.036

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
PIK3CAKinaseyes2.7.1.137PI3K_Ras-bd_dom, PI3/4_kinase_cat_dom, PI3K_accessory_dom

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)1
unknown0

Top tissues across cohort

TissueCohort genes
adrenal tissue1
calcaneal tendon1
tendon1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
PIK3CA284ubiquitousmarkercalcaneal tendon, adrenal tissue, tendon

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
PIK3CA5,157

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
PIK3CAP42336135

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 60. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
MET activates PI3K/AKT signaling11903.3×0.004PIK3CA
Activated NTRK3 signals through PI3K11903.3×0.004PIK3CA
Activated NTRK2 signals through PI3K11631.4×0.004PIK3CA
Signaling by LTK in cancer11631.4×0.004PIK3CA
PI3K/AKT activation11268.9×0.004PIK3CA
IRS-mediated signalling11038.2×0.004PIK3CA
PI3K events in ERBB4 signaling11038.2×0.004PIK3CA
Co-stimulation by ICOS11038.2×0.004PIK3CA
Signaling by FGFR4 in disease1951.7×0.004PIK3CA
Erythropoietin activates Phosphoinositide-3-kinase (PI3K)1951.7×0.004PIK3CA
Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants1878.5×0.004PIK3CA
Signaling by PDGFRA extracellular domain mutants1878.5×0.004PIK3CA
Signaling by LTK1878.5×0.004PIK3CA
Signaling by FLT3 ITD and TKD mutants1761.3×0.004PIK3CA
Constitutive Signaling by EGFRvIII1713.8×0.004PIK3CA
PI3K events in ERBB2 signaling1671.8×0.004PIK3CA
Signaling by ERBB2 ECD mutants1671.8×0.004PIK3CA
GAB1 signalosome1634.4×0.004PIK3CA
Signaling by cytosolic FGFR1 fusion mutants1634.4×0.004PIK3CA
PI-3K cascade:FGFR31634.4×0.004PIK3CA
Tie2 Signaling1601.0×0.004PIK3CA
Role of LAT2/NTAL/LAB on calcium mobilization1601.0×0.004PIK3CA
Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants1571.0×0.004PIK3CA
Signaling by ALK1571.0×0.004PIK3CA
PI-3K cascade:FGFR41571.0×0.004PIK3CA
Signaling by FLT3 fusion proteins1571.0×0.004PIK3CA
PI-3K cascade:FGFR11519.1×0.004PIK3CA
Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants1519.1×0.004PIK3CA
PI-3K cascade:FGFR21496.5×0.004PIK3CA
Signaling by FGFR3 in disease1496.5×0.004PIK3CA

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
response to muscle inactivity116852.0×0.001PIK3CA
response to butyrate116852.0×0.001PIK3CA
response to L-leucine15617.3×0.002PIK3CA
cellular response to hydrostatic pressure15617.3×0.002PIK3CA
negative regulation of actin filament depolymerization12808.7×0.002PIK3CA
regulation of cellular respiration12808.7×0.002PIK3CA
regulation of actin filament organization12407.4×0.002PIK3CA
autosome genomic imprinting12407.4×0.002PIK3CA
negative regulation of fibroblast apoptotic process12407.4×0.002PIK3CA
cardiac muscle cell contraction11685.2×0.002PIK3CA
positive regulation of protein localization to membrane11685.2×0.002PIK3CA
TORC2 signaling11532.0×0.002PIK3CA
phosphatidylinositol-3-phosphate biosynthetic process11296.3×0.002PIK3CA
anoikis11296.3×0.002PIK3CA
relaxation of cardiac muscle11296.3×0.002PIK3CA
response to dexamethasone11203.7×0.002PIK3CA
vasculature development11123.5×0.002PIK3CA
negative regulation of macroautophagy11123.5×0.002PIK3CA
vascular endothelial growth factor signaling pathway11053.2×0.002PIK3CA
negative regulation of anoikis1887.0×0.003PIK3CA
response to muscle stretch1766.0×0.003PIK3CA
phosphatidylinositol-mediated signaling1702.2×0.003PIK3CA
regulation of multicellular organism growth1648.1×0.003PIK3CA
positive regulation of lamellipodium assembly1601.9×0.003PIK3CA
positive regulation of TOR signaling1495.6×0.004PIK3CA
insulin-like growth factor receptor signaling pathway1495.6×0.004PIK3CA
phosphatidylinositol phosphate biosynthetic process1481.5×0.004PIK3CA
endothelial cell migration1411.0×0.004PIK3CA
cardiac muscle contraction1401.2×0.004PIK3CA
adipose tissue development1401.2×0.004PIK3CA

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 0

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
PIK3CAIDELALISIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
PIK3CA674

