Megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome

disease
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Also known as megalencephaly and perisylvian polymicrogyria with postaxial polydactyly and hydrocephalusmegalencephaly, polymicrogyria, and hydrocephalus (MPPH) syndromemegalencephaly-polymicrogyria-polydactyly-hydrocephalus syndromeMPPH syndrome

Summary

Megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome (MONDO:0019375) is a disease with 3 cohort genes.

At a glance

  • Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
  • Cohort genes: 3
  • ClinVar variants: 339
  • Phenotypes (HPO): 16

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Cases/families62WorldwideValidated
Point prevalence<1 / 1 000 000WorldwideValidated

Signs & symptoms

Clinical features (HPO)

16 HPO clinical features (Orphanet curated; top 16 by frequency):

HPO IDTermFrequency
HP:0000238HydrocephalusVery frequent (80-99%)
HP:0000256MacrocephalyVery frequent (80-99%)
HP:0001162Postaxial hand polydactylyVery frequent (80-99%)
HP:0001355MegalencephalyVery frequent (80-99%)
HP:0002126PolymicrogyriaVery frequent (80-99%)
HP:0000160Narrow mouthFrequent (30-79%)
HP:0000316HypertelorismFrequent (30-79%)
HP:0000348High foreheadFrequent (30-79%)
HP:0000506TelecanthusFrequent (30-79%)
HP:0001250SeizureFrequent (30-79%)
HP:0001629Ventricular septal defectFrequent (30-79%)
HP:0001653Mitral regurgitationFrequent (30-79%)
HP:0001671Abnormal cardiac septum morphologyFrequent (30-79%)
HP:0005105Abnormal nasal morphologyFrequent (30-79%)
HP:0005280Depressed nasal bridgeFrequent (30-79%)
HP:0100542Abnormal localization of kidneyFrequent (30-79%)

Identifiers

Disease identifiers

FieldValue
Canonical namemegalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome
Mondo IDMONDO:0019375
OMIM603387
Orphanet83473
SNOMED CT722036008
UMLSC1863924
MedGen355095
GARD0010341
Is cancer (heuristic)no

Also known as: megalencephaly and perisylvian polymicrogyria with postaxial polydactyly and hydrocephalus · megalencephaly, polymicrogyria, and hydrocephalus (MPPH) syndrome · megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome · MPPH syndrome

Data availability: 339 ClinVar variants · 3 GenCC gene-disease records · 6 cell lines.

Disease family

An umbrella term covering 3 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › nervous system disordercentral nervous system disorderbrain disorderhydrocephalusmegalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome

Related subtypes (6): obstructive hydrocephalus, communicating hydrocephalus, craniosynostosis-Dandy-Walker malformation-hydrocephalus syndrome, congenital hydrocephalus, baker Vinters syndrome, palmer pagon syndrome

Subtypes (3): megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1, megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 3

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

339 retrieved; paginated sample, class counts are floors:

158 likely benign, 101 uncertain significance, 50 benign, 17 conflicting classifications of pathogenicity, 12 benign/likely benign, 1 pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
39808NM_005027.4(PIK3R2):c.1117G>A (p.Gly373Arg)PIK3R2Pathogenicreviewed by expert panel
856239NM_005027.4(PIK3R2):c.706G>A (p.Ala236Thr)LOC130063979Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2109735NM_005027.4(PIK3R2):c.1766A>G (p.Lys589Arg)LOC130063980Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1190673NM_005027.4(PIK3R2):c.734C>A (p.Ala245Asp)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1296705NM_005027.4(PIK3R2):c.1243G>A (p.Ala415Thr)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1319057NM_005027.4(PIK3R2):c.1217G>A (p.Arg406His)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1381828NM_005027.4(PIK3R2):c.527G>A (p.Ser176Asn)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1392796NM_005027.4(PIK3R2):c.271C>T (p.Arg91Trp)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1565321NM_005027.4(PIK3R2):c.46C>T (p.Arg16Cys)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1600096NM_005027.4(PIK3R2):c.2171C>T (p.Pro724Leu)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2077921NM_005027.4(PIK3R2):c.1987G>C (p.Gly663Arg)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2086146NM_005027.4(PIK3R2):c.827G>A (p.Ser276Asn)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2212053NM_005027.4(PIK3R2):c.517G>A (p.Gly173Ser)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2387831NM_005027.4(PIK3R2):c.1522C>T (p.Arg508Cys)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
429932NM_005027.4(PIK3R2):c.1694C>G (p.Pro565Arg)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
661297NM_005027.4(PIK3R2):c.1076G>C (p.Ser359Thr)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
859412NM_005027.4(PIK3R2):c.107C>T (p.Ala36Val)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
864121NM_005027.4(PIK3R2):c.380T>C (p.Leu127Pro)PIK3R2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1711475NM_005027.4(PIK3R2):c.811G>T (p.Asp271Tyr)LOC130063979Uncertain significancecriteria provided, multiple submitters, no conflicts
1925630NM_005027.4(PIK3R2):c.766_783dup (p.Pro261_Ser262insArgAlaProProProPro)LOC130063979Uncertain significancecriteria provided, single submitter
1954122NM_005027.4(PIK3R2):c.595C>T (p.Arg199Trp)LOC130063979Uncertain significancecriteria provided, multiple submitters, no conflicts
2737997NM_005027.4(PIK3R2):c.565G>A (p.Glu189Lys)LOC130063979Uncertain significancecriteria provided, single submitter
3698949NM_005027.4(PIK3R2):c.560C>A (p.Thr187Asn)LOC130063979Uncertain significancecriteria provided, single submitter
3710461NM_005027.4(PIK3R2):c.755C>A (p.Pro252Gln)LOC130063979Uncertain significancecriteria provided, single submitter
3718370NM_005027.4(PIK3R2):c.655G>A (p.Ala219Thr)LOC130063979Uncertain significancecriteria provided, single submitter
3719478NM_005027.4(PIK3R2):c.583C>T (p.Arg195Cys)LOC130063979Uncertain significancecriteria provided, single submitter
3725567NM_005027.4(PIK3R2):c.576dup (p.Glu193fs)LOC130063979Uncertain significancecriteria provided, single submitter
4136879NM_005027.4(PIK3R2):c.572C>T (p.Ser191Leu)LOC130063979Uncertain significancecriteria provided, multiple submitters, no conflicts
4751733NM_005027.4(PIK3R2):c.700_701delinsCA (p.Ser234His)LOC130063979Uncertain significancecriteria provided, single submitter
536232NM_005027.4(PIK3R2):c.721C>A (p.Pro241Thr)LOC130063979Uncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 20 · Orphanet: 4 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
CCND2DefinitiveAutosomal dominantmegalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 35
PIK3R2DefinitiveAutosomal dominantmegalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 17
AKT3StrongAutosomal dominantmegalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 28

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
PIK3R2Orphanet:83473Megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome
CCND2Orphanet:83473Megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome
AKT3Orphanet:83473Megalencephaly-polymicrogyria-postaxial polydactyly-hydrocephalus syndrome
AKT3Orphanet:99802Hemimegalencephaly

Cohort genes → proteins

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence3

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
PIK3R2HGNC:8980ENSG00000105647O00459Phosphatidylinositol 3-kinase regulatory subunit betagencc,clinvar
CCND2HGNC:1583ENSG00000118971P30279G1/S-specific cyclin-D2gencc
AKT3HGNC:393ENSG00000117020Q9Y243RAC-gamma serine/threonine-protein kinasegencc

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
PIK3R2Phosphatidylinositol 3-kinase regulatory subunit betaRegulatory subunit of phosphoinositide-3-kinase (PI3K), a kinase that phosphorylates PtdIns(4,5)P2 (Phosphatidylinositol 4,5-bisphosphate) to generate phosphatidylinositol 3,4,5-trisphosphate (PIP3).
CCND2G1/S-specific cyclin-D2Regulatory component of the cyclin D2-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family including RB1 and regulates the cell-cycle during G(1)/S transition.
AKT3RAC-gamma serine/threonine-protein kinaseAKT3 is one of 3 closely related serine/threonine-protein kinases (AKT1, AKT2 and AKT3) called the AKT kinase, and which regulate many processes including metabolism, proliferation, cell survival, growth and angiogenesis.

