Hereditary pulmonary alveolar proteinosis

disease
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Also known as congenital PAPcongenital pulmonary alveolar proteinosisinborn error of pulmonary surfactant metabolisminborn error of surfactant metabolismpulmonary alveolar proteinosis, congenital

Summary

Hereditary pulmonary alveolar proteinosis (MONDO:0012580) is a disease (an umbrella term covering 8 Mondo subtypes) with 6 cohort genes and 2 clinical trials. The dominant Reactome pathway is Defective CSF2RB causes SMDP5 (4 cohort genes). Top therapeutic interventions include sargramostim.

At a glance

  • Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
  • Umbrella term: 8 Mondo subtypes
  • Cohort genes: 6
  • ClinVar variants: 781
  • Phenotypes (HPO): 15
  • Clinical trials: 2

Clinical features

Epidemiology

Prevalence records

1 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Point prevalence<1 / 1 000 000WorldwideValidated

Signs & symptoms

Clinical features (HPO)

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

HPO IDTermFrequency
HP:0010876Abnormal circulating protein levelVery frequent (80-99%)
HP:0001531Failure to thrive in infancyFrequent (30-79%)
HP:0002091Restrictive ventilatory defectFrequent (30-79%)
HP:0002098Respiratory distressFrequent (30-79%)
HP:0004887Respiratory failure requiring assisted ventilationFrequent (30-79%)
HP:0012418HypoxemiaFrequent (30-79%)
HP:0025391Crazy paving pattern on pulmonary HRCTFrequent (30-79%)
HP:0001649TachycardiaOccasional (5-29%)
HP:0002789TachypneaOccasional (5-29%)
HP:0003651Foam cellsOccasional (5-29%)
HP:0011949Acute infectious pneumoniaOccasional (5-29%)
HP:0012735CoughOccasional (5-29%)
HP:0030057Autoimmune antibody positivityOccasional (5-29%)
HP:0030830CracklesOccasional (5-29%)
HP:0031029Elevated carcinoembryonic antigen levelOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical namehereditary pulmonary alveolar proteinosis
Mondo IDMONDO:0012580
MeSHC535832
OMIM265120
Orphanet264675
SNOMED CT707442002
UMLSC3711368
MedGen777976
GARD0004582
Is cancer (heuristic)no

Also known as: congenital PAP · congenital pulmonary alveolar proteinosis · hereditary pulmonary alveolar proteinosis · inborn error of pulmonary surfactant metabolism · inborn error of surfactant metabolism · pulmonary alveolar proteinosis, congenital

Data availability: 781 ClinVar variants · 3 GenCC gene-disease records.

Disease family

An umbrella term covering 8 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › respiratory system disorderlower respiratory tract disorderlung disorderpulmonary alveolar proteinosishereditary pulmonary alveolar proteinosis

Related subtypes (2): autoimmune pulmonary alveolar proteinosis, secondary pulmonary alveolar proteinosis

Subtypes (8): surfactant metabolism dysfunction, pulmonary, 1, surfactant metabolism dysfunction, pulmonary, 4, interstitial lung disease due to ABCA3 deficiency, surfactant metabolism dysfunction, pulmonary, 5, severe early-onset pulmonary alveolar proteinosis due to MARS deficiency, chronic respiratory distress with surfactant metabolism deficiency, SFTPC-related interstitial lung disease, surfactant metabolism dysfunction, pulmonary, 2

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:

295 uncertain significance, 142 likely benign, 75 conflicting classifications of pathogenicity, 26 benign/likely benign, 26 benign, 18 pathogenic, 9 pathogenic/likely pathogenic, 9 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
1068619NM_001089.3(ABCA3):c.1729_1730del (p.Ser577fs)ABCA3Pathogeniccriteria provided, multiple submitters, no conflicts
1211382NM_001089.3(ABCA3):c.3863-98C>TABCA3Pathogeniccriteria provided, multiple submitters, no conflicts
1317554NM_001089.3(ABCA3):c.3997_3998del (p.Arg1333fs)ABCA3Pathogeniccriteria provided, multiple submitters, no conflicts
1331730NM_001089.3(ABCA3):c.4141_4142del (p.Leu1381fs)ABCA3Pathogeniccriteria provided, multiple submitters, no conflicts
1730473NM_001089.3(ABCA3):c.3348_3360del (p.Ile1117fs)ABCA3Pathogeniccriteria provided, single submitter
1735105NM_001089.3(ABCA3):c.3805G>T (p.Glu1269Ter)ABCA3Pathogeniccriteria provided, single submitter
1736036NM_001089.3(ABCA3):c.3902dup (p.Val1303fs)ABCA3Pathogeniccriteria provided, multiple submitters, no conflicts
1738591NM_001089.3(ABCA3):c.4195G>A (p.Val1399Met)ABCA3Pathogeniccriteria provided, multiple submitters, no conflicts
1740383NM_001089.3(ABCA3):c.440C>T (p.Pro147Leu)ABCA3Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1758921NM_001089.3(ABCA3):c.743C>T (p.Pro248Leu)ABCA3Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1767530NM_001089.3(ABCA3):c.127C>T (p.Arg43Cys)ABCA3Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1769442NM_001089.3(ABCA3):c.1302G>A (p.Trp434Ter)ABCA3Pathogeniccriteria provided, single submitter
1772770NM_001089.3(ABCA3):c.1444C>T (p.Gln482Ter)ABCA3Pathogeniccriteria provided, single submitter
1773031NM_001089.3(ABCA3):c.1455C>A (p.Tyr485Ter)ABCA3Pathogeniccriteria provided, single submitter
1773032NM_001089.3(ABCA3):c.1455C>G (p.Tyr485Ter)ABCA3Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1799308NM_001089.3(ABCA3):c.3057dup (p.Asn1020Ter)ABCA3Pathogeniccriteria provided, single submitter
203381NM_001089.3(ABCA3):c.875A>T (p.Glu292Val)ABCA3Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
228321NM_001089.3(ABCA3):c.128G>A (p.Arg43His)ABCA3Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2982329NM_001089.3(ABCA3):c.737C>T (p.Pro246Leu)ABCA3Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
13201NM_000542.5(SFTPB):c.361delinsGAA (p.Pro121fs)SFTPBPathogeniccriteria provided, multiple submitters, no conflicts
1752055NM_000542.5(SFTPB):c.581del (p.Gln194fs)SFTPBPathogeniccriteria provided, single submitter
1761177NM_000542.5(SFTPB):c.754C>T (p.Arg252Cys)SFTPBPathogeniccriteria provided, single submitter
1766142NM_000542.5(SFTPB):c.883C>T (p.Arg295Ter)SFTPBPathogeniccriteria provided, single submitter
13208NM_001317778.2(SFTPC):c.218T>C (p.Ile73Thr)SFTPCPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1729939NM_001317778.2(SFTPC):c.329T>C (p.Leu110Pro)SFTPCPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1738082NM_001317778.2(SFTPC):c.413_430delinsAGGTGATC (p.Thr138fs)SFTPCPathogeniccriteria provided, single submitter
1744578NM_001317778.2(SFTPC):c.480dup (p.Arg161fs)SFTPCPathogeniccriteria provided, single submitter
1740119NM_001089.3(ABCA3):c.4376G>A (p.Gly1459Asp)ABCA3Likely pathogeniccriteria provided, multiple submitters, no conflicts
1741928NM_001089.3(ABCA3):c.4618G>A (p.Glu1540Lys)ABCA3Likely pathogeniccriteria provided, multiple submitters, no conflicts
1742161NM_001089.3(ABCA3):c.4648C>T (p.Arg1550Trp)ABCA3Likely pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 7 · 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
CSF2RADefinitiveAutosomal recessivesurfactant metabolism dysfunction, pulmonary, 43
CSF2RBModerateAutosomal recessivesurfactant metabolism dysfunction, pulmonary, 53
ACADLLimitedAutosomal recessivehereditary pulmonary alveolar proteinosis

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
CSF2RAOrphanet:264675Hereditary pulmonary alveolar proteinosis
CSF2RBOrphanet:264675Hereditary pulmonary alveolar proteinosis
SFTPBOrphanet:217563Neonatal acute respiratory distress syndrome
SFTPBOrphanet:685082Pediatric acute respiratory distress syndrome
SFTPCOrphanet:2032Idiopathic pulmonary fibrosis
SFTPCOrphanet:217566Chronic respiratory distress with surfactant metabolism deficiency
SFTPCOrphanet:440392Interstitial lung disease due to SP-C deficiency
SFTPCOrphanet:685082Pediatric acute respiratory distress syndrome
ABCA3Orphanet:2032Idiopathic pulmonary fibrosis
ABCA3Orphanet:217563Neonatal acute respiratory distress syndrome
ABCA3Orphanet:440402Interstitial lung disease due to ABCA3 deficiency
ABCA3Orphanet:685082Pediatric acute respiratory distress syndrome

