Niemann-Pick disease

disease
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Also known as lipoid histiocytosis (classical phosphatide)Niemann-Pick disease with cholesterol esterification blockNiemann-Pick disease, subacute juvenile formsphingomyelin/cholesterol lipidosistype A Niemann-Pick disease

Summary

Niemann-Pick disease (MONDO:0001982) is a disease caused by SMPD1 (GenCC Definitive), with 4 cohort genes and 17 clinical trials. Top therapeutic interventions include olipudase alfa, busulfan, and cyclophosphamide anhydrous.

At a glance

  • Causal gene: SMPD1 (GenCC Definitive)
  • Cohort genes: 4
  • ClinVar variants: 130
  • Clinical trials: 17

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameNiemann-Pick disease
Mondo IDMONDO:0001982
EFOEFO:1001380
MeSHD009542
DOIDDOID:14504
ICD-10-CME75.24
ICD-11398872780
NCITC61269
SNOMED CT58459009
UMLSC0028064
MedGen10348
GARD0013334
Is cancer (heuristic)no

Also known as: lipoid histiocytosis (classical phosphatide) · Niemann-Pick disease with cholesterol esterification block · Niemann-Pick disease, subacute juvenile form · sphingomyelin/cholesterol lipidosis · type A Niemann-Pick disease

Data availability: 130 ClinVar variants · 1 GenCC gene-disease record · 10 cell lines.

Disease family

An umbrella term covering 4 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › immune system disorder › lymphoid system disorder › lymphatic system disorderhistiocytosisnon-Langerhans cell histiocytosisNiemann-Pick disease

Related subtypes (14): sinus histiocytosis with massive lymphadenopathy, hereditary progressive mucinous histiocytosis, sea-blue histiocyte syndrome, multicentric reticulohistiocytosis, generalized eruptive histiocytosis, benign cephalic histiocytosis, juvenile xanthogranuloma, xanthoma disseminatum, papular xanthoma, necrobiotic xanthogranuloma, indeterminate dendritic cell tumor, progressive nodular histiocytosis, Erdheim-Chester disease, xanthogranuloma

Subtypes (4): Niemann-Pick disease type C, Niemann-Pick disease type E, acid sphingomyelinase deficiency, chronic neurovisceral acid sphingomyelinase deficiency

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

130 retrieved; paginated sample, class counts are floors:

36 pathogenic/likely pathogenic, 27 conflicting classifications of pathogenicity, 26 pathogenic, 16 likely pathogenic, 16 uncertain significance, 4 benign/likely benign, 4 likely benign, 1 not provided

ClinVarVariant (HGVS)GeneClassificationReview
198093NM_000543.5(SMPD1):c.1826GCC[1] (p.Arg610del)APBB1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2980NM_000543.5(SMPD1):c.1493G>T (p.Arg498Leu)APBB1Pathogeniccriteria provided, multiple submitters, no conflicts
551367NM_000543.5(SMPD1):c.84del (p.Gly29fs)LOC130005193Pathogeniccriteria provided, multiple submitters, no conflicts
2967NM_000271.5(NPC1):c.3182T>C (p.Ile1061Thr)NPC1Pathogeniccriteria provided, multiple submitters, no conflicts
558706NM_000271.5(NPC1):c.3634G>T (p.Val1212Leu)NPC1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
986364NM_000271.5(NPC1):c.99_100del (p.Ala34fs)NPC1Pathogeniccriteria provided, multiple submitters, no conflicts
3383995NM_006432.5(NPC2):c.289del (p.Ile97fs)NPC2Pathogeniccriteria provided, single submitter
100731NM_000543.5(SMPD1):c.739G>A (p.Gly247Ser)SMPD1Pathogeniccriteria provided, multiple submitters, no conflicts
1173968NM_000543.5(SMPD1):c.668G>C (p.Cys223Ser)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1173972NM_000543.5(SMPD1):c.1148A>G (p.Asn383Ser)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1475471NM_000543.5(SMPD1):c.1497_1498inv (p.Tyr500His)SMPD1Pathogeniccriteria provided, multiple submitters, no conflicts
167709NM_000543.5(SMPD1):c.475T>C (p.Cys159Arg)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
167710NM_000543.5(SMPD1):c.573del (p.Ser192fs)SMPD1Pathogeniccriteria provided, multiple submitters, no conflicts
167712NM_000543.5(SMPD1):c.1493G>A (p.Arg498His)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
188955NM_000543.5(SMPD1):c.1805G>A (p.Arg602His)SMPD1Pathogeniccriteria provided, multiple submitters, no conflicts
189075NM_000543.5(SMPD1):c.1430C>T (p.Pro477Leu)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
189096NM_000543.5(SMPD1):c.538_539del (p.Leu180fs)SMPD1Pathogeniccriteria provided, multiple submitters, no conflicts
189153NM_000543.5(SMPD1):c.518dup (p.Ser174fs)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
195086NM_000543.5(SMPD1):c.785_807del (p.Leu262fs)SMPD1Pathogeniccriteria provided, multiple submitters, no conflicts
198095NM_000543.5(SMPD1):c.1492C>T (p.Arg498Cys)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
203424NM_000543.5(SMPD1):c.416T>C (p.Leu139Pro)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
203427NM_000543.5(SMPD1):c.1076C>A (p.Ala359Asp)SMPD1Pathogeniccriteria provided, single submitter
2136989NM_000543.5(SMPD1):c.1268A>G (p.His423Arg)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
225624NM_000543.5(SMPD1):c.1673T>C (p.Leu558Pro)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2982NM_000543.5(SMPD1):c.1735G>A (p.Gly579Ser)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2984NM_000543.5(SMPD1):c.788T>A (p.Leu263Ter)SMPD1Pathogeniccriteria provided, multiple submitters, no conflicts
2986NM_000543.5(SMPD1):c.1152G>A (p.Met384Ile)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2987NM_000543.5(SMPD1):c.730G>A (p.Gly244Arg)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2989NM_000543.5(SMPD1):c.911T>C (p.Leu304Pro)SMPD1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2990NM_000543.5(SMPD1):c.996del (p.Phe333fs)SMPD1Pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 9 · Orphanet: 12 · 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
SMPD1DefinitiveAutosomal recessiveNiemann-Pick disease9