Protein-family classification

Druggable: 2 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.67

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
Kinase218.5×0.008
Other/Unknown10.6×0.914

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
PIK3R2Kinaseyes2.7.1.137RhoGAP_dom, SH2, SH3_domain
CCND2Other/UnknownnoCyclin_C-dom, Cyclin_N, Cyclin-like_dom
AKT3Kinaseyes2.7.11.1Prot_kinase_dom, AGC-kinase_C, PH_domain

Expression context

Cohort genes with no expression data: 0.

3 cohort genes 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)3
unknown0

Top tissues across cohort

TissueCohort genes
cortical plate2
ganglionic eminence1
stromal cell of endometrium1
adrenal tissue1
cauda epididymis1
seminal vesicle1
calcaneal tendon1
embryo1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
PIK3R2138ubiquitousmarkercortical plate, ganglionic eminence, stromal cell of endometrium
CCND2293ubiquitousmarkeradrenal tissue, seminal vesicle, cauda epididymis
AKT3231ubiquitousmarkercortical plate, calcaneal tendon, embryo

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
CCND23,569
AKT33,392
PIK3R22,751

Intra-cohort edges

ABSources
AKT3PIK3R2string_interaction

Structural data

PDB: 3 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
PIK3R2O004598
AKT3Q9Y2432
CCND2P302791

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 136. Enrichment computed across 3 evidence-associated genes (3 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 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
CD28 dependent PI3K/Akt signaling2262.5×0.003PIK3R2, AKT3
Mitotic G1 phase and G1/S transition2122.8×0.005CCND2, AKT3
Extra-nuclear estrogen signaling2113.6×0.005PIK3R2, AKT3
VEGFA-VEGFR2 Pathway292.8×0.005PIK3R2, AKT3
PIP3 activates AKT signaling244.5×0.018PIK3R2, AKT3
AKT-mediated inactivation of FOXO1A1951.7×0.019AKT3
Inhibition of TSC complex formation by AKT (PKB)1761.3×0.019AKT3
Drug-mediated inhibition of CDK4/CDK6 activity1761.3×0.019CCND2
G-protein beta:gamma signalling1634.4×0.019AKT3
Signaling by LTK in cancer1543.8×0.019PIK3R2
RUNX2 regulates genes involved in cell migration1475.8×0.019AKT3
PI3K/AKT activation1423.0×0.019PIK3R2
AKT phosphorylates targets in the nucleus1380.7×0.019AKT3
IRS-mediated signalling1346.1×0.019PIK3R2
Co-stimulation by ICOS1346.1×0.019PIK3R2
Regulation of localization of FOXO transcription factors1317.2×0.019AKT3
Aberrant regulation of mitotic G1/S transition in cancer due to RB1 defects1292.8×0.019CCND2
Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants1292.8×0.019PIK3R2
Signaling by PDGFRA extracellular domain mutants1292.8×0.019PIK3R2
SARS-CoV-2 targets host intracellular signalling and regulatory pathways1292.8×0.019AKT3
Signaling by LTK1292.8×0.019PIK3R2
Downregulation of ERBB2:ERBB3 signaling1271.9×0.019AKT3
AKT phosphorylates targets in the cytosol1271.9×0.019AKT3
Regulation of TP53 Activity through Association with Co-factors1271.9×0.019AKT3
Activation of BAD and translocation to mitochondria1253.8×0.019AKT3
Regulation of beta-cell development1237.9×0.019AKT3
Regulation of RUNX1 Expression and Activity1223.9×0.019CCND2
Defective binding of RB1 mutants to E2F1,(E2F2, E2F3)1211.5×0.019CCND2
Tie2 Signaling1200.3×0.019PIK3R2
Role of LAT2/NTAL/LAB on calcium mobilization1200.3×0.019PIK3R2

