Bilateral perisylvian polymicrogyria

disease
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Summary

Bilateral perisylvian polymicrogyria (MONDO:0020340) is a disease with 6 cohort genes.

At a glance

  • Cohort genes: 6
  • ClinVar variants: 8
  • Phenotypes (HPO): 49

Clinical features

Signs & symptoms

Clinical features (HPO)

49 HPO clinical features (Orphanet curated; top 49 by frequency):

HPO IDTermFrequency
HP:0002269Abnormality of neuronal migrationVery frequent (80-99%)
HP:0032407Bilateral perisylvian polymicrogyriaVery frequent (80-99%)
HP:0000750Delayed speech and language developmentFrequent (30-79%)
HP:0001249Intellectual disabilityFrequent (30-79%)
HP:0001250SeizureFrequent (30-79%)
HP:0001257SpasticityFrequent (30-79%)
HP:0001263Global developmental delayFrequent (30-79%)
HP:0001328Specific learning disabilityFrequent (30-79%)
HP:0001347HyperreflexiaFrequent (30-79%)
HP:0001371Flexion contractureFrequent (30-79%)
HP:0002392EEG with polyspike wave complexesFrequent (30-79%)
HP:0002463Language impairmentFrequent (30-79%)
HP:0005684Distal arthrogryposisFrequent (30-79%)
HP:0007359Focal-onset seizureFrequent (30-79%)
HP:0008947Floppy infantFrequent (30-79%)
HP:0012014EEG with central focal spikesFrequent (30-79%)
HP:0012017EEG with parietal focal spikesFrequent (30-79%)
HP:0020190Perisylvian predominant thick cortex pachygyriaFrequent (30-79%)
HP:0030319Weakness of facial musculatureFrequent (30-79%)
HP:0000252MicrocephalyOccasional (5-29%)
HP:0000347MicrognathiaOccasional (5-29%)
HP:0000365Hearing impairmentOccasional (5-29%)
HP:0000453Choanal atresiaOccasional (5-29%)
HP:0000639NystagmusOccasional (5-29%)
HP:0000767Pectus excavatumOccasional (5-29%)
HP:0001260DysarthriaOccasional (5-29%)
HP:0001310DysmetriaOccasional (5-29%)
HP:0001320Cerebellar vermis hypoplasiaOccasional (5-29%)
HP:0001349Facial diplegiaOccasional (5-29%)
HP:0001511Intrauterine growth retardationOccasional (5-29%)
HP:0002015DysphagiaOccasional (5-29%)
HP:0002020Gastroesophageal refluxOccasional (5-29%)
HP:0002061Lower limb spasticityOccasional (5-29%)
HP:0002104ApneaOccasional (5-29%)
HP:0002307DroolingOccasional (5-29%)
HP:0002385ParaparesisOccasional (5-29%)
HP:0002509Limb hypertoniaOccasional (5-29%)
HP:0002510Spastic tetraplegiaOccasional (5-29%)
HP:0002835AspirationOccasional (5-29%)
HP:0007024Pseudobulbar paralysisOccasional (5-29%)
HP:0007033Cerebellar dysplasiaOccasional (5-29%)
HP:0007301Oromotor apraxiaOccasional (5-29%)
HP:0010808Protruding tongueOccasional (5-29%)
HP:0011157Focal sensory seizureOccasional (5-29%)
HP:0011755Ectopic posterior pituitaryOccasional (5-29%)
HP:0011968Feeding difficultiesOccasional (5-29%)
HP:0012015EEG with frontal focal spikesOccasional (5-29%)
HP:0012469Infantile spasmsOccasional (5-29%)
HP:0410011Abnormality of masticatory muscleOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical namebilateral perisylvian polymicrogyria
Mondo IDMONDO:0020340
Orphanet98889
DOIDDOID:0080924
ICD-111882677643
UMLSC1845668
MedGen337000
GARD0006011
Is cancer (heuristic)no

Data availability: 8 ClinVar variants.

Disease family

An umbrella term covering 3 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › nervous system disordercongenital nervous system disorderpolymicrogyriabilateral polymicrogyriabilateral perisylvian polymicrogyria

Related subtypes (4): bilateral frontoparietal polymicrogyria, bilateral parasagittal parieto-occipital polymicrogyria, bilateral generalized polymicrogyria, bilateral frontal polymicrogyria

Subtypes (3): polymicrogyria, bilateral perisylvian, X-linked, polymicrogyria, bilateral perisylvian, autosomal recessive, polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis

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

8 retrieved; paginated sample, class counts are floors:

3 conflicting classifications of pathogenicity, 2 pathogenic, 2 likely pathogenic, 1 pathogenic/likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
432534NM_006922.4(SCN3A):c.4862G>A (p.Arg1621Gln)SCN3APathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2664153NM_006009.4(TUBA1A):c.303T>A (p.Asn101Lys)TUBA1APathogeniccriteria provided, single submitter
1708143NM_178012.5(TUBB2B):c.776C>T (p.Pro259Leu)TUBB2BPathogeniccriteria provided, multiple submitters, no conflicts
2664152NM_004818.3(DDX23):c.2437C>T (p.Arg813Cys)DDX23Likely pathogeniccriteria provided, single submitter
2664151NM_138459.5(NUS1):c.616G>T (p.Asp206Tyr)NUS1Likely pathogeniccriteria provided, single submitter
988578NM_006009.4(TUBA1A):c.1216C>G (p.His406Asp)TUBA1AConflicting classifications of pathogenicitycriteria provided, conflicting classifications
988580NM_006009.4(TUBA1A):c.1193T>G (p.Met398Arg)TUBA1AConflicting classifications of pathogenicitycriteria provided, conflicting classifications
1496445NM_006005.3(WFS1):c.923C>G (p.Ser308Cys)WFS1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications

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
SCN3AOrphanet:442835Non-specific early-onset epileptic encephalopathy
SCN3AOrphanet:98820Familial focal epilepsy with variable foci
WFS1Orphanet:3463Wolfram syndrome
WFS1Orphanet:411590Wolfram-like syndrome
WFS1Orphanet:90635Rare autosomal dominant non-syndromic sensorineural deafness type DFNA
WFS1Orphanet:98991Early-onset nuclear cataract
TUBA1AOrphanet:171680Lissencephaly due to TUBA1A mutation
TUBA1AOrphanet:45358Congenital fibrosis of extraocular muscles
TUBA1AOrphanet:467166Tubulinopathy-associated dysgyria
TUBA1AOrphanet:994Fetal akinesia deformation sequence
NUS1Orphanet:442835Non-specific early-onset epileptic encephalopathy
TUBB2BOrphanet:1766Dysequilibrium syndrome
TUBB2BOrphanet:300573Polymicrogyria due to TUBB2B mutation
TUBB2BOrphanet:45358Congenital fibrosis of extraocular muscles
TUBB2BOrphanet:467166Tubulinopathy-associated dysgyria

Cohort genes → proteins

6 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SCN3AHGNC:10590ENSG00000153253Q9NY46Sodium channel protein type 3 subunit alphaclinvar
WFS1HGNC:12762ENSG00000109501O76024Wolframinclinvar
DDX23HGNC:17347ENSG00000174243Q9BUQ8Probable ATP-dependent RNA helicase DDX23clinvar
TUBA1AHGNC:20766ENSG00000167552Q71U36Tubulin alpha-1A chainclinvar
NUS1HGNC:21042ENSG00000153989Q96E22Dehydrodolichyl diphosphate synthase complex subunit NUS1clinvar
TUBB2BHGNC:30829ENSG00000137285Q9BVA1Tubulin beta-2B chainclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SCN3ASodium channel protein type 3 subunit alphaPore-forming subunit of Nav1.3, a voltage-gated sodium (Nav) channel that directly mediates the depolarizing phase of action potentials in excitable membranes.
WFS1WolframinParticipates in the regulation of cellular Ca(2+) homeostasis, at least partly, by modulating the filling state of the endoplasmic reticulum Ca(2+) store.
DDX23Probable ATP-dependent RNA helicase DDX23Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation.
TUBA1ATubulin alpha-1A chainTubulin is the major constituent of microtubules, a cylinder consisting of laterally associated linear protofilaments composed of alpha- and beta-tubulin heterodimers.
NUS1Dehydrodolichyl diphosphate synthase complex subunit NUS1With DHDDS, forms the dehydrodolichyl diphosphate synthase (DDS) complex, an essential component of the dolichol monophosphate (Dol-P) biosynthetic machinery.
TUBB2BTubulin beta-2B chainTubulin is the major constituent of microtubules, a cylinder consisting of laterally associated linear protofilaments composed of alpha- and beta-tubulin heterodimers.

Protein-family classification

Druggable: 2 · Difficult: 0 · Unknown: 4 · Druggable fraction: 0.33

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
Ion channel118.6×0.158
Enzyme (other)12.0×0.458
Other/Unknown41.2×0.458

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SCN3AIon channelyesNa_channel_asu, Ion_trans_dom, Na_trans_assoc_dom
WFS1Other/UnknownnoTPR-like_helical_dom_sf, Wolframin, Wolframin_fam
DDX23Other/UnknownnoRNA-helicase_DEAD-box_CS, Helicase_C-like, DEAD/DEAH_box_helicase_dom
TUBA1AOther/UnknownnoTubulin, Alpha_tubulin, Tubulin_FtsZ_GTPase
NUS1Enzyme (other)yes2.5.1.87UPP_synth-like, UPP_synth-like_sf, Nus1/NgBR
TUBB2BOther/UnknownnoTubulin, Beta_tubulin, Tubulin_FtsZ_GTPase

Expression context

Cohort genes with no expression data: 0.