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SMPD1Orphanet:77292Infantile neurovisceral acid sphingomyelinase deficiency
SMPD1Orphanet:77293Chronic visceral acid sphingomyelinase deficiency
NPC2Orphanet:216972Niemann-Pick disease type C, severe perinatal form
NPC2Orphanet:216975Niemann-Pick disease type C, severe early infantile neurologic onset
NPC2Orphanet:216978Niemann-Pick disease type C, late infantile neurologic onset
NPC2Orphanet:216981Niemann-Pick disease type C, juvenile neurologic onset
NPC2Orphanet:216986Niemann-Pick disease type C, adult neurologic onset
NPC1Orphanet:216972Niemann-Pick disease type C, severe perinatal form
NPC1Orphanet:216975Niemann-Pick disease type C, severe early infantile neurologic onset
NPC1Orphanet:216978Niemann-Pick disease type C, late infantile neurologic onset
NPC1Orphanet:216981Niemann-Pick disease type C, juvenile neurologic onset
NPC1Orphanet:216986Niemann-Pick disease type C, adult neurologic onset

Cohort genes → proteins

4 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence4

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SMPD1HGNC:11120ENSG00000166311P17405Sphingomyelin phosphodiesterasegencc,clinvar
NPC2HGNC:14537ENSG00000119655P61916NPC intracellular cholesterol transporter 2clinvar
APBB1HGNC:581ENSG00000166313O00213Amyloid beta precursor protein binding family B member 1clinvar
NPC1HGNC:7897ENSG00000141458O15118NPC intracellular cholesterol transporter 1clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SMPD1Sphingomyelin phosphodiesteraseConverts sphingomyelin to ceramide.
NPC2NPC intracellular cholesterol transporter 2Intracellular cholesterol transporter which acts in concert with NPC1 and plays an important role in the egress of cholesterol from the lysosomal compartment.
APBB1Amyloid beta precursor protein binding family B member 1Transcription coregulator that can have both coactivator and corepressor functions.
NPC1NPC intracellular cholesterol transporter 1Intracellular cholesterol transporter which acts in concert with NPC2 and plays an important role in the egress of cholesterol from the endosomal/lysosomal compartment.

Protein-family classification

Druggable: 1 · Difficult: 1 · Unknown: 2 · Druggable fraction: 0.25

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
Scaffold/PPI14.3×0.441
Enzyme (other)13.0×0.441
Other/Unknown20.9×0.769

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SMPD1Enzyme (other)yes3.1.4.12Calcineurin-like_PHP, SaposinB_dom, Saposin-like
NPC2Other/UnknownnoML_dom, Ig_E-set, ML_Npc2-like
APBB1Scaffold/PPInoWW_dom, PTB/PI_dom, PH-like_dom_sf
NPC1Other/UnknownnoSSD, NPC1-like, NPC1_N

Expression context

Cohort genes with no expression data: 0.

