Multicystic dysplastic kidney

disease
On this page

Also known as MCDKmulticystic renal dysplasia

Summary

Multicystic dysplastic kidney (MONDO:0015988) is a disease with 9 cohort genes and 3 clinical trials.

At a glance

  • Prevalence: Unknown (Worldwide) [Orphanet-validated]
  • Cohort genes: 9
  • ClinVar variants: 10
  • Phenotypes (HPO): 15
  • Clinical trials: 3

Clinical features

Epidemiology

Prevalence records

1 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Prevalence at birth1-5 / 10 00023.26WorldwideValidated

Signs & symptoms

Clinical features (HPO)

15 HPO clinical features (Orphanet curated; top 15 by frequency):

HPO IDTermFrequency
HP:0000003Multicystic kidney dysplasiaVery frequent (80-99%)
HP:0002643Neonatal respiratory distressVery frequent (80-99%)
HP:0001622Premature birthFrequent (30-79%)
HP:0003270Abdominal distentionFrequent (30-79%)
HP:0031500Abdominal massFrequent (30-79%)
HP:0000028CryptorchidismOccasional (5-29%)
HP:0000076Vesicoureteral refluxOccasional (5-29%)
HP:0000105Enlarged kidneyOccasional (5-29%)
HP:0000122Unilateral renal agenesisOccasional (5-29%)
HP:0001562OligohydramniosOccasional (5-29%)
HP:0000070UreteroceleVery rare (<1-4%)
HP:0000074Ureteropelvic junction obstructionVery rare (<1-4%)
HP:0000085Horseshoe kidneyVery rare (<1-4%)
HP:0000822HypertensionVery rare (<1-4%)
HP:0030735Ureterovesical junction obstructionVery rare (<1-4%)

Identifiers

Disease identifiers

FieldValue
Canonical namemulticystic dysplastic kidney
Mondo IDMONDO:0015988
MeSHD021782
Orphanet1851
ICD-111178642763
NCITC123031
SNOMED CT204962002
UMLSC3714581
MedGen811388
GARD0018748
Is cancer (heuristic)no

Also known as: MCDK · multicystic renal dysplasia

Data availability: 10 ClinVar variants.

Disease family

An umbrella term covering 2 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › urinary system disorderkidney disordercystic kidney diseasemulticystic dysplastic kidney

Related subtypes (3): non-congenital cyst of kidney, medullary sponge kidney, familial cystic renal disease

Subtypes (2): unilateral multicystic dysplastic kidney, bilateral multicystic dysplastic kidney

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

10 retrieved; paginated sample, class counts are floors:

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

ClinVarVariant (HGVS)GeneClassificationReview
523524NM_170784.3(MKKS):c.958_959del (p.Leu320fs)MKKSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
523354NM_000297.4(PKD2):c.2284_2287del (p.Tyr762fs)PKD2Pathogeniccriteria provided, single submitter
1804040NM_020706.2(SCAF4):c.1295_1296del (p.Arg432fs)SCAF4Pathogeniccriteria provided, single submitter
632606NM_017412.4(FZD3):c.1616dup (p.Asp539fs)FZD3Likely pathogenicno assertion criteria provided
632604NM_012310.5(KIF4A):c.794G>T (p.Arg265Leu)KIF4ALikely pathogenicno assertion criteria provided
977155NM_001429.4(EP300):c.1781C>T (p.Thr594Met)EP300Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
523387NM_001009944.3(PKD1):c.5896GTG[1] (p.Val1967del)PKD1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
26792846;Y;inv(X)(p11.2q28)matUncertain significancecriteria provided, single submitter
523520NM_017777.4(MKS1):c.1274-3C>TMKS1Uncertain significancecriteria provided, single submitter
374206NM_001009944.3(PKD1):c.3785A>G (p.His1262Arg)PKD1Uncertain significancecriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 13 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SCAF4Orphanet:528084Non-specific syndromic intellectual disability
EP300Orphanet:353284Rubinstein-Taybi syndrome due to EP300 haploinsufficiency
MKKSOrphanet:110Bardet-Biedl syndrome
MKKSOrphanet:2473McKusick-Kaufman syndrome
MKS1Orphanet:110Bardet-Biedl syndrome
MKS1Orphanet:220493Joubert syndrome with ocular defect
MKS1Orphanet:475Isolated Joubert syndrome
MKS1Orphanet:564Meckel syndrome
PKD1Orphanet:730Autosomal dominant polycystic kidney disease
PKD1Orphanet:88924Autosomal dominant polycystic kidney disease type 1 with tuberous sclerosis
PKD2Orphanet:730Autosomal dominant polycystic kidney disease
PRKD1Orphanet:276145Malignant epithelial tumor of salivary glands
PRKD1Orphanet:708019Congenital heart defect-ectodermal dysplasia- brachydactyly-telangiectasia syndrome