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
insulin receptor signaling pathway2147.8×0.002PIK3R2, AKT3
positive regulation of artery morphogenesis11123.5×0.014AKT3
cellular response to X-ray1561.7×0.014CCND2
negative regulation of PERK-mediated unfolded protein response1468.1×0.014AKT3
positive regulation of cell size1432.1×0.014AKT3
regulation of stress fiber assembly1330.4×0.014PIK3R2
regulation of mitochondrion organization1280.9×0.014AKT3
positive regulation of vascular endothelial cell proliferation1280.9×0.014AKT3
brain morphogenesis1244.2×0.014AKT3
positive regulation of cell migration involved in sprouting angiogenesis1244.2×0.014AKT3
regulation of protein localization to plasma membrane1216.1×0.014PIK3R2
negative regulation of cellular senescence1216.1×0.014AKT3
intracellular glucose homeostasis1193.7×0.014PIK3R2
regulation of actin filament polymerization1193.7×0.014PIK3R2
negative regulation of apoptotic process223.2×0.014CCND2, AKT3
positive regulation of TOR signaling1165.2×0.014AKT3
homeostasis of number of cells within a tissue1147.8×0.014AKT3
long-term memory1140.4×0.014CCND2
positive regulation of protein import into nucleus1140.4×0.014PIK3R2
positive regulation of G1/S transition of mitotic cell cycle1133.8×0.014CCND2
positive regulation of blood vessel endothelial cell migration1130.6×0.014AKT3
T cell differentiation1127.7×0.014PIK3R2
adult locomotory behavior1100.3×0.017CCND2
negative regulation of MAPK cascade1100.3×0.017PIK3R2
positive regulation of cell adhesion190.6×0.018PIK3R2
regulation of autophagy180.2×0.019PIK3R2
positive regulation of endothelial cell proliferation177.0×0.019AKT3
B cell differentiation173.0×0.019PIK3R2
phosphatidylinositol 3-kinase/protein kinase B signal transduction170.2×0.020PIK3R2
G1/S transition of mitotic cell cycle166.9×0.020CCND2

Therapeutics

Drug target analysis

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

Druggability breadth: 3 of 3 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
PIK3R2IDELALISIB
CCND2PALBOCICLIB
AKT3CAPIVASERTIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
AKT3184
PIK3R264
CCND234

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
IDELALISIB4PIK3R2
INAVOLISIB4PIK3R2
PALBOCICLIB4CCND2
CAPIVASERTIB4AKT3
MIDOSTAURIN4AKT3
TASELISIB3PIK3R2
ALVOCIDIB3CCND2
IPATASERTIB3AKT3
AFURESERTIB3AKT3
ENZASTAURIN3AKT3
FASUDIL3AKT3
LESTAURTINIB3AKT3
RUBOXISTAURIN3AKT3
ROGINOLISIB2PIK3R2
AMDIZALISIB2PIK3R2
PICTILISIB2PIK3R2
MIRANSERTIB2AKT3
MK-22062AKT3
UPROSERTIB2AKT3
BMS-3870321CCND2
AT-131481AKT3
GSK-6906931AKT3
GSK-10709161AKT3
JNJ-264833271AKT3
PF-037583091AKT3
BAY-11259761AKT3
VEVORISERTIB1AKT3

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

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

SymbolAssaysType breakdown
AKT3660Binding:644, Functional:16
CCND228Binding:28
PIK3R227Binding:27

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PIK3R22.7.1.137phosphatidylinositol 3-kinase
AKT32.7.11.1non-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
AKT3660

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

27 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)
IDELALISIB4PIK3R2
INAVOLISIB4PIK3R2
PALBOCICLIB4CCND2
CAPIVASERTIB4AKT3
MIDOSTAURIN4AKT3
TASELISIB3PIK3R2
ALVOCIDIB3CCND2
IPATASERTIB3AKT3
AFURESERTIB3AKT3
ENZASTAURIN3AKT3
FASUDIL3AKT3
LESTAURTINIB3AKT3
RUBOXISTAURIN3AKT3
ROGINOLISIB2PIK3R2
AMDIZALISIB2PIK3R2
PICTILISIB2PIK3R2
MIRANSERTIB2AKT3
MK-22062AKT3
UPROSERTIB2AKT3
BMS-3870321CCND2
AT-131481AKT3
GSK-6906931AKT3
GSK-10709161AKT3
JNJ-264833271AKT3
PF-037583091AKT3
BAY-11259761AKT3
VEVORISERTIB1AKT3

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3PIK3R2, CCND2, AKT3
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: 0.