Congenital hydrocephalus

disease
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Also known as HYC3

Summary

Congenital hydrocephalus (MONDO:0016349) is a disease (an umbrella term covering 8 Mondo subtypes) caused by LDB1 (GenCC Strong), with 11 cohort genes and 1 clinical trial.

At a glance

  • Prevalence: 1-5 / 10 000 (Europe) [Orphanet-validated]
  • Causal gene: LDB1 (GenCC Strong)
  • Umbrella term: 8 Mondo subtypes
  • Cohort genes: 11
  • ClinVar variants: 19
  • Phenotypes (HPO): 21
  • Clinical trials: 1

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Prevalence at birth1-5 / 10 00046.5EuropeValidated
Prevalence at birth6-9 / 10 00059United StatesValidated

Signs & symptoms

Clinical features (HPO)

21 HPO clinical features (Orphanet curated; top 21 by frequency):

HPO IDTermFrequency
HP:0000238HydrocephalusVery frequent (80-99%)
HP:0000256MacrocephalyFrequent (30-79%)
HP:0000324Facial asymmetryFrequent (30-79%)
HP:0000358Posteriorly rotated earsFrequent (30-79%)
HP:0000414Bulbous noseFrequent (30-79%)
HP:0000486StrabismusFrequent (30-79%)
HP:0000494Downslanted palpebral fissuresFrequent (30-79%)
HP:0000612Iris colobomaFrequent (30-79%)
HP:0001249Intellectual disabilityFrequent (30-79%)
HP:0001250SeizureFrequent (30-79%)
HP:0001270Motor delayFrequent (30-79%)
HP:0002007Frontal bossingFrequent (30-79%)
HP:0002119VentriculomegalyFrequent (30-79%)
HP:0002472Small cerebral cortexFrequent (30-79%)
HP:0002536Abnormal cortical gyrationFrequent (30-79%)
HP:0030048ColpocephalyFrequent (30-79%)
HP:0000407Sensorineural hearing impairmentVery rare (<1-4%)
HP:0000648Optic atrophyVery rare (<1-4%)
HP:0001104Macular hypoplasiaVery rare (<1-4%)
HP:0001339LissencephalyVery rare (<1-4%)
HP:0001627Abnormal heart morphologyVery rare (<1-4%)

Identifiers

Disease identifiers

FieldValue
Canonical namecongenital hydrocephalus
Mondo IDMONDO:0016349
OMIM236600
Orphanet2185
ICD-10-CMQ03
ICD-111878746673
NCITC98876
SNOMED CT47032000
UMLSC0020256
MedGen9336
GARD0006682
MedDRA10010506
Is cancer (heuristic)no

Also known as: congenital hydrocephalus · HYC3

Data availability: 19 ClinVar variants · 1 GenCC gene-disease record · 7 cell lines.

Disease family

An umbrella term covering 8 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › nervous system disordercentral nervous system disorderbrain disorderhydrocephaluscongenital hydrocephalus

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

Subtypes (8): hydrocephalus, nonsyndromic, autosomal recessive 1, autosomal recessive hydrocephalus due to congenital stenosis of aqueduct of Sylvius, X-linked hydrocephalus with stenosis of the aqueduct of Sylvius, hydrocephalus, nonsyndromic, autosomal recessive 2, hydrocephalus-blue sclerae-nephropathy syndrome, congenital communicating hydrocephalus, congenital non-communicating hydrocephalus, hydrocephalus, congenital, 3, with brain anomalies

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

19 retrieved; paginated sample, class counts are floors:

9 likely pathogenic, 6 uncertain significance, 2 likely pathogenic; risk factor, 1 conflicting classifications of pathogenicity, 1 pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
684696NM_000264.5(PTCH1):c.1991_1997del (p.Leu664fs)LOC100507346Pathogeniccriteria provided, single submitter
684697NC_000005.9:g.154735732_155604899dupLikely pathogenicno assertion criteria provided
39862NM_001080414.4(CCDC88C):c.5841_5842del (p.Glu1949fs)CCDC88CLikely pathogeniccriteria provided, single submitter
684695NM_000264.5(PTCH1):c.456_457del (p.Met152fs)PTCH1Likely pathogenicno assertion criteria provided
684721NC_000005.9:g.155599390_155755985dupSGCDLikely pathogenicno assertion criteria provided
4536632NM_003074.4(SMARCC1):c.1676T>A (p.Leu559Ter)SMARCC1Likely pathogeniccriteria provided, single submitter
684690NM_003074.4(SMARCC1):c.1589_1590insAGTGGGGACTC (p.Gln531fs)SMARCC1Likely pathogenicno assertion criteria provided
684691NM_003074.4(SMARCC1):c.1577A>C (p.His526Pro)SMARCC1Likely pathogenic; risk factorno assertion criteria provided
684692NM_003074.4(SMARCC1):c.2672del (p.Lys891fs)SMARCC1Likely pathogenic; risk factorno assertion criteria provided
684693NM_003074.4(SMARCC1):c.535A>T (p.Lys179Ter)SMARCC1Likely pathogenicno assertion criteria provided
684694NM_003074.4(SMARCC1):c.1242_1243dup (p.Thr415fs)SMARCC1Likely pathogenicno assertion criteria provided
684689NM_001039111.3(TRIM71):c.1886G>A (p.Arg629His)TRIM71Likely pathogenicno assertion criteria provided
667381NM_001378778.1(MPDZ):c.4171C>T (p.Arg1391Ter)MPDZConflicting classifications of pathogenicitycriteria provided, conflicting classifications
684725NC_000005.9:g.172068277_172342131dupDUSP1Uncertain significanceno assertion criteria provided
684723NC_000005.9:g.170814836_171100000dupFGF18Uncertain significanceno assertion criteria provided
684698NM_016338.5(IPO11):c.-6-1400_138+1704dupIPO11Uncertain significanceno assertion criteria provided
237456NM_000264.5(PTCH1):c.1503+3A>GPTCH1Uncertain significancecriteria provided, single submitter
684722NC_000005.9:g.170591818_170713790dupRANBP17Uncertain significanceno assertion criteria provided
684688NM_001039111.3(TRIM71):c.2450G>A (p.Arg817Gln)TRIM71Uncertain significancecriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 1 · Orphanet: 15 · 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
LDB1StrongAutosomal dominantcongenital hydrocephalus

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SGCDOrphanet:154Familial isolated dilated cardiomyopathy
SGCDOrphanet:219Delta-sarcoglycan-related limb-girdle muscular dystrophy R6
CCDC88COrphanet:269510Congenital non-communicating hydrocephalus
CCDC88COrphanet:423275Spinocerebellar ataxia type 40
TRIM71Orphanet:269505Congenital communicating hydrocephalus
MPDZOrphanet:269505Congenital communicating hydrocephalus
PTCH1Orphanet:220386Semilobar holoprosencephaly
PTCH1Orphanet:2353Schilbach-Rott syndrome
PTCH1Orphanet:280195Septopreoptic holoprosencephaly
PTCH1Orphanet:280200Microform holoprosencephaly
PTCH1Orphanet:377Gorlin syndrome
PTCH1Orphanet:77301Monosomy 9q22.3 syndrome
PTCH1Orphanet:93924Lobar holoprosencephaly
PTCH1Orphanet:93925Alobar holoprosencephaly
PTCH1Orphanet:93926Midline interhemispheric variant of holoprosencephaly