Cohort genes → proteins

9 cohort genes, 9 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence9

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
KIF4AHGNC:13339ENSG00000090889O95239Chromosome-associated kinesin KIF4Aclinvar
SCAF4HGNC:19304ENSG00000156304O95104SR-related and CTD-associated factor 4clinvar
EP300HGNC:3373ENSG00000100393Q09472Histone acetyltransferase p300clinvar
FZD3HGNC:4041ENSG00000104290Q9NPG1Frizzled-3clinvar
MKKSHGNC:7108ENSG00000125863Q9NPJ1Molecular chaperone MKKSclinvar
MKS1HGNC:7121ENSG00000011143Q9NXB0Tectonic-like complex member MKS1clinvar
PKD1HGNC:9008ENSG00000008710P98161Polycystin-1clinvar
PKD2HGNC:9009ENSG00000118762Q13563Polycystin-2clinvar
PRKD1HGNC:9407ENSG00000184304Q15139Serine/threonine-protein kinase D1clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
KIF4AChromosome-associated kinesin KIF4AIron-sulfur (Fe-S) cluster binding motor protein that has a role in chromosome segregation during mitosis.
SCAF4SR-related and CTD-associated factor 4Anti-terminator protein required to prevent early mRNA termination during transcription.
EP300Histone acetyltransferase p300Functions as a histone acetyltransferase and regulates transcription via chromatin remodeling.
FZD3Frizzled-3Receptor for Wnt proteins.
MKKSMolecular chaperone MKKSProbable molecular chaperone that assists the folding of proteins upon ATP hydrolysis.
MKS1Tectonic-like complex member MKS1Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes.
PKD1Polycystin-1Component of a heteromeric calcium-permeable ion channel formed by PKD1 and PKD2 that is activated by interaction between PKD1 and a Wnt family member, such as WNT3A and WNT9B.
PKD2Polycystin-2Forms a nonselective cation channel.
PRKD1Serine/threonine-protein kinase D1Serine/threonine-protein kinase that converts transient diacylglycerol (DAG) signals into prolonged physiological effects downstream of PKC, and is involved in the regulation of MAPK8/JNK1 and Ras signaling, Golgi membrane integrity and tr…

Protein-family classification

Druggable: 3 · Difficult: 1 · Unknown: 5 · 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
Antibody/Immunoglobulin13.2×0.532
Kinase13.1×0.532
GPCR12.7×0.532
Other/Unknown51.0×0.687
Transcription factor10.9×0.687

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
KIF4AOther/UnknownnoKinesin_motor_dom, Kinesin_motor_CS, P-loop_NTPase
SCAF4Other/UnknownnoRRM_dom, CID_dom, ENTH_VHS
EP300Transcription factorno2.3.1.48Znf_TAZ, Znf_ZZ, Bromodomain
FZD3GPCRyesFrizzled/Smoothened_7TM, Frizzled/SFRP, GPCR_2-like_7TM
MKKSOther/UnknownnoCpn60/GroEL/TCP-1, GroEL-like_apical_dom_sf, TCP-1-like_intermed_sf
MKS1Other/UnknownnoC2_B9-type_dom
PKD1Antibody/ImmunoglobulinyesGPS, LRRNT, PC1
PKD2Other/UnknownnoEF_hand_dom, PKD_2, EF-hand-dom_pair
PRKD1Kinaseyes2.7.11.13Prot_kinase_dom, PH_domain, PKC_DAG/PE

Expression context

Cohort genes with no expression data: 0.

9 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)9
unknown0

Top tissues across cohort

TissueCohort genes
secondary oocyte2
ventricular zone2
oocyte1
buccal mucosa cell1
sperm1
tendon of biceps brachii1
adrenal tissue1
bone marrow cell1
colonic epithelium1
Brodmann (1909) area 231
corpus epididymis1
endothelial cell1
middle temporal gyrus1
prefrontal cortex1
left ovary1
olfactory segment of nasal mucosa1
right uterine tube1
cerebellar cortex1
cerebellar hemisphere1
right hemisphere of cerebellum1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
KIF4A179broadmarkeroocyte, secondary oocyte, ventricular zone
SCAF4267ubiquitousmarkertendon of biceps brachii, buccal mucosa cell, sperm
EP300292ubiquitousmarkercolonic epithelium, adrenal tissue, bone marrow cell
FZD3257ubiquitousmarkerBrodmann (1909) area 23, secondary oocyte, corpus epididymis
MKKS277ubiquitousmarkermiddle temporal gyrus, endothelial cell, prefrontal cortex
MKS1182ubiquitousmarkerright uterine tube, olfactory segment of nasal mucosa, left ovary
PKD1290markerright hemisphere of cerebellum, cerebellar hemisphere, cerebellar cortex
PKD2288ubiquitousmarkerblood vessel layer, calcaneal tendon, saphenous vein
PRKD1239ubiquitousmarkerventricular zone, seminal vesicle, thoracic aorta

Protein interactions among cohort

Intra-cohort edges: 3.