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
IDELALISIB4PIK3CA
ALPELISIB4PIK3CA
DUVELISIB4PIK3CA
COPANLISIB4PIK3CA
FEDRATINIB4PIK3CA
ROMIDEPSIN4PIK3CA
COPANLISIB HYDROCHLORIDE4PIK3CA
LENIOLISIB4PIK3CA
BELINOSTAT4PIK3CA
INAVOLISIB4PIK3CA
SUNITINIB4PIK3CA
DASATINIB4PIK3CA
CRIZOTINIB4PIK3CA
MIDOSTAURIN4PIK3CA
DACTOLISIB3PIK3CA
BUPARLISIB3PIK3CA
RESVERATROL3PIK3CA
IPATASERTIB3PIK3CA
TASELISIB3PIK3CA
EPIGALOCATECHIN GALLATE3PIK3CA
GEDATOLISIB3PIK3CA
LESTAURTINIB3PIK3CA
OMIPALISIB2PIK3CA
VISTUSERTIB2PIK3CA
FIMEPINOSTAT2PIK3CA
EGANELISIB2PIK3CA
BERZOSERTIB2PIK3CA
BIMIRALISIB2PIK3CA
PICTILISIB2PIK3CA
ZSTK-4742PIK3CA

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
PIK3CA2,034Binding:2009, ADMET:19, Toxicity:4, Functional:2

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PIK3CA2.7.1.137, 2.7.1.153, 2.7.11.1phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
PIK3CA2,034

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

29 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
IDELALISIB4PIK3CA
DUVELISIB4PIK3CA
COPANLISIB4PIK3CA
FEDRATINIB4PIK3CA
ROMIDEPSIN4PIK3CA
COPANLISIB HYDROCHLORIDE4PIK3CA
LENIOLISIB4PIK3CA
BELINOSTAT4PIK3CA
INAVOLISIB4PIK3CA
SUNITINIB4PIK3CA
DASATINIB4PIK3CA
CRIZOTINIB4PIK3CA
MIDOSTAURIN4PIK3CA
DACTOLISIB3PIK3CA
BUPARLISIB3PIK3CA
RESVERATROL3PIK3CA
IPATASERTIB3PIK3CA
TASELISIB3PIK3CA
EPIGALOCATECHIN GALLATE3PIK3CA
GEDATOLISIB3PIK3CA
LESTAURTINIB3PIK3CA
OMIPALISIB2PIK3CA
VISTUSERTIB2PIK3CA
FIMEPINOSTAT2PIK3CA
EGANELISIB2PIK3CA
BERZOSERTIB2PIK3CA
BIMIRALISIB2PIK3CA
PICTILISIB2PIK3CA
ZSTK-4742PIK3CA

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1PIK3CA
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug0

Undrugged target profiles

0 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Clinical trials & evidence

Clinical trials

Clinical trials: 14.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified7
PHASE26
PHASE1/PHASE21

Top trials by phase / activity

NCTPhaseStatusTitle
NCT04589650PHASE2ACTIVE_NOT_RECRUITINGStudy Assessing the Efficacy, Safety and PK of Alpelisib (BYL719) in Pediatric and Adult Patients With PIK3CA-related Overgrowth Spectrum
NCT04980833PHASE2ACTIVE_NOT_RECRUITINGStudy Assessing Long-term Safety and Efficacy of Alpelisib in Patients With PIK3CA-Related Overgrowth Spectrum (PROS) Who Previously Participated in Study CBYL719F12002 (EPIK-P1)
NCT05983159PHASE2RECRUITINGA Trial of Targeted Therapies for Patients With Slow-Flow or Fast-Flow Vascular Malformations
NCT06789913PHASE2RECRUITINGA Phase 2 Study of Mutant-selective PI3Kα Inhibitor, RLY-2608, in Adults and Children With PIK3CA Related Overgrowth Spectrum and Malformations Driven by PIK3CA Mutation
NCT06975618PHASE1/PHASE2RECRUITINGStudy to Evaluate the Safety, Tolerability, Pharmacokinetics and Preliminary Efficacy of CYH33 in Patients With PIK3CA-related Overgrowth Spectrum (PROS) and PIK3CA-related Vascular Malformations (PRVM)
NCT06997588PHASE2RECRUITINGEPIK-P4: A Phase II Single-arm Study to Assess the Efficacy, Safety and Pharmacokinetics of Alpelisib (BYL719) in Pediatric and Adult Patients With PIK3CA-related Overgrowth Spectrum (PROS)
NCT02428296PHASE2COMPLETEDStudy of Sirolimus Therapy for Segmental Overgrowth Caused by Somatic PI3K Activation
NCT00001403Not specifiedRECRUITINGStudy of Proteus Syndrome and Related Congenital Disorders
NCT04085653Not specifiedAVAILABLEManaged Access Programs for BYL719, Alpelisib
NCT03317366Not specifiedNO_LONGER_AVAILABLEExpanded Access to Provide ARQ 092 for the Treatment of Overgrowth Diseases and/or Vascular Anomalies
NCT04285723Not specifiedCOMPLETEDRetrospective Chart Review Study of Patients With PIK3CA-Related Overgrowth Spectrum Who Have Received Alpelisib
NCT05294289Not specifiedCOMPLETEDHealth-related Quality of Life, Symptom Severity, and Pain Among Patients With PIK3CA-related Overgrowth Spectrum: A Mixed-methods Observational Study
NCT05563831Not specifiedCOMPLETEDNational Evaluation of Patients With PIK3CA-Related Overgrowth Spectrum (PROS)
NCT07222423Not specifiedCOMPLETEDA Study of the Epidemiology and Hospital Management of Patients With PROS in France

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
ALPELISIB47
SIROLIMUS41
MIRANSERTIB21
MIRDAMETINIB21
RISOVALISIB21
RLY-260811