Cystinosis

disease
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Also known as cystine diathesiscystine diseasecystine storage diseaseCystinosesProtein defect of cystin transport

Summary

Cystinosis (MONDO:0016239) is a disease caused by CTNS (GenCC Definitive), with 3 cohort genes and 38 clinical trials. Top therapeutic interventions include cysteamine, fludarabine phosphate, and elx-02.

At a glance

  • Prevalence: 1-9 / 100 000 (Europe) [Orphanet-validated]
  • Causal gene: CTNS (GenCC Definitive)
  • Cohort genes: 3
  • ClinVar variants: 159
  • Phenotypes (HPO): 56
  • Clinical trials: 38

Clinical features

Epidemiology

Prevalence records

10 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Prevalence at birth1-9 / 1 000 0000.75WorldwideValidated
Point prevalence1-9 / 100 0001.5EuropeValidated
Prevalence at birth1-9 / 1 000 0000.5EuropeValidated
Prevalence at birth1-9 / 1 000 0000.31FranceValidated
Prevalence at birth1-9 / 1 000 0000.59GermanyValidated
Prevalence at birth1-9 / 100 0002.1United KingdomValidated
Prevalence at birth1-9 / 1 000 0000.52AustraliaValidated
Prevalence at birth1-9 / 1 000 0000.87DenmarkValidated
Prevalence at birth1-9 / 1 000 0000.38SwedenValidated
Prevalence at birth1-9 / 100 0001.6Specific populationValidated

Signs & symptoms

Clinical features (HPO)

56 HPO clinical features (Orphanet curated; top 50 by frequency):

HPO IDTermFrequency
HP:0000093ProteinuriaVery frequent (80-99%)
HP:0000112NephropathyVery frequent (80-99%)
HP:0000124Renal tubular dysfunctionVery frequent (80-99%)
HP:0000613PhotophobiaVery frequent (80-99%)
HP:0000821HypothyroidismVery frequent (80-99%)
HP:0000823Delayed pubertyVery frequent (80-99%)
HP:0001324Muscle weaknessVery frequent (80-99%)
HP:0001508Failure to thriveVery frequent (80-99%)
HP:0001944DehydrationVery frequent (80-99%)
HP:0001959PolydipsiaVery frequent (80-99%)
HP:0001994Renal Fanconi syndromeVery frequent (80-99%)
HP:0002013VomitingVery frequent (80-99%)
HP:0002148HypophosphatemiaVery frequent (80-99%)
HP:0002900HypokalemiaVery frequent (80-99%)
HP:0003198MyopathyVery frequent (80-99%)
HP:0003355AminoaciduriaVery frequent (80-99%)
HP:0004322Short statureVery frequent (80-99%)
HP:0007957Corneal opacityVery frequent (80-99%)
HP:0009806Nephrogenic diabetes insipidusVery frequent (80-99%)
HP:0012378FatigueVery frequent (80-99%)
HP:0100651Type I diabetes mellitusVery frequent (80-99%)
HP:0000083Renal insufficiencyFrequent (30-79%)
HP:0000121NephrocalcinosisFrequent (30-79%)
HP:0000135HypogonadismFrequent (30-79%)
HP:0000488RetinopathyFrequent (30-79%)
HP:0000585Band keratopathyFrequent (30-79%)
HP:0000787NephrolithiasisFrequent (30-79%)
HP:0001510Growth delayFrequent (30-79%)
HP:0001744SplenomegalyFrequent (30-79%)
HP:0002240HepatomegalyFrequent (30-79%)
HP:0002748RicketsFrequent (30-79%)
HP:0002749OsteomalaciaFrequent (30-79%)
HP:0002901HypocalcemiaFrequent (30-79%)
HP:0003076GlycosuriaFrequent (30-79%)
HP:0003109HyperphosphaturiaFrequent (30-79%)
HP:0003155Elevated circulating alkaline phosphatase concentrationFrequent (30-79%)
HP:0003458EMG: myopathic abnormalitiesFrequent (30-79%)
HP:0011968Feeding difficultiesFrequent (30-79%)
HP:0012072AciduriaFrequent (30-79%)
HP:0001942Metabolic acidosisOccasional (5-29%)
HP:0000027AzoospermiaOccasional (5-29%)
HP:0000505Visual impairmentOccasional (5-29%)
HP:0001252HypotoniaOccasional (5-29%)
HP:0001256Intellectual disability, mildOccasional (5-29%)
HP:0001288Gait disturbanceOccasional (5-29%)
HP:0001409Portal hypertensionOccasional (5-29%)
HP:0001738Exocrine pancreatic insufficiencyOccasional (5-29%)
HP:0001945FeverOccasional (5-29%)
HP:0001952Glucose intoleranceOccasional (5-29%)
HP:0002019ConstipationOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical namecystinosis
Mondo IDMONDO:0016239
MeSHD003554
Orphanet213
DOIDDOID:1064
ICD-10-CME72.04
ICD-11733715856
NCITC2976
SNOMED CT190681003
UMLSC4316899
MedGen1384792
GARD0006236
MedDRA10011777
NORD1028
Is cancer (heuristic)no

Also known as: cystine diathesis · cystine disease · cystine storage disease · Cystinoses · cystinosis · Protein defect of cystin transport

Data availability: 159 ClinVar variants · 1 GenCC gene-disease record · 5 cell lines.

