Pantothenate kinase-associated neurodegeneration

disease
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Also known as brain iron accumulation type I syndromeHallervorden-Spatz diseaseHallervorden-Spatz syndromeNBIA1neuroaxonal dystrophy, late infantileneurodegeneration with brain iron accumulation 1neurodegeneration with brain iron accumulation type 1pigmentary pallidal degenerationPKAN

Summary

Pantothenate kinase-associated neurodegeneration (MONDO:0009319) is a disease caused by PANK2 (GenCC Definitive), with 5 cohort genes and 8 clinical trials. Top therapeutic interventions include deferiprone and fosmetpantotenate.

At a glance

  • Prevalence: 1-9 / 1 000 000 (Europe) [Orphanet-validated]
  • Causal gene: PANK2 (GenCC Definitive)
  • Cohort genes: 5
  • ClinVar variants: 658
  • Phenotypes (HPO): 60
  • Clinical trials: 8

Clinical features

Epidemiology

Prevalence records

1 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Point prevalence1-9 / 1 000 0000.15EuropeValidated

Signs & symptoms

Clinical features (HPO)

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

HPO IDTermFrequency
HP:0000505Visual impairmentVery frequent (80-99%)
HP:0000546Retinal degenerationVery frequent (80-99%)
HP:0001257SpasticityVery frequent (80-99%)
HP:0001266ChoreoathetosisVery frequent (80-99%)
HP:0001288Gait disturbanceVery frequent (80-99%)
HP:0001332DystoniaVery frequent (80-99%)
HP:0002071Abnormality of extrapyramidal motor functionVery frequent (80-99%)
HP:0002505Loss of ambulationVery frequent (80-99%)
HP:0000496Abnormality of eye movementFrequent (30-79%)
HP:0000510Rod-cone dystrophyFrequent (30-79%)
HP:0000580Pigmentary retinopathyFrequent (30-79%)
HP:0000662NyctalopiaFrequent (30-79%)
HP:0000708Atypical behaviorFrequent (30-79%)
HP:0000938OsteopeniaFrequent (30-79%)
HP:0001260DysarthriaFrequent (30-79%)
HP:0001268Mental deteriorationFrequent (30-79%)
HP:0001300ParkinsonismFrequent (30-79%)
HP:0001927AcanthocytosisFrequent (30-79%)
HP:0002063RigidityFrequent (30-79%)
HP:0002451Limb dystoniaFrequent (30-79%)
HP:0002454Eye of the tiger anomaly of globus pallidusFrequent (30-79%)
HP:0002483Bulbar signsFrequent (30-79%)
HP:0007994Peripheral visual field lossFrequent (30-79%)
HP:0008181AbetalipoproteinemiaFrequent (30-79%)
HP:0009763Limb painFrequent (30-79%)
HP:0012045Retinal flecksFrequent (30-79%)
HP:0012179Craniofacial dystoniaFrequent (30-79%)
HP:0012678Iron accumulation in substantia nigraFrequent (30-79%)
HP:0031959Leg dystoniaFrequent (30-79%)
HP:0000712Emotional labilityOccasional (5-29%)
HP:0000716DepressionOccasional (5-29%)
HP:0000722Compulsive behaviorsOccasional (5-29%)
HP:0000726DementiaOccasional (5-29%)
HP:0001123Visual field defectOccasional (5-29%)
HP:0001152Saccadic smooth pursuitOccasional (5-29%)
HP:0001249Intellectual disabilityOccasional (5-29%)
HP:0001263Global developmental delayOccasional (5-29%)
HP:0001270Motor delayOccasional (5-29%)
HP:0001347HyperreflexiaOccasional (5-29%)
HP:0001350Slurred speechOccasional (5-29%)
HP:0002167Abnormality of speech or vocalizationOccasional (5-29%)
HP:0003084Fractures of the long bonesOccasional (5-29%)
HP:0007018Attention deficit hyperactivity disorderOccasional (5-29%)
HP:0007132Pallidal degenerationOccasional (5-29%)
HP:0009088Speech articulation difficultiesOccasional (5-29%)
HP:0011504Bull’s eye maculopathyOccasional (5-29%)
HP:0011916Toe extensor amyotrophyOccasional (5-29%)
HP:0025402Square-wave jerksOccasional (5-29%)
HP:0030051Tip-toe gaitOccasional (5-29%)
HP:0031814PalilaliaOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical namepantothenate kinase-associated neurodegeneration
Mondo IDMONDO:0009319
MeSHD006211
OMIM234200
Orphanet157850
DOIDDOID:3981
ICD-10-CMG23.0
NCITC84988
SNOMED CT2992000
UMLSC0018523
MedGen6708
GARD0006564
NORD1550
Is cancer (heuristic)no