6 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)6
unknown0

Top tissues across cohort

TissueCohort genes
cortical plate3
endothelial cell2
ganglionic eminence2
middle temporal gyrus1
body of uterus1
left ovary1
right ovary1
calcaneal tendon1
granulocyte1
sural nerve1
endometrium1
islet of Langerhans1
tibia1
ventricular zone1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SCN3A221broadmarkerendothelial cell, cortical plate, middle temporal gyrus
WFS1280ubiquitousmarkerright ovary, left ovary, body of uterus
DDX23296ubiquitousmarkercalcaneal tendon, sural nerve, granulocyte
TUBA1A288ubiquitousmarkerendothelial cell, cortical plate, ganglionic eminence
NUS1255broadmarkerendometrium, tibia, islet of Langerhans
TUBB2B265ubiquitousmarkercortical plate, ganglionic eminence, ventricular zone

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
DDX234,764
TUBB2B4,736
WFS13,409
NUS12,058
SCN3A1,454
TUBA1A1,436

Intra-cohort edges

ABSources
TUBA1ATUBB2Bintact

Structural data

PDB: 5 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
DDX23Q9BUQ824
TUBA1AQ71U3615
NUS1Q96E229
TUBB2BQ9BVA13
SCN3AQ9NY462

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
WFS1O7602473.85

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 108. Enrichment computed across 6 evidence-associated genes (6 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 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane2181.3×0.001TUBA1A, TUBB2B
Transport of connexons to the plasma membrane2181.3×0.001TUBA1A, TUBB2B
Gap junction trafficking and regulation2158.6×0.001TUBA1A, TUBB2B
Gap junction trafficking2158.6×0.001TUBA1A, TUBB2B
Post-chaperonin tubulin folding pathway2158.6×0.001TUBA1A, TUBB2B
Formation of tubulin folding intermediates by CCT/TriC2141.0×0.001TUBA1A, TUBB2B
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding2135.9×0.001TUBA1A, TUBB2B
Prefoldin mediated transfer of substrate to CCT/TriC2131.3×0.001TUBA1A, TUBB2B
Activation of AMPK downstream of NMDARs2126.9×0.001TUBA1A, TUBB2B
L1CAM interactions360.1×0.001SCN3A, TUBA1A, TUBB2B
RHO GTPases activate IQGAPs2115.3×0.001TUBA1A, TUBB2B
Sealing of the nuclear envelope (NE) by ESCRT-III2115.3×0.001TUBA1A, TUBB2B
HCMV Infection2108.8×0.001TUBA1A, TUBB2B
Chaperonin-mediated protein folding2100.2×0.001TUBA1A, TUBB2B
Gap junction assembly297.6×0.001TUBA1A, TUBB2B
Nuclear Envelope (NE) Reassembly297.6×0.001TUBA1A, TUBB2B
Selective autophagy292.8×0.001TUBA1A, TUBB2B
Protein folding286.5×0.001TUBA1A, TUBB2B
Assembly and cell surface presentation of NMDA receptors284.6×0.001TUBA1A, TUBB2B
Cargo trafficking to the periciliary membrane282.8×0.001TUBA1A, TUBB2B
Aggrephagy282.8×0.001TUBA1A, TUBB2B
Axon guidance322.6×0.001SCN3A, TUBA1A, TUBB2B
Nervous system development321.5×0.001SCN3A, TUBA1A, TUBB2B
Carboxyterminal post-translational modifications of tubulin279.3×0.001TUBA1A, TUBB2B
Recycling pathway of L1274.6×0.001TUBA1A, TUBB2B
COPI-independent Golgi-to-ER retrograde traffic269.2×0.001TUBA1A, TUBB2B
Post NMDA receptor activation events268.0×0.001TUBA1A, TUBB2B
Intraflagellar transport266.8×0.001TUBA1A, TUBB2B
Antimicrobial mechanism of IFN-stimulated genes265.6×0.001TUBA1A, TUBB2B
HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand264.5×0.001TUBA1A, TUBB2B