4 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)4
unknown0

Top tissues across cohort

TissueCohort genes
islet of Langerhans1
stromal cell of endometrium1
type B pancreatic cell1
cauda epididymis1
corpus epididymis1
epididymis1
cerebellar cortex1
cerebellar hemisphere1
right hemisphere of cerebellum1
adrenal tissue1
oocyte1
secondary oocyte1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SMPD1262ubiquitousmarkertype B pancreatic cell, stromal cell of endometrium, islet of Langerhans
NPC2296ubiquitousmarkercorpus epididymis, cauda epididymis, epididymis
APBB1242ubiquitousmarkerright hemisphere of cerebellum, cerebellar hemisphere, cerebellar cortex
NPC1292ubiquitousmarkersecondary oocyte, oocyte, adrenal tissue

Protein interactions among cohort

Intra-cohort edges: 2.

Hub genes (top 10 by interactor count)

SymbolInteractor count
APBB12,826
NPC12,648
SMPD11,729
NPC21,706

Intra-cohort edges

ABSources
NPC1NPC2intact, string_interaction
NPC2SMPD1string_interaction

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
NPC1O1511820
APBB1O0021311
SMPD1P174054
NPC2P619162

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 12. Enrichment computed across 4 evidence-associated genes (4 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 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
LDL clearance2271.9×2e-04NPC2, NPC1
DNA Double Strand Break Response1119.0×0.034APBB1
Glycosphingolipid metabolism175.1×0.034SMPD1
Glycosphingolipid catabolism173.2×0.034SMPD1
DNA Double-Strand Break Repair162.1×0.034APBB1
Regulation of clotting cascade158.3×0.034SMPD1
Sphingolipid metabolism142.0×0.040SMPD1
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks136.6×0.041APBB1
DNA Repair124.6×0.053APBB1
Metabolism of lipids17.9×0.145SMPD1
Neutrophil degranulation15.8×0.177NPC2
Metabolism12.9×0.302SMPD1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
cholesterol storage21203.7×3e-05NPC2, NPC1
cholesterol metabolic process3147.0×3e-05SMPD1, NPC2, NPC1
intracellular cholesterol transport2648.1×7e-05NPC2, NPC1
cholesterol transport2366.4×2e-04NPC2, NPC1
cholesterol efflux2263.3×3e-04NPC2, NPC1
symbiont entry into host cell2200.6×4e-04SMPD1, NPC1
regulation of isoprenoid metabolic process14213.0×0.002NPC2
cyclodextrin metabolic process14213.0×0.002NPC1
cholesterol homeostasis278.0×0.002NPC2, NPC1
response to virus272.0×0.002SMPD1, NPC2
termination of signal transduction11404.3×0.004SMPD1
intracellular lipid transport11404.3×0.004NPC1
glycolipid transport11404.3×0.004NPC2
sphingomyelin metabolic process1842.6×0.004SMPD1
sphingomyelin catabolic process1842.6×0.004SMPD1
membrane raft organization1842.6×0.004NPC1
intracellular sterol transport1842.6×0.004NPC2
gene expression239.9×0.004NPC2, NPC1
response to xenobiotic stimulus234.5×0.004SMPD1, NPC1
sterol transport1702.2×0.005NPC1
negative regulation of cell cycle G1/S phase transition1601.9×0.005APBB1
positive regulation of apoptotic process228.4×0.006SMPD1, APBB1
response to type I interferon1468.1×0.006SMPD1
establishment of protein localization to membrane1468.1×0.006NPC1
glycosphingolipid catabolic process1383.0×0.007SMPD1
intestinal cholesterol absorption1351.1×0.007NPC1
programmed cell death1324.1×0.008NPC1
positive regulation of viral entry into host cell1300.9×0.008SMPD1
negative regulation of epithelial cell apoptotic process1300.9×0.008NPC1
negative regulation of macroautophagy1280.9×0.008NPC1

Therapeutics

Drugs indicated for this disease

2 approved. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
MiglustatApproved (phase 4)
Olipudase AlfaApproved (phase 4)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Busulfan.

Drug target analysis

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

Druggability breadth: 2 of 4 evidence-associated genes (50%) 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
SMPD1IMIPRAMINE
NPC1NABUMETONE

Top cohort targets by molecule count

SymbolMoleculesMax phase
NPC1904
SMPD134
NPC200
APBB100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
IMIPRAMINE4SMPD1
CHLORPROMAZINE4SMPD1
NABUMETONE4NPC1
PHENELZINE4NPC1
AMLEXANOX4NPC1
IDARUBICIN4NPC1
RABEPRAZOLE SODIUM4NPC1
NITAZOXANIDE4NPC1
NICLOSAMIDE4NPC1
NITROXOLINE4NPC1
NICARDIPINE4NPC1
DAUNORUBICIN HYDROCHLORIDE4NPC1
INDOPROFEN4NPC1
CYCLOSPORINE4NPC1
TERFENADINE4NPC1
DIGOXIN4NPC1
PRAZOSIN4NPC1
MAPROTILINE4NPC1
DIGITOXIN4NPC1
HYDRALAZINE4NPC1
EBASTINE4NPC1
DEQUALINIUM4NPC1
DOXORUBICIN HYDROCHLORIDE4NPC1
VINBLASTINE SULFATE4NPC1
FLUOXETINE4NPC1
DITHIAZANINE IODIDE4NPC1
TRIFLUOPERAZINE4NPC1
PACLITAXEL4NPC1
NORTRIPTYLINE4NPC1
MIBEFRADIL4NPC1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
SMPD142Binding:40, Functional:2
NPC118Binding:13, Functional:5

