IEMbase 0307: CLN3-related lysosomal transmembrane protein deficiency
Scope
| Field | Value |
|---|---|
| IEMbase ID | 307 |
| Nosology | 20.4.02.01 |
| Gene | CLN3 |
| External IDs | OMIM:204200; ORPHA:228346 |
| Generated mapping | MAPPED; Neuronal_Ceroid_Lipofuscinosis_3.yaml |
| Candidate DisMech targets | Neuronal_Ceroid_Lipofuscinosis_3.yaml |
| Review date | 2026-07-07 |
IEMbase phenotype signal
IEMbase represents CLN3 disease as juvenile NCL/Batten disease with cerebral atrophy, electron-microscopy storage material, movement disorder, pigmentary retinopathy, retinal dystrophy, seizures, vacuolated lymphocytes, and vision loss or optic atrophy. Additional rows include anxiety, aggressive behavior, behavioral disorder, cardiac arrhythmia, cardiomyopathy, cerebellar atrophy, cerebellar white matter abnormalities, cognitive dysfunction, depression, developmental regression, dysarthria, abnormal EEG, abnormal ERG, extrapyramidal movement disorder, gait disturbance, hallucinations, hypokinesia, muscular atrophy, neurodegenerative disease, optic atrophy, psychiatric disturbances, rigidity, sea-blue histiocytes, complex partial and tonic-clonic seizures, abnormal somatosensory evoked potentials, spinal muscular atrophy, and abnormal VEP.
No biochemical or treatment rows are present in the cached IEMbase record.
DisMech phenotype coverage
Neuronal_Ceroid_Lipofuscinosis_3.yaml is the correct local target. It models
CLN3 biallelic pathogenic variants, CLN3 endolysosomal membrane dysfunction,
lysosomal cholesterol storage, progressive retinal degeneration, and
progressive neurobehavioral decline. Phenotype coverage includes visual
impairment, retinal degeneration, cognitive impairment, atypical behavior,
sleep disturbance, motor deterioration, and seizure.
The local file also represents supportive care and experimental AAV9-CLN3 gene therapy, even though the cached IEMbase record does not list treatments.
Concordance and completeness
Judgement: correct high-confidence mapping to
Neuronal_Ceroid_Lipofuscinosis_3.yaml.
Concordance is strong for CLN3 disease identity, juvenile NCL scope, early retinal/visual disease, cognitive and behavioral decline, seizures, motor deterioration, lysosomal storage inclusions, and endolysosomal mechanism. DisMech is richer for mechanism and treatment-development context.
IEMbase is much more granular for movement-disorder subphenotypes, psychiatric features, imaging/electrophysiology rows, vacuolated lymphocytes, sea-blue histiocytes, optic atrophy, pigmentary retinopathy, and possible cardiac arrhythmia/cardiomyopathy. The cardiac and spinal muscular atrophy rows should be evidence-reviewed before import.
Curation actions
- Keep the generated NCL3 mapping.
- Review vacuolated lymphocytes and electron-microscopy storage material as diagnostic/pathology readouts.
- Consider phenotype expansion for psychiatric symptoms, extrapyramidal signs, gait disturbance, rigidity/hypokinesia, EEG/ERG/VEP, and optic atrophy.
- Treat cardiac arrhythmia, cardiomyopathy, sea-blue histiocytes, and spinal muscular atrophy as higher-caution prompts.