Also known as: brain iron accumulation type I syndrome · Hallervorden-Spatz disease · Hallervorden-Spatz syndrome · NBIA1 · neuroaxonal dystrophy, late infantile · neurodegeneration with brain iron accumulation 1 · neurodegeneration with brain iron accumulation type 1 · pantothenate kinase-associated neurodegeneration · pigmentary pallidal degeneration · PKAN

Data availability: 658 ClinVar variants · 3 GenCC gene-disease records · 7 cell lines.

Disease family

An umbrella term covering 2 Mondo subtypes.

Classification path: disease › human disease › disease by developmental or physiological process › metabolic diseasemineral metabolism diseaseiron metabolism diseaseneurodegeneration with brain iron accumulationpantothenate kinase-associated neurodegeneration

Related subtypes (13): Woodhouse-Sakati syndrome, neurodegeneration with brain iron accumulation 5, aceruloplasminemia, neuroferritinopathy, Kufor-Rakeb syndrome, neurodegeneration with brain iron accumulation 4, neurodegeneration with brain iron accumulation 6, PLA2G6-associated neurodegeneration, fatty acid hydroxylase-associated neurodegeneration, early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome, neurodegeneration with brain iron accumulation 7, neurodegeneration with brain iron accumulation 8, neurodegeneration with brain iron accumulation 9

Subtypes (2): classic pantothenate kinase-associated neurodegeneration, atypical pantothenate kinase-associated neurodegeneration

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

600 retrieved; paginated sample, class counts are floors:

287 likely benign, 146 uncertain significance, 71 pathogenic, 31 likely pathogenic, 29 conflicting classifications of pathogenicity, 18 pathogenic/likely pathogenic, 12 benign/likely benign, 6 benign