Cohort genes → proteins

11 cohort genes, 11 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence11

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
LDB1HGNC:6532ENSG00000198728Q86U70LIM domain-binding protein 1gencc
SGCDHGNC:10807ENSG00000170624Q92629Delta-sarcoglycanclinvar
SMARCC1HGNC:11104ENSG00000173473Q92922SWI/SNF complex subunit SMARCC1clinvar
RANBP17HGNC:14428ENSG00000204764Q9H2T7Ran-binding protein 17clinvar
CCDC88CHGNC:19967ENSG00000015133Q9P219Protein Dapleclinvar
IPO11HGNC:20628ENSG00000086200Q9UI26Importin-11clinvar
DUSP1HGNC:3064ENSG00000120129P28562Dual specificity protein phosphatase 1clinvar
TRIM71HGNC:32669ENSG00000206557Q2Q1W2E3 ubiquitin-protein ligase TRIM71clinvar
FGF18HGNC:3674ENSG00000156427O76093Fibroblast growth factor 18clinvar
MPDZHGNC:7208ENSG00000107186O75970Multiple PDZ domain proteinclinvar
PTCH1HGNC:9585ENSG00000185920Q13635Protein patched homolog 1clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
LDB1LIM domain-binding protein 1Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors.
SGCDDelta-sarcoglycanComponent of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a link between the F-actin cytoskeleton and the extracellular matrix.
SMARCC1SWI/SNF complex subunit SMARCC1Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology).
RANBP17Ran-binding protein 17May function as a nuclear transport receptor.
CCDC88CProtein DapleRequired for activation of guanine nucleotide-binding proteins (G-proteins) during non-canonical Wnt signaling.
IPO11Importin-11Functions in nuclear protein import as nuclear transport receptor.
DUSP1Dual specificity protein phosphatase 1Dual specificity phosphatase that dephosphorylates MAP kinase MAPK1/ERK2 on both ‘Thr-183’ and ‘Tyr-185’, regulating its activity during the meiotic cell cycle.
TRIM71E3 ubiquitin-protein ligase TRIM71E3 ubiquitin-protein ligase that cooperates with the microRNAs (miRNAs) machinery and promotes embryonic stem cells proliferation and maintenance.
FGF18Fibroblast growth factor 18Plays an important role in the regulation of cell proliferation, cell differentiation and cell migration.
MPDZMultiple PDZ domain proteinMember of the NMDAR signaling complex that may play a role in control of AMPAR potentiation and synaptic plasticity in excitatory synapses.
PTCH1Protein patched homolog 1Acts as a receptor for sonic hedgehog (SHH), indian hedgehog (IHH) and desert hedgehog (DHH).

Protein-family classification

Druggable: 1 · Difficult: 3 · Unknown: 7 · Druggable fraction: 0.09

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
Phosphatase17.6×0.481
Scaffold/PPI11.6×0.481
Transcription factor21.5×0.481
Other/Unknown71.1×0.481

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
LDB1Other/UnknownnoLIM-bd/SEUSS, LID
SGCDOther/UnknownnoSarcoglycan, Sarcoglycan_gamma/delta/zeta
SMARCC1Transcription factornoChromo/chromo_shadow_dom, SANT/Myb, SWIRM
RANBP17Other/UnknownnoImportin-beta_N, ARM-like, ARM-type_fold
CCDC88COther/UnknownnoCH_dom, CH_dom_sf, HOOK_N
IPO11Other/UnknownnoImportin-beta_N, ARM-like, ARM-type_fold
DUSP1Phosphataseyes3.1.3.16Dual-sp_phosphatase_cat-dom, Tyr_Pase_dom, Rhodanese-like_dom
TRIM71Transcription factornoZnf_B-box, NHL_repeat, Filamin/ABP280_rpt
FGF18Other/UnknownnoFibroblast_GF_fam, IL1/FGF
MPDZScaffold/PPInoPDZ, L27_dom, L27_2
PTCH1Other/UnknownnoSSD, TM_rcpt_patched, HMGCR/SNAP/NPC1-like_SSD

Expression context

Cohort genes with no expression data: 0.