Disease family

An umbrella term covering 2 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseaseinborn errors of metabolismlysosomal storage disease › inborn disorder of lysosomal amino acid transport › cystinosis

Related subtypes (1): free sialic acid storage disease

Subtypes (2): ocular cystinosis, nephropathic cystinosis

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

159 retrieved; paginated sample, class counts are floors:

38 uncertain significance, 36 pathogenic, 25 pathogenic/likely pathogenic, 18 likely pathogenic, 17 likely benign, 12 conflicting classifications of pathogenicity, 8 benign, 4 benign/likely benign, 1 not provided

ClinVarVariant (HGVS)GeneClassificationReview
1020638NM_004937.3(CTNS):c.635C>T (p.Ala212Val)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1067346NM_004937.3(CTNS):c.839A>G (p.Lys280Arg)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1425663NM_004937.3(CTNS):c.699_700del (p.Ser234fs)CTNSPathogeniccriteria provided, multiple submitters, no conflicts
1451713NM_004937.3(CTNS):c.970+5G>ACTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1452938NM_004937.3(CTNS):c.1000del (p.Thr334fs)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1698582NM_004937.3(CTNS):c.565C>T (p.Gln189Ter)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1705665NM_004937.3(CTNS):c.751_752del (p.Thr251fs)CTNSPathogeniccriteria provided, multiple submitters, no conflicts
188714NM_004937.3(CTNS):c.926dup (p.Ser310fs)CTNSPathogeniccriteria provided, multiple submitters, no conflicts
188718NM_004937.3(CTNS):c.611ACG[1] (p.Asp205del)CTNSPathogeniccriteria provided, multiple submitters, no conflicts
188834NM_004937.3(CTNS):c.18_21del (p.Thr7fs)CTNSPathogeniccriteria provided, multiple submitters, no conflicts
188893NM_004937.3(CTNS):c.225+5_225+6delinsCCCTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
189020NM_004937.3(CTNS):c.809_811del (p.Ser270del)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
189067NM_004937.3(CTNS):c.561+1delCTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
21438NM_004937.3(CTNS):c.198_218del (p.Ile67_Pro73del)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
21439NM_004937.3(CTNS):c.473T>C (p.Leu158Pro)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
21440NM_004937.3(CTNS):c.613G>A (p.Asp205Asn)CTNSPathogeniccriteria provided, multiple submitters, no conflicts
21441NM_004937.3(CTNS):c.696dup (p.Val233fs)CTNSPathogeniccriteria provided, multiple submitters, no conflicts
21442NM_004937.3(CTNS):c.559_561+24delCTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2429208NM_004937.3(CTNS):c.1027_1038del (p.Ile343_Asp346del)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2501161NC_000017.10:g.(?_3539761)_3561464delCTNSPathogeniccriteria provided, single submitter
253205NM_004937.3(CTNS):c.323del (p.Gln108fs)CTNSPathogeniccriteria provided, multiple submitters, no conflicts
253206NM_004937.3(CTNS):c.257_258del (p.Ser86fs)CTNSPathogeniccriteria provided, single submitter
253207NM_004937.2:c.661insTCTNSPathogenicno assertion criteria provided
253208NM_004937.3(CTNS):c.91dup (p.Val31fs)CTNSPathogenicno assertion criteria provided
253209NM_004937.3(CTNS):c.120del (p.Asn41fs)CTNSPathogenicno assertion criteria provided
2577044NM_004937.3(CTNS):c.741del (p.Phe247fs)CTNSPathogeniccriteria provided, single submitter
267306NM_004937.3(CTNS):c.382C>T (p.Gln128Ter)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
267310NM_004937.3(CTNS):c.922G>A (p.Gly308Arg)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2681007NM_004937.3(CTNS):c.225+3A>TCTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2681026NM_004937.3(CTNS):c.955C>T (p.Gln319Ter)CTNSPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 10 · Orphanet: 3 · 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
CTNSDefinitiveAutosomal recessivenephropathic cystinosis10

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
CTNSOrphanet:411629Infantile nephropathic cystinosis
CTNSOrphanet:411634Juvenile nephropathic cystinosis
CTNSOrphanet:411641Ocular cystinosis

Cohort genes → proteins

3 cohort genes, 2 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence3

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
CTNSHGNC:2518ENSG00000040531O60931Cystinosingencc,clinvar
TAX1BP3HGNC:30684ENSG00000213977O14907Tax1-binding protein 3clinvar
CTNS-AS1HGNC:56090ENSG00000262903CTNS antisense RNA 1clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
CTNSCystinosinCystine/H(+) symporter that mediates export of cystine, the oxidized dimer of cysteine, from lysosomes.
TAX1BP3Tax1-binding protein 3May regulate a number of protein-protein interactions by competing for PDZ domain binding sites.