ClinVarVariant (HGVS)GeneClassificationReview
526631NC_000020.11:g.(?3889081)(3912654_?)delLOC125384566Pathogeniccriteria provided, single submitter
1878518NM_001386393.1(PANK2):c.215_216insA (p.Arg73fs)LOC130065345Pathogeniccriteria provided, multiple submitters, no conflicts
2634258NM_001386393.1(PANK2):c.104C>A (p.Ser35Ter)LOC130065345Pathogeniccriteria provided, multiple submitters, no conflicts
2736936NM_001386393.1(PANK2):c.185_197del (p.Val62fs)LOC130065345Pathogeniccriteria provided, single submitter
2784668NM_001386393.1(PANK2):c.225del (p.Arg76fs)LOC130065345Pathogeniccriteria provided, single submitter
2844377NM_001386393.1(PANK2):c.189_201del (p.Ala64fs)LOC130065345Pathogeniccriteria provided, single submitter
284671NM_001386393.1(PANK2):c.-21G>TLOC130065345Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2852428NM_001386393.1(PANK2):c.262del (p.Arg88fs)LOC130065345Pathogeniccriteria provided, single submitter
3384757NM_001386393.1(PANK2):c.84_100dup (p.Val34fs)LOC130065345Pathogeniccriteria provided, single submitter
4549NM_001386393.1(PANK2):c.240C>G (p.Tyr80Ter)LOC130065345Pathogeniccriteria provided, multiple submitters, no conflicts
4561NM_001386393.1(PANK2):c.203C>A (p.Ser68Ter)LOC130065345Pathogeniccriteria provided, single submitter
3248221NC_000020.10:g.(?3869748)(3903941_?)delMIR103A2Pathogeniccriteria provided, single submitter
4556NM_001386393.1(PANK2):c.1253C>T (p.Thr418Met)MIR103A2Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1030294NM_001386393.1(PANK2):c.905+1G>CPANK2Pathogeniccriteria provided, multiple submitters, no conflicts
1068023NM_001386393.1(PANK2):c.353T>C (p.Phe118Ser)PANK2Pathogeniccriteria provided, single submitter
1321409NM_001386393.1(PANK2):c.1277A>G (p.Tyr426Cys)PANK2Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1323413NM_001386393.1(PANK2):c.682G>T (p.Glu228Ter)PANK2Pathogeniccriteria provided, multiple submitters, no conflicts
1363985NM_001386393.1(PANK2):c.1086del (p.Phe362fs)PANK2Pathogeniccriteria provided, single submitter
1416528NM_001386393.1(PANK2):c.944T>C (p.Leu315Pro)PANK2Pathogeniccriteria provided, single submitter
1419098NM_001386393.1(PANK2):c.906-99_929delPANK2Pathogeniccriteria provided, single submitter
1439787NM_001386393.1(PANK2):c.317dup (p.Asp107fs)PANK2Pathogeniccriteria provided, single submitter
1452444NM_001386393.1(PANK2):c.440_441insCT (p.Tyr148fs)PANK2Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1458749NM_001386393.1(PANK2):c.652-1G>CPANK2Pathogeniccriteria provided, single submitter
1696025NM_001386393.1(PANK2):c.664C>T (p.Gln222Ter)PANK2Pathogeniccriteria provided, multiple submitters, no conflicts
1933981NM_001386393.1(PANK2):c.1370T>A (p.Leu457Ter)PANK2Pathogeniccriteria provided, single submitter
2138325NM_001386393.1(PANK2):c.885C>G (p.Tyr295Ter)PANK2Pathogeniccriteria provided, single submitter
2138326NM_001386393.1(PANK2):c.1094T>C (p.Met365Thr)PANK2Pathogeniccriteria provided, single submitter
2427434NC_000020.10:g.(?3888553)(3888945_?)delPANK2Pathogeniccriteria provided, single submitter
2427435NC_000020.10:g.(?3869748)(3891497_?)delPANK2Pathogeniccriteria provided, single submitter
2427436NC_000020.10:g.(?3891204)(3893301_?)delPANK2Pathogeniccriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 3 · Orphanet: 2 · 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
PANK2DefinitiveAutosomal recessivepantothenate kinase-associated neurodegeneration3

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
PANK2Orphanet:216866Classic pantothenate kinase-associated neurodegeneration
PANK2Orphanet:216873Atypical pantothenate kinase-associated neurodegeneration

Cohort genes → proteins

5 cohort genes, 3 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
PANK2HGNC:15894ENSG00000125779Q9BZ23Pantothenate kinase 2, mitochondrialgencc,clinvar
AP5S1HGNC:15875ENSG00000125843Q9NUS5AP-5 complex subunit sigma-1clinvar
MAVSHGNC:29233ENSG00000088888Q7Z434Mitochondrial antiviral-signaling proteinclinvar
MIR103A2HGNC:31491ENSG00000199024microRNA 103a-2clinvar
PANK2-AS1HGNC:40732ENSG00000229539PANK2 antisense RNA 1clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
PANK2Pantothenate kinase 2, mitochondrialMitochondrial isoform that catalyzes the phosphorylation of pantothenate to generate 4’-phosphopantothenate in the first and rate-determining step of coenzyme A (CoA) synthesis.
AP5S1AP-5 complex subunit sigma-1As part of AP-5, a probable fifth adaptor protein complex it may be involved in endosomal transport.
MAVSMitochondrial antiviral-signaling proteinAdapter required for innate immune defense against viruses.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 4 · Druggable fraction: 0.2