Cohort genes → proteins

6 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
CSF2RAHGNC:2435ENSG00000198223P15509Granulocyte-macrophage colony-stimulating factor receptor subunit alphagencc
CSF2RBHGNC:2436ENSG00000100368P32927Cytokine receptor common subunit betagencc
ACADLHGNC:88ENSG00000115361P28330Long-chain specific acyl-CoA dehydrogenase, mitochondrialgencc
SFTPBHGNC:10801ENSG00000168878P07988Pulmonary surfactant-associated protein Bclinvar
SFTPCHGNC:10802ENSG00000168484P11686Surfactant protein Cclinvar
ABCA3HGNC:33ENSG00000167972Q99758Phospholipid-transporting ATPase ABCA3clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
CSF2RAGranulocyte-macrophage colony-stimulating factor receptor subunit alphaLow affinity receptor for granulocyte-macrophage colony-stimulating factor.
CSF2RBCytokine receptor common subunit betaCell surface receptor that plays a role in immune response and controls the production and differentiation of hematopoietic progenitor cells into lineage-restricted cells.
ACADLLong-chain specific acyl-CoA dehydrogenase, mitochondrialLong-chain specific acyl-CoA dehydrogenase is one of the acyl-CoA dehydrogenases that catalyze the first step of mitochondrial fatty acid beta-oxidation (FAO), breaking down fatty acids into acetyl-CoA and allowing the production of energy…
SFTPBPulmonary surfactant-associated protein BPulmonary surfactant-associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces.
SFTPCSurfactant protein CPulmonary surfactant associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces.
ABCA3Phospholipid-transporting ATPase ABCA3Catalyzes the ATP-dependent transport of phospholipids such as phosphatidylcholine and phosphoglycerol from the cytoplasm into the lumen side of lamellar bodies, in turn participates in the lamellar bodies biogenesis and homeostasis of pul…

Protein-family classification

Druggable: 3 · Difficult: 0 · Unknown: 3 · Druggable fraction: 0.5

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/Immunoglobulin29.7×0.048
Transporter113.0×0.112
Other/Unknown30.9×0.758

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
CSF2RAAntibody/ImmunoglobulinyesShort_hematopoietin_rcpt_2_CS, FN3_dom, Ig-like_fold
CSF2RBAntibody/ImmunoglobulinyesHempt_rcpt_S_F1_CS, FN3_dom, IL3_rcpt_beta
ACADLOther/UnknownnoAcyl-CoA_DH_CS, AcylCoA_DH/ox_M, AcylCo_DH/oxidase_C
SFTPBOther/UnknownnoSAP_A, SapB_1, SapB_2
SFTPCOther/UnknownnoSP-C, BRICHOS_dom, Surfactant_protein_propep
ABCA3TransporteryesABC_transporter-like_ATP-bd, AAA+_ATPase, ABC2_TM

Expression context

Cohort genes with no expression data: 0.

6 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)6
unknown0

Top tissues across cohort

TissueCohort genes
lower lobe of lung3
upper lobe of lung2
leukocyte1
monocyte1
mononuclear cell1
blood1
decidua1
periodontal ligament1
body of pancreas1
popliteal artery1
tibial artery1
visceral pleura1
adult organism1
right lung1
upper lobe of left lung1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
CSF2RA193markermonocyte, mononuclear cell, leukocyte
CSF2RB230broadmarkerblood, periodontal ligament, decidua
ACADL208broadmarkerbody of pancreas, popliteal artery, tibial artery
SFTPB231tissue_specificmarkerlower lobe of lung, visceral pleura, upper lobe of lung
SFTPC208tissue_specificmarkerlower lobe of lung, right lung, adult organism
ABCA3222ubiquitousmarkerlower lobe of lung, upper lobe of lung, upper lobe of left lung

Protein interactions among cohort

Intra-cohort edges: 7.

Hub genes (top 10 by interactor count)

SymbolInteractor count
ACADL2,251
CSF2RB1,948
SFTPC1,613
ABCA31,436
CSF2RA1,335
SFTPB899

Intra-cohort edges

ABSources
ABCA3CSF2RAstring_interaction
ABCA3CSF2RBstring_interaction
ABCA3SFTPBstring_interaction
ABCA3SFTPCstring_interaction
CSF2RACSF2RBstring_interaction
CSF2RASFTPBstring_interaction
SFTPBSFTPCstring_interaction

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
CSF2RBP3292710
SFTPBP079889
ACADLP283303
SFTPCP116863
CSF2RAP155092
ABCA3Q997582