Protein-family classification

Druggable: 1 · Difficult: 1 · Unknown: 1 · 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
Transporter125.9×0.114
Scaffold/PPI15.8×0.246
Other/Unknown10.6×0.914

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
CTNSTransporteryesLC_transporter, PQ-loop_rpt
TAX1BP3Scaffold/PPIno3.5.1.2PDZ, Tax1-binding_p3, PDZ_sf
CTNS-AS1Other/Unknownno

Expression context

Cohort genes with no expression data: 0.

2 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
right adrenal gland cortex2
left adrenal gland cortex1
right adrenal gland1
apex of heart1
esophagus mucosa1
tibial nerve1
male germ line stem cell (sensu Vertebrata) in testis1
right uterine tube1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
CTNS251ubiquitousmarkerright adrenal gland cortex, left adrenal gland cortex, right adrenal gland
TAX1BP3134ubiquitousmarkertibial nerve, apex of heart, esophagus mucosa
CTNS-AS1131yesmale germ line stem cell (sensu Vertebrata) in testis, right uterine tube, right adrenal gland cortex

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
TAX1BP31,111
CTNS850
CTNS-AS10

Structural data

PDB: 2 · AlphaFold-only: 0 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
TAX1BP3O149079
CTNSO609316

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 3. Enrichment computed across 3 evidence-associated genes (2 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 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
SLC-mediated transport of oligopeptides15710.0×5e-04CTNS
RHO GTPases Activate Rhotekin and Rhophilins1634.4×0.002TAX1BP3
Miscellaneous transport and binding events1219.6×0.005CTNS

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
regulation of melanin biosynthetic process12808.7×0.006CTNS
L-cystine transport11404.3×0.006CTNS
regulation of TORC1 signaling1842.6×0.006CTNS
regulation of Cdc42 protein signal transduction1702.2×0.006TAX1BP3
melanin biosynthetic process1648.1×0.006CTNS
negative regulation of protein localization to cell surface1648.1×0.006TAX1BP3
grooming behavior1561.7×0.006CTNS
amino acid metabolic process1401.2×0.007CTNS
adult walking behavior1247.8×0.010CTNS
ATP metabolic process1234.1×0.010CTNS
long-term memory1210.7×0.010CTNS
lens development in camera-type eye1187.2×0.010CTNS
glutathione metabolic process1175.5×0.010CTNS
negative regulation of Wnt signaling pathway1172.0×0.010TAX1BP3
visual learning1153.2×0.010CTNS
positive regulation of TORC1 signaling1147.8×0.010CTNS
cognition1142.8×0.010CTNS
Rho protein signal transduction1123.9×0.011TAX1BP3
transmembrane transport184.3×0.015CTNS
monoatomic ion transport178.0×0.015CTNS
Wnt signaling pathway149.9×0.023TAX1BP3
brain development139.8×0.027CTNS
protein transport121.9×0.047CTNS
negative regulation of cell population proliferation121.1×0.047TAX1BP3

Therapeutics

Drugs indicated or in trials for this disease

No drug has an approved disease-direct ChEMBL indication for this disease.

1 drug in clinical trials for this disease (phase 2–3, investigational): efficacy not established — a trial record, not an indication.

DrugHighest phase
CysteaminePhase 3

Drug target analysis

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

Druggability breadth: 1 of 3 evidence-associated genes (33%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
CTNS00
TAX1BP300
CTNS-AS100

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
CTNS2Binding:2

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
TAX1BP33.5.1.2glutaminase

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

0 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.

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1CTNS
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2TAX1BP3, CTNS-AS1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
CTNS2
TAX1BP30
CTNS-AS10