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
Enzyme (other)12.4×0.353
Other/Unknown41.4×0.353

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
PANK2Enzyme (other)yes2.7.1.33Type_II_PanK, ATPase_NBD
AP5S1Other/UnknownnoAP-5_subunit_s1
MAVSOther/UnknownnoDEATH-like_dom_sf, CARD_dom, CARD_IPS1
MIR103A2Other/Unknownno
PANK2-AS1Other/Unknownno

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)5
unknown0

Top tissues across cohort

TissueCohort genes
primordial germ cell in gonad3
monocyte2
buccal mucosa cell2
endothelial cell1
stromal cell of endometrium1
biceps brachii1
skeletal muscle tissue of biceps brachii1
colonic mucosa1
heart right ventricle1
skeletal muscle tissue of rectus abdominis1
male germ line stem cell (sensu Vertebrata) in testis1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
PANK2282ubiquitousmarkerendothelial cell, stromal cell of endometrium, monocyte
AP5S1226ubiquitousmarkerprimordial germ cell in gonad, biceps brachii, skeletal muscle tissue of biceps brachii
MAVS277ubiquitousmarkerskeletal muscle tissue of rectus abdominis, heart right ventricle, colonic mucosa
MIR103A2149markerprimordial germ cell in gonad, buccal mucosa cell, monocyte
PANK2-AS1173yesbuccal mucosa cell, male germ line stem cell (sensu Vertebrata) in testis, primordial germ cell in gonad

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
MAVS3,769
PANK21,312
AP5S1527
MIR103A20
PANK2-AS10

Structural data

PDB: 3 · AlphaFold-only: 0 · No structure: 2

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
MAVSQ7Z43411
AP5S1Q9NUS52
PANK2Q9BZ231

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 31. Enrichment computed across 5 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
Coenzyme A biosynthesis1713.8×0.022PANK2
NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -101439.2×0.022MAVS
TRAF3-dependent IRF activation pathway1380.7×0.022MAVS
TRAF6 mediated NF-kB activation1228.4×0.022MAVS
TRAF6 mediated IRF7 activation1190.3×0.022MAVS
Dengue virus activates/modulates innate and adaptive immune responses1167.9×0.022MAVS
Negative regulators of DDX58/IFIH1 signaling1163.1×0.022MAVS
Evasion by RSV of host interferon responses1163.1×0.022MAVS
Ovarian tumor domain proteases1139.3×0.022MAVS
SARS-CoV-1 activates/modulates innate immune responses1135.9×0.022MAVS
DDX58/IFIH1-mediated induction of interferon-alpha/beta1126.9×0.022MAVS
Antimicrobial mechanism of IFN-stimulated genes198.5×0.024MAVS
Respiratory Syncytial Virus Infection Pathway198.5×0.024MAVS
SARS-CoV-1-host interactions187.8×0.025MAVS
RSV-host interactions178.2×0.026MAVS
SARS-CoV-1 Infection171.4×0.026MAVS
PKR-mediated signaling170.5×0.026MAVS
Deubiquitination162.1×0.026MAVS
Interferon Signaling160.1×0.026MAVS
SARS-CoV-2-host interactions159.5×0.026MAVS
SARS-CoV-2 activates/modulates innate and adaptive immune responses144.6×0.033MAVS
SARS-CoV-2 Infection140.2×0.035MAVS
SARS-CoV Infections127.7×0.048MAVS
Cytokine Signaling in Immune system120.4×0.063MAVS
Viral Infection Pathways115.4×0.079MAVS
Innate Immune System112.8×0.091MAVS
Infectious disease112.4×0.091MAVS
Post-translational protein modification19.6×0.112MAVS
Disease16.5×0.153MAVS
Immune System16.5×0.153MAVS