Hub genes (top 10 by interactor count)

SymbolInteractor count
EP30010,122
MKKS2,728
PRKD12,131
SCAF42,068
KIF4A1,982
PKD21,644
FZD31,413
PKD11,370
MKS11,087

Intra-cohort edges

ABSources
PKD1PKD2biogrid_interaction, intact, string_interaction
PKD1PRKD1string_interaction
PKD2PRKD1string_interaction

Structural data

PDB: 6 · AlphaFold-only: 3 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
EP300Q0947260
PKD2Q1356331
PKD1P9816113
FZD3Q9NPG14
KIF4AO952391
SCAF4O951041

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
MKKSQ9NPJ189.05
MKS1Q9NXB074.05
PRKD1Q1513968.99

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 95. Enrichment computed across 9 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
VxPx cargo-targeting to cilium2129.8×0.009PKD1, PKD2
LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production1285.5×0.047EP300
NFE2L2 regulating inflammation associated genes1285.5×0.047EP300
NFE2L2 regulating ER-stress associated genes1285.5×0.047EP300
NFE2L2 regulates pentose phosphate pathway genes1178.4×0.047EP300
NFE2L2 regulating MDR associated enzymes1178.4×0.047EP300
Regulation of NFE2L2 gene expression1178.4×0.047EP300
PI5P Regulates TP53 Acetylation1158.6×0.047EP300
RUNX3 regulates p14-ARF1142.8×0.047EP300
Regulation of FOXO transcriptional activity by acetylation1142.8×0.047EP300
STAT3 nuclear events downstream of ALK signaling1129.8×0.047EP300
Regulation of gene expression by Hypoxia-inducible Factor1119.0×0.047EP300
NOTCH2 intracellular domain regulates transcription1119.0×0.047EP300
Activation of the TFAP2 (AP-2) family of transcription factors1119.0×0.047EP300
NFE2L2 regulating tumorigenic genes1119.0×0.047EP300
Cilium Assembly227.2×0.047MKKS, MKS1
Organelle biogenesis and maintenance216.5×0.047MKKS, MKS1
RUNX3 regulates NOTCH signaling1102.0×0.049EP300
TRAF3-dependent IRF activation pathway195.2×0.049EP300
Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells189.2×0.049EP300
FOXO-mediated transcription of cell death genes189.2×0.049EP300
SARS-CoV-1 targets host intracellular signalling and regulatory pathways184.0×0.049EP300
Zygotic genome activation (ZGA)184.0×0.049EP300
Polo-like kinase mediated events179.3×0.050EP300
TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest175.1×0.050EP300
NOTCH4 Intracellular Domain Regulates Transcription171.4×0.050EP300
Regulation of TP53 Activity through Methylation168.0×0.050EP300
NFE2L2 regulating anti-oxidant/detoxification enzymes168.0×0.050EP300
CD209 (DC-SIGN) signaling164.9×0.050EP300
BBSome-mediated cargo-targeting to cilium162.1×0.051MKKS

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 9 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
mesonephric tubule development21872.4×7e-05PKD1, PKD2
metanephric ascending thin limb development2936.2×2e-04PKD1, PKD2
mesonephric duct development2749.0×2e-04PKD1, PKD2
heart development435.0×2e-04EP300, MKKS, PKD1, PKD2
determination of left/right symmetry385.1×2e-04MKKS, MKS1, PKD2
placenta blood vessel development2312.1×7e-04PKD1, PKD2
detection of mechanical stimulus2267.5×8e-04PKD1, PKD2
protein heterotetramerization2234.1×1e-03PKD1, PKD2
embryonic placenta development2170.2×0.002PKD1, PKD2
branching morphogenesis of an epithelial tube2162.8×0.002MKS1, PKD1
neural tube development2117.0×0.003PKD1, PKD2
spinal cord development2113.5×0.003PKD1, PKD2
positive regulation of protein import into nucleus293.6×0.004EP300, PRKD1
behavioral defense response11872.4×0.005EP300
smoothened signaling pathway involved in regulation of secondary heart field cardioblast proliferation11872.4×0.005MKS1
negative regulation of protein oligomerization11872.4×0.005EP300
swimming11872.4×0.005EP300
peptidyl-lysine propionylation11872.4×0.005EP300
metanephric cortex development11872.4×0.005PKD2
metanephric cortical collecting duct development11872.4×0.005PKD2
metanephric distal tubule development11872.4×0.005PKD2
metanephric distal tubule morphogenesis11872.4×0.005PKD1
regulation of tubulin deacetylation11872.4×0.005EP300
peptidyl-lysine crotonylation11872.4×0.005EP300
peptidyl-lysine butyrylation11872.4×0.005EP300
cell surface receptor signaling pathway via JAK-STAT264.6×0.005PKD1, PKD2
non-motile cilium assembly264.6×0.005MKKS, MKS1
heart looping259.4×0.005MKKS, PKD2
cartilage development255.9×0.005MKKS, PKD1
liver development249.3×0.006PKD1, PKD2