11 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)11
unknown0

Top tissues across cohort

TissueCohort genes
male germ line stem cell (sensu Vertebrata) in testis3
ganglionic eminence2
right uterine tube2
heart right ventricle2
ventricular zone2
calcaneal tendon2
vena cava2
left ovary1
left ventricle myocardium1
skeletal muscle tissue of rectus abdominis1
embryo1
adrenal tissue1
granulocyte1
olfactory segment of nasal mucosa1
colonic epithelium1
primordial germ cell in gonad1
nipple1
urethra1
oocyte1
secondary oocyte1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
LDB1236ubiquitousmarkerright uterine tube, ganglionic eminence, left ovary
SGCD247broadmarkerleft ventricle myocardium, skeletal muscle tissue of rectus abdominis, heart right ventricle
SMARCC1290ubiquitousmarkerventricular zone, embryo, ganglionic eminence
RANBP17197ubiquitousmarkercalcaneal tendon, male germ line stem cell (sensu Vertebrata) in testis, adrenal tissue
CCDC88C220ubiquitousmarkerright uterine tube, granulocyte, olfactory segment of nasal mucosa
IPO11241ubiquitousmarkerprimordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis, colonic epithelium
DUSP1302ubiquitousmarkervena cava, nipple, urethra
TRIM7169broadmarkersecondary oocyte, oocyte, male germ line stem cell (sensu Vertebrata) in testis
FGF18172broadmarkertendon of biceps brachii, heart right ventricle, vena cava
MPDZ274ubiquitousmarkercalcaneal tendon, corpus callosum, ventricular zone
PTCH1275ubiquitousmarkertibia, dorsal root ganglion, trigeminal ganglion

Protein interactions among cohort

Intra-cohort edges: 2.

Hub genes (top 10 by interactor count)

SymbolInteractor count
SMARCC13,999
FGF183,769
DUSP13,610
MPDZ3,527
PTCH13,368
LDB11,845
IPO111,218
SGCD1,102
TRIM711,101
CCDC88C906

Intra-cohort edges

ABSources
CCDC88CMPDZstring_interaction
IPO11RANBP17string_interaction

Structural data

PDB: 7 · AlphaFold-only: 4 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
PTCH1Q1363516
LDB1Q86U709
MPDZO759709
SMARCC1Q929225
DUSP1P285624
TRIM71Q2Q1W22
FGF18O760931

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
IPO11Q9UI2693.53
RANBP17Q9H2T785.42
SGCDQ9262981.43
CCDC88CQ9P21965.69

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 74. Enrichment computed across 11 evidence-associated genes (8 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 8 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Negative regulation of TCF-dependent signaling by DVL-interacting proteins1285.5×0.042CCDC88C
FGFR3b ligand binding and activation1203.9×0.042FGF18
GLI proteins bind promoters of Hh responsive genes to promote transcription1203.9×0.042PTCH1
Ligand-receptor interactions1178.4×0.042PTCH1
Signaling by activated point mutants of FGFR31119.0×0.042FGF18
FGFR3c ligand binding and activation1109.8×0.042FGF18
FGFR2c ligand binding and activation1109.8×0.042FGF18
Phospholipase C-mediated cascade; FGFR31109.8×0.042FGF18
FGFRL1 modulation of FGFR1 signaling1109.8×0.042FGF18
FGFR4 ligand binding and activation1102.0×0.042FGF18
Phospholipase C-mediated cascade; FGFR4195.2×0.042FGF18
Activated point mutants of FGFR2184.0×0.042FGF18
Formation of the non-canonical BAF (ncBAF) complex184.0×0.042SMARCC1
RAF-independent MAPK1/3 activation179.3×0.042DUSP1
Activation of SMO179.3×0.042PTCH1
Phospholipase C-mediated cascade; FGFR2179.3×0.042FGF18
PI-3K cascade:FGFR3179.3×0.042FGF18
Formation of the canonical BAF (cBAF) complex179.3×0.042SMARCC1
Formation of the polybromo-BAF (pBAF) complex179.3×0.042SMARCC1
SHC-mediated cascade:FGFR3175.1×0.042FGF18
Formation of the embryonic stem cell BAF (esBAF) complex175.1×0.042SMARCC1
PI-3K cascade:FGFR4171.4×0.042FGF18
FRS-mediated FGFR3 signaling168.0×0.042FGF18
SHC-mediated cascade:FGFR4168.0×0.042FGF18
PI-3K cascade:FGFR2162.1×0.042FGF18
FRS-mediated FGFR4 signaling162.1×0.042FGF18
Signaling by FGFR3 in disease162.1×0.042FGF18
SHC-mediated cascade:FGFR2159.5×0.042FGF18
Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)157.1×0.042SMARCC1
FRS-mediated FGFR2 signaling154.9×0.042FGF18