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
positive regulation of IP-10 production15617.3×0.008MAVS
regulation of peroxisome organization11872.4×0.008MAVS
obsolete regulation of bile acid metabolic process11872.4×0.008PANK2
positive regulation of myeloid dendritic cell cytokine production1936.2×0.008MAVS
positive regulation of chemokine (C-C motif) ligand 5 production1936.2×0.008MAVS
positive regulation of response to cytokine stimulus1802.5×0.008MAVS
pantothenate metabolic process1702.2×0.008PANK2
regulation of triglyceride metabolic process1702.2×0.008PANK2
regulation of fatty acid metabolic process1624.1×0.008PANK2
coenzyme A biosynthetic process1510.7×0.009PANK2
protein localization to mitochondrion1432.1×0.009MAVS
cellular response to exogenous dsRNA1351.1×0.011MAVS
cytoplasmic pattern recognition receptor signaling pathway1295.6×0.011MAVS
positive regulation of type I interferon-mediated signaling pathway1280.9×0.011MAVS
positive regulation of interferon-alpha production1216.1×0.013MAVS
protein tetramerization1208.1×0.013MAVS
positive regulation of NLRP3 inflammasome complex assembly1193.7×0.013MAVS
regulation of mitochondrial membrane potential1181.2×0.013PANK2
positive regulation of defense response to virus by host1175.5×0.013MAVS
cellular response to interferon-beta1175.5×0.013MAVS
activation of innate immune response1160.5×0.013MAVS
positive regulation of type I interferon production1140.4×0.014MAVS
positive regulation of protein import into nucleus1140.4×0.014MAVS
positive regulation of interferon-beta production1130.6×0.014MAVS
negative regulation of viral genome replication1124.8×0.014MAVS
type I interferon-mediated signaling pathway1114.6×0.015MAVS
aerobic respiration182.6×0.019PANK2
endosomal transport181.4×0.019AP5S1
positive regulation of interleukin-8 production181.4×0.019MAVS
antiviral innate immune response175.9×0.020MAVS

Therapeutics

Drugs indicated for this disease

0 approved, 2 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
DeferipronePhase 3 (in late-stage trials)
FosmetpantotenatePhase 3 (in late-stage trials)

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 5

Druggability breadth: 2 of 5 evidence-associated genes (40%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
PANK200
AP5S100
MAVS00
MIR103A200
PANK2-AS100

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
MAVS3Binding:3
PANK21Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PANK22.7.1.33pantothenate kinase

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

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 drug1PANK2
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug4AP5S1, MAVS, MIR103A2, PANK2-AS1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
PANK21
AP5S10
MAVS3
MIR103A20
PANK2-AS10

Clinical trials & evidence

Clinical trials

Clinical trials: 8.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified5
PHASE33

Top trials by phase / activity

NCTPhaseStatusTitle
NCT01741532PHASE3COMPLETEDEfficacy and Safety Study of Deferiprone in Patients With Pantothenate Kinase-associated Neurodegeneration (PKAN)
NCT02174848PHASE3COMPLETEDLong-term Deferiprone Treatment in Patients With Pantothenate Kinase-Associated Neurodegeneration
NCT03041116PHASE3TERMINATEDEfficacy and Safety Study of Fosmetpantotenate (RE-024) in PKAN Participants
NCT03333200Not specifiedRECRUITINGLongitudinal Study of Neurodegenerative Disorders
NCT05522374Not specifiedRECRUITINGTIRCON International NBIA Registry
NCT01838018Not specifiedCOMPLETEDBrain Perfusion in Pantothenate Kinase-associated Neurodegeneration (PKAN)
NCT02635841Not specifiedNO_LONGER_AVAILABLECompassionate Use of Deferiprone in Patients With PKAN
NCT04182763Not specifiedCOMPLETEDCoA-Z in Pantothenate Kinase-associated Neurodegeneration (PKAN)

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
DEFERIPRONE43
FOSMETPANTOTENATE31