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 2 · Phased (≥1): 2 · Undrugged: 7

Druggability breadth: 5 of 9 evidence-associated genes (56%) 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
PRKD1INGENOL MEBUTATE

Top cohort targets by molecule count

SymbolMoleculesMax phase
PRKD1264
EP30093
KIF4A00
SCAF400
FZD300
MKKS00
MKS100
PKD100
PKD200

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
INGENOL MEBUTATE4PRKD1
MIDOSTAURIN4PRKD1
TAMOXIFEN4PRKD1
NERATINIB4PRKD1
BRIGATINIB4PRKD1
NINTEDANIB4PRKD1
SUNITINIB4PRKD1
CRIZOTINIB4PRKD1
GEFITINIB4PRKD1
COENZYME_A3EP300
CURCUMIN3EP300
EPIGALOCATECHIN GALLATE3EP300
SURAMIN3PRKD1
FASUDIL3PRKD1
ALVOCIDIB3PRKD1
LESTAURTINIB3PRKD1
MOLIBRESIB2EP300
MIVEBRESIB2EP300
STREPTONIGRIN2EP300
PHORBOL MYRISTATE ACETATE2PRKD1
EDELFOSINE2PRKD1
UPROSERTIB2PRKD1
UCN-012PRKD1
SU-0148132PRKD1
AT-92832PRKD1
BI-25362PRKD1
BERBERINE CHLORIDE1EP300
PLUMBAGIN1EP300
INOBRODIB1EP300
KW-24491PRKD1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

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

SymbolAssaysType breakdown
EP300767Binding:763, Functional:3, ADMET:1
PRKD1660Binding:650, Functional:10
PKD127Binding:27
KIF4A20Binding:20
PKD212Binding:12

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
EP3002.3.1.48histone acetyltransferase
PRKD12.7.11.13protein kinase C

Cohort genes with high screening signal

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

SymbolChEMBL assays
EP300767
PRKD1660

Pharmacogenomics

Cohort genes with a PharmGKB record: 9; 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)
INGENOL MEBUTATE4PRKD1
MIDOSTAURIN4PRKD1
TAMOXIFEN4PRKD1
NERATINIB4PRKD1
BRIGATINIB4PRKD1
NINTEDANIB4PRKD1
SUNITINIB4PRKD1
CRIZOTINIB4PRKD1
GEFITINIB4PRKD1
COENZYME_A3EP300
CURCUMIN3EP300
EPIGALOCATECHIN GALLATE3EP300
SURAMIN3PRKD1
FASUDIL3PRKD1
ALVOCIDIB3PRKD1
LESTAURTINIB3PRKD1
MOLIBRESIB2EP300
MIVEBRESIB2EP300
STREPTONIGRIN2EP300
PHORBOL MYRISTATE ACETATE2PRKD1
EDELFOSINE2PRKD1
UPROSERTIB2PRKD1
UCN-012PRKD1
SU-0148132PRKD1
AT-92832PRKD1
BI-25362PRKD1
BERBERINE CHLORIDE1EP300
PLUMBAGIN1EP300
INOBRODIB1EP300
KW-24491PRKD1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1PRKD1
BPhased (≥1) drug, not yet approved1EP300
CDruggable family + PDB, no drug2FZD3, PKD1
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug5KIF4A, SCAF4, MKKS, MKS1, PKD2

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
PKD127PRKD1
KIF4A20
SCAF40
FZD30
MKKS0
MKS10
PKD212

Clinical trials & evidence

Clinical trials

Clinical trials: 3.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified2
PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT03101891PHASE1ACTIVE_NOT_RECRUITINGRenal Anhydramnios Fetal Therapy
NCT06728228Not specifiedRECRUITINGAmnioinfusion for Fetal Renal Failure
NCT00764543Not specifiedNO_LONGER_AVAILABLEAmbulatory Blood Pressure Measurement in Children With Congenital Urine Flow Obstruction