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
microtubule-based process2330.4×0.001TUBA1A, TUBB2B
cis assembly of pre-catalytic spliceosome11404.3×0.009DDX23
dolichyl diphosphate biosynthetic process11404.3×0.009NUS1
positive regulation of axon guidance11404.3×0.009TUBB2B
negative regulation of ATF6-mediated unfolded protein response11404.3×0.009WFS1
cerebral cortex development268.5×0.009TUBA1A, TUBB2B
mitotic cell cycle244.6×0.009TUBA1A, TUBB2B
neuron migration244.6×0.009TUBA1A, TUBB2B
microtubule cytoskeleton organization240.4×0.009TUBA1A, TUBB2B
regulation of intracellular cholesterol transport1702.2×0.011NUS1
positive regulation of growth1702.2×0.011WFS1
pyramidal neuron differentiation1561.7×0.013TUBA1A
cerebellar cortex morphogenesis1468.1×0.014TUBA1A
negative regulation of response to endoplasmic reticulum stress1401.2×0.014WFS1
negative regulation of type B pancreatic cell apoptotic process1351.1×0.014WFS1
olfactory behavior1312.1×0.014WFS1
dolichyl monophosphate biosynthetic process1312.1×0.014NUS1
neuron projection arborization1312.1×0.014TUBA1A
R-loop processing1280.9×0.014DDX23
membrane depolarization during action potential1280.9×0.014SCN3A
response to L-glutamate1280.9×0.014TUBA1A
positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis1280.9×0.014NUS1
ER overload response1255.3×0.015WFS1
forebrain morphogenesis1234.1×0.015TUBA1A
nervous system process1200.6×0.016WFS1
organelle transport along microtubule1200.6×0.016TUBA1A
startle response1187.2×0.017TUBA1A
vascular endothelial growth factor signaling pathway1175.5×0.017NUS1
locomotory exploration behavior1165.2×0.017TUBA1A
positive regulation of protein metabolic process1165.2×0.017WFS1

Therapeutics

Drug target analysis

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

Druggability breadth: 4 of 6 evidence-associated genes (67%) 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
SCN3ABEPRIDIL
TUBA1ACOLCHICINE
TUBB2BCOLCHICINE

Top cohort targets by molecule count

SymbolMoleculesMax phase
SCN3A934
TUBA1A224
TUBB2B214
WFS100
DDX2300
NUS100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BEPRIDIL4SCN3A
DIBUCAINE4SCN3A
ARTICAINE4SCN3A
BUPIVACAINE4SCN3A
IMIPRAMINE4SCN3A
DROPERIDOL4SCN3A
DICYCLOMINE4SCN3A
TETRABENAZINE4SCN3A
PHENIRAMINE4SCN3A
PRILOCAINE4SCN3A
PROPOXYCAINE4SCN3A
PROPARACAINE4SCN3A
HEXYLCAINE4SCN3A
PRAMOXINE4SCN3A
BENOXINATE4SCN3A
QUINIDINE4SCN3A
FELODIPINE4SCN3A
PHENYTOIN4SCN3A
QUININE4SCN3A
NISOLDIPINE4SCN3A
NIFEDIPINE4SCN3A
PRAZOSIN4SCN3A
DILTIAZEM4SCN3A
PRENYLAMINE4SCN3A
COCAINE4SCN3A
TRIFLUOPERAZINE4SCN3A
CINNARIZINE4SCN3A
THIORIDAZINE4SCN3A
ETIDOCAINE4SCN3A
CHLORPHENIRAMINE4SCN3A

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
TUBB2B1,757Binding:1717, Functional:34, ADMET:6
TUBA1A1,696Binding:1655, Functional:35, ADMET:6
SCN3A102Binding:79, Functional:18, ADMET:4, Toxicity:1
WFS11Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
NUS12.5.1.87ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]

Cohort genes with high screening signal

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

SymbolChEMBL assays
SCN3A102
TUBA1A1,696
TUBB2B1,757

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

30 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)
BEPRIDIL4SCN3A
DIBUCAINE4SCN3A
ARTICAINE4SCN3A
BUPIVACAINE4SCN3A
IMIPRAMINE4SCN3A
DROPERIDOL4SCN3A
DICYCLOMINE4SCN3A
TETRABENAZINE4SCN3A
PHENIRAMINE4SCN3A
PRILOCAINE4SCN3A
PROPOXYCAINE4SCN3A
PROPARACAINE4SCN3A
HEXYLCAINE4SCN3A
PRAMOXINE4SCN3A
BENOXINATE4SCN3A
QUINIDINE4SCN3A
FELODIPINE4SCN3A
PHENYTOIN4SCN3A
QUININE4SCN3A
NISOLDIPINE4SCN3A
NIFEDIPINE4SCN3A
PRAZOSIN4SCN3A
DILTIAZEM4SCN3A
PRENYLAMINE4SCN3A
COCAINE4SCN3A
TRIFLUOPERAZINE4SCN3A
CINNARIZINE4SCN3A
THIORIDAZINE4SCN3A
ETIDOCAINE4SCN3A
CHLORPHENIRAMINE4SCN3A

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3SCN3A, TUBA1A, TUBB2B
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1NUS1
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2WFS1, DDX23

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
WFS11
DDX230
NUS10

Clinical trials & evidence

Clinical trials

Clinical trials: 0.