Clinical trials & evidence

Clinical trials

Clinical trials: 38.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified23
PHASE35
PHASE1/PHASE25
PHASE22
PHASE41
PHASE11
EARLY_PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT01614431PHASE4COMPLETEDN Acetyl Cysteine for Cystinosis Patients
NCT01000961PHASE3COMPLETEDPhase 3 Study of Cysteamine Bitartrate Delayed-release (RP103) Compared to Cystagon® in Patients With Cystinosis
NCT01197378PHASE3COMPLETEDLong-Term Safety Follow-up Study of Cysteamine Bitartrate Delayed-release Capsules (RP103)
NCT01733316PHASE3COMPLETEDOpen-Label, Safety and Superior Effectiveness Study of Cysteamine Bitartrate Delayed-Release Capsules (RP103) in Cystinosis
NCT01744782PHASE3COMPLETEDSafety/Effectiveness Study of Cysteamine Bitartrate Delayed-release Capsules (RP103) in Cysteamine Treatment Naive Patients With Cystinosis
NCT04125927PHASE3COMPLETEDCystadrops in Pediatric Cystinosis Patients From Six Months to Less Than Two Years Old (SCOB2)
NCT05508009PHASE1/PHASE2RECRUITINGEarly Trial of Allogeneic Hematopoietic Stem Cell Transplantation for Patients Who Will Receive a Kidney Transplant From the Same Donor
NCT05994534PHASE1/PHASE2RECRUITINGPK and PD Study of NPI-001 and Cysteamine Bitartrate
NCT00001213PHASE2COMPLETEDCysteamine Eye Drops to Treat Corneal Crystals in Cystinosis
NCT00872729PHASE1/PHASE2COMPLETEDPilot Study of Safety, Tolerability, Pharmacokinetics/Pharmacodynamics of RP103 Compared to Cystagon® in Patients With Cystinosis
NCT02124070PHASE1/PHASE2WITHDRAWNTherapeutic Effect of Recombinant Human Growth Hormone (rhGH) on the Myopathy of Cystinosis
NCT03897361PHASE1/PHASE2COMPLETEDStem Cell Gene Therapy for Cystinosis
NCT04069260PHASE2TERMINATEDA Phase 2 Study of ELX-02 in Patients With Nephropathic Cystinosis
NCT00001736PHASE1COMPLETEDNew Cysteamine Eye Drops Formulation to Treat Corneal Crystals in Cystinosis
NCT02533076EARLY_PHASE1COMPLETEDThe Functional Consequences of the CTNS-deletion for the TRPV1-receptor in Cystinosis Patients
NCT00359684Not specifiedRECRUITINGUse of Cysteamine in the Treatment of Cystinosis
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT03655223Not specifiedENROLLING_BY_INVITATIONEarly Check: Expanded Screening in Newborns
NCT05146830Not specifiedENROLLING_BY_INVITATIONA Long-Term Follow-Up Study of Participants With Cystinosis Who Previously Received CTNS-RD-04
NCT05843851Not specifiedRECRUITINGGenetic Newborn Screening for Cystinosis and Primary Hyperoxaluria
NCT05901077Not specifiedRECRUITINGEuropean Cystinosis Cohort
NCT05959668Not specifiedRECRUITINGDevelopment of Health-related Quality of Life Instrument for Patients With Cystinosis
NCT06065852Not specifiedRECRUITINGNational Registry of Rare Kidney Diseases
NCT07319091Not specifiedNOT_YET_RECRUITINGCystinosis and Mitochondrial Metabolism
NCT00004312Not specifiedCOMPLETEDEstablishment of a Database for Long-Term Monitoring of Patients With Nephropathic Cystinosis
NCT00004350Not specifiedCOMPLETEDEvaluation of Fanconi Syndrome and Cystinosis
NCT00010426Not specifiedCOMPLETEDRandomized Study of New Formulation Ophthalmic Cysteamine Hydrochloride for Corneal Cystine Accumulation in Patients With Cystinosis
NCT00071903Not specifiedCOMPLETEDThe Role of Susceptibility to Thrombosis in the Pseudotumor Cerebri of Nephropathic Cystinosis: A Case-Control Study
NCT00074516Not specifiedCOMPLETEDKidney Transplantation in Patients With Cystinosis
NCT00100204Not specifiedCOMPLETEDSalivary Proteins in Disease and Health
NCT00822250Not specifiedCOMPLETEDClinical and Biological Study of Sub-pigmentation During Infantile Cystinosis
NCT01327807Not specifiedUNKNOWNCure Cystinosis International Registry
NCT01432561Not specifiedCOMPLETEDStudy in Healthy Adults to Determine the Effect That Food Has on the Absorption and Delivery of the Drug Cystagon™
NCT02012114Not specifiedCOMPLETEDA Cohort of Patients With Cystinosis : Compliance to Cysteamine and Neurological Complications
NCT04071548Not specifiedCOMPLETEDThe Effect of Exercise on Muscle Dysfunction in Cystinosis
NCT05545774Not specifiedCOMPLETEDNeuromuscular Characterisation in Late Adolescent and Adult Cystinosis Patients
NCT05687474Not specifiedCOMPLETEDBaby Detect : Genomic Newborn Screening
NCT06027385Not specifiedCOMPLETEDGenetic Newborn Screening for Cystinosis and Spinal Muscular Atrophy

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
CYSTEAMINE48
FLUDARABINE PHOSPHATE41
ELX-0221