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 11 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
prostate gland development2255.3×0.004SMARCC1, PTCH1
response to chlorate1766.0×0.022PTCH1
neural plate axis specification1766.0×0.022PTCH1
coronary vasculature morphogenesis1766.0×0.022SGCD
cell proliferation involved in metanephros development1766.0×0.022PTCH1
respiratory basal cell differentiation1766.0×0.022CCDC88C
response to retinoic acid269.6×0.022DUSP1, PTCH1
stem cell proliferation256.7×0.022TRIM71, PTCH1
fibroblast growth factor receptor signaling pathway251.9×0.022TRIM71, FGF18
response to estradiol236.0×0.022DUSP1, PTCH1
animal organ morphogenesis234.8×0.022SMARCC1, PTCH1
neural tube closure234.0×0.022TRIM71, PTCH1
cell differentiation involved in kidney development1510.7×0.023PTCH1
peptidyl-serine dephosphorylation1510.7×0.023DUSP1
positive regulation of endothelial cell chemotaxis to fibroblast growth factor1510.7×0.023FGF18
transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery1383.0×0.023LDB1
regulation of kinase activity1383.0×0.023LDB1
negative regulation of meiotic cell cycle1383.0×0.023DUSP1
regulation of cell migration228.6×0.023FGF18, LDB1
protein import into nucleus226.2×0.023RANBP17, IPO11
apical constriction1306.4×0.024CCDC88C
ribosomal protein import into nucleus1306.4×0.024IPO11
epidermal cell fate specification1306.4×0.024PTCH1
intramembranous ossification1255.3×0.024FGF18
neural tube patterning1255.3×0.024PTCH1
hindlimb morphogenesis1255.3×0.024PTCH1
positive regulation of hemoglobin biosynthetic process1255.3×0.024LDB1
negative regulation of monocyte chemotaxis1255.3×0.024DUSP1
negative regulation of cell division1218.9×0.025PTCH1
mammary gland duct morphogenesis1218.9×0.025PTCH1

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 1 · Undrugged: 10

Druggability breadth: 4 of 11 evidence-associated genes (36%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
SMARCC112
LDB100
SGCD00
RANBP1700
CCDC88C00
IPO1100
DUSP100
TRIM7100
FGF1800
MPDZ00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
MOLIBRESIB2SMARCC1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
SMARCC18Binding:8
DUSP18Binding:8
PTCH14Binding:4
IPO111Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
DUSP13.1.3.16protein-serine/threonine phosphatase

Pharmacogenomics

Cohort genes with a PharmGKB record: 11; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

1 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)
MOLIBRESIB2SMARCC1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved1SMARCC1
CDruggable family + PDB, no drug1DUSP1
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug9LDB1, SGCD, RANBP17, CCDC88C, IPO11, TRIM71, FGF18, MPDZ, PTCH1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
LDB10
SGCD0
RANBP170
CCDC88C0
IPO111
DUSP18
TRIM710
FGF180
MPDZ0
PTCH14

Clinical trials & evidence

Clinical trials

Clinical trials: 1.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified1

Top trials by phase / activity

NCTPhaseStatusTitle
NCT06664372Not specifiedNOT_YET_RECRUITINGInsertion of Frontal Ventricular Catheter of VP Shunt in Congenital Hydrocephalus Guided by Trans Fontanelle Ultrasound