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
SMPD13.1.4.12sphingomyelin phosphodiesterase

Pharmacogenomics

Cohort genes with a PharmGKB record: 4; 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)
IMIPRAMINE4SMPD1
CHLORPROMAZINE4SMPD1
NABUMETONE4NPC1
PHENELZINE4NPC1
AMLEXANOX4NPC1
IDARUBICIN4NPC1
RABEPRAZOLE SODIUM4NPC1
NITAZOXANIDE4NPC1
NICLOSAMIDE4NPC1
NITROXOLINE4NPC1
NICARDIPINE4NPC1
DAUNORUBICIN HYDROCHLORIDE4NPC1
INDOPROFEN4NPC1
CYCLOSPORINE4NPC1
TERFENADINE4NPC1
DIGOXIN4NPC1
PRAZOSIN4NPC1
MAPROTILINE4NPC1
DIGITOXIN4NPC1
HYDRALAZINE4NPC1
EBASTINE4NPC1
DEQUALINIUM4NPC1
DOXORUBICIN HYDROCHLORIDE4NPC1
VINBLASTINE SULFATE4NPC1
FLUOXETINE4NPC1
DITHIAZANINE IODIDE4NPC1
TRIFLUOPERAZINE4NPC1
PACLITAXEL4NPC1
NORTRIPTYLINE4NPC1
MIBEFRADIL4NPC1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)2SMPD1, NPC1
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2NPC2, APBB1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
NPC20NPC1
APBB10

Clinical trials & evidence

Clinical trials

Clinical trials: 17.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified11
PHASE13
PHASE1/PHASE22
PHASE2/PHASE31

Top trials by phase / activity

NCTPhaseStatusTitle
NCT00176904PHASE2/PHASE3COMPLETEDStem Cell Transplant for Inborn Errors of Metabolism
NCT00730314PHASE1/PHASE2COMPLETEDUnrelated Hematopoietic Stem Cell Transplantation(HSCT) for Genetic Diseases of Blood Cells
NCT01372228PHASE1/PHASE2TERMINATEDPhase I/II Pilot Study of Mixed Chimerism to Treat Inherited Metabolic Disorders
NCT00316498PHASE1COMPLETEDSaccadic Eye Movements in Patients With Niemann-Pick Type C Disease
NCT00410566PHASE1TERMINATEDSafety Study of rhASM Enzyme Replacement Therapy in Adults With Acid Sphingomyelinase Deficiency (Niemann-Pick Disease)
NCT01586455PHASE1COMPLETEDHuman Placental-Derived Stem Cell Transplantation
NCT03333200Not specifiedRECRUITINGLongitudinal Study of Neurodegenerative Disorders
NCT06192576Not specifiedRECRUITINGA Real-world Long-term Safety and Immunogenicity Study of Olipudase Alfa Therapy in Pediatric Patients Less Than 2 Years of Age With Acid Sphingomyelinase Deficiency (ASMD)
NCT06985212Not specifiedNOT_YET_RECRUITINGNational Multicentre Study of the Natural History of Acid Sphingo-myelinase Deficiency in Adults and Children
NCT07545473Not specifiedRECRUITINGRetinal Hyperspectral Imaging in Neurodegenerative Diseases
NCT00001972Not specifiedCOMPLETEDPET Scan of Brain Metabolism in Relation to Age and Disease
NCT00005900Not specifiedUNKNOWNStudy of Pulmonary Complications in Pediatric Patients With Storage Disorders Undergoing Allogeneic Hematopoietic Stem Cell Transplantation
NCT01306604Not specifiedWITHDRAWNBiomarker for Niemann Pick Type C Disease (BioNPC)
NCT02120235Not specifiedUNKNOWNInvestigating Lysosomal Storage Diseases in Minority Groups
NCT03883750Not specifiedCOMPLETEDInduced Pluripotent Stem Cells for Niemann Pick Disease
NCT04469894Not specifiedCOMPLETEDHealth Insurance Literacy and Challenges in Accessing Health Services in Niemann-Pick
NCT05641103Not specifiedCOMPLETEDPREDIGA 2: Spanish Acronym of Educational and Diagnostic Project for Gaucher and ASMD

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
OLIPUDASE ALFA42
BUSULFAN41
CYCLOPHOSPHAMIDE ANHYDROUS41