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 27. Enrichment computed across 6 evidence-associated genes (6 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 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Defective CSF2RB causes SMDP541087.6×7e-12SFTPB, SFTPC, CSF2RA, CSF2RB
Defective CSF2RA causes SMDP441087.6×7e-12SFTPB, SFTPC, CSF2RA, CSF2RB
Surfactant metabolism5307.0×7e-12SFTPB, SFTPC, CSF2RA, CSF2RB, ABCA3
Interleukin receptor SHC signaling2135.9×6e-04CSF2RA, CSF2RB
Interleukin-3, Interleukin-5 and GM-CSF signaling2105.7×8e-04CSF2RA, CSF2RB
Defective ABCA3 causes SMDP311903.3×0.002ABCA3
Defective pro-SFTPB causes SMDP1 and RDS11903.3×0.002SFTPB
Defective pro-SFTPC causes SMDP2 and RDS11903.3×0.002SFTPC
Beta oxidation of myristoyl-CoA to lauroyl-CoA1634.4×0.004ACADL
Diseases associated with surfactant metabolism1475.8×0.005ABCA3
Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA1380.7×0.006ACADL
mitochondrial fatty acid beta-oxidation of unsaturated fatty acids1317.2×0.007ACADL
mitochondrial fatty acid beta-oxidation of saturated fatty acids1271.9×0.007ACADL
RAF/MAP kinase cascade220.4×0.007CSF2RA, CSF2RB
ABC transporters in lipid homeostasis1100.2×0.017ABCA3
ABC transporter disorders173.2×0.022ABCA3
Mitochondrial Fatty Acid Beta-Oxidation163.4×0.023ACADL
Disorders of transmembrane transporters123.2×0.060ABCA3
Fatty acid metabolism121.9×0.061ACADL
ABC-family protein mediated transport120.2×0.062ABCA3
Diseases of metabolism113.4×0.089ABCA3
Metabolism of lipids15.3×0.206ACADL
Transport of small molecules14.2×0.243ABCA3
Disease12.2×0.410ABCA3
Metabolism of proteins12.1×0.412ABCA3
Metabolism11.9×0.417ACADL

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
respiratory gaseous exchange by respiratory system3312.1×3e-06SFTPB, SFTPC, CSF2RB
granulocyte-macrophage colony-stimulating factor signaling pathway21404.3×1e-05CSF2RA, CSF2RB
positive regulation of leukocyte proliferation2936.2×2e-05CSF2RA, CSF2RB
cell surface receptor signaling pathway via JAK-STAT296.8×0.002CSF2RA, CSF2RB
positive regulation of protein homooligomerization12808.7×0.003ABCA3
carnitine catabolic process12808.7×0.003ACADL
regulation of phosphatidylcholine metabolic process11404.3×0.005ABCA3
carnitine metabolic process, CoA-linked1936.2×0.005ACADL
xenobiotic export from cell1936.2×0.005ABCA3
positive regulation of phospholipid efflux1702.2×0.006ABCA3
cellular response to interleukin-31468.1×0.006CSF2RB
interleukin-5-mediated signaling pathway1468.1×0.006CSF2RB
long-chain fatty acid catabolic process1468.1×0.006ACADL
regulation of lipid biosynthetic process1468.1×0.006ABCA3
organelle assembly1468.1×0.006ABCA3
interleukin-3-mediated signaling pathway1401.2×0.007CSF2RB
positive regulation of phospholipid transport1401.2×0.007ABCA3
negative regulation of fatty acid oxidation1280.9×0.009ACADL
fatty acid beta-oxidation using acyl-CoA dehydrogenase1234.1×0.010ACADL
phosphatidylglycerol metabolic process1234.1×0.010ABCA3
growth hormone receptor signaling pathway1200.6×0.011CSF2RA
regulation of cholesterol metabolic process1187.2×0.011ACADL
sphingolipid metabolic process1165.2×0.011SFTPB
phospholipid homeostasis1165.2×0.011ABCA3
xenobiotic transmembrane transport1156.0×0.012ABCA3
negative regulation of fatty acid biosynthetic process1147.8×0.012ACADL
xenobiotic transport1140.4×0.012ABCA3
surfactant homeostasis1133.8×0.012ABCA3
phosphatidylcholine metabolic process1133.8×0.012ABCA3
phospholipid transport1117.0×0.012ABCA3

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 6

Druggability breadth: 2 of 6 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
CSF2RA00
CSF2RB00
ACADL00
SFTPB00
SFTPC00
ABCA300

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; 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 drug3CSF2RA, CSF2RB, ABCA3
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug3ACADL, SFTPB, SFTPC

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
CSF2RA0
CSF2RB0
ACADL0
SFTPB0
SFTPC0
ABCA30

Clinical trials & evidence

Clinical trials

Clinical trials: 2.

Phase distribution (across all retrieved trials)

PhaseTrials
PHASE21
PHASE1/PHASE21

Top trials by phase / activity

NCTPhaseStatusTitle
NCT05761899PHASE1/PHASE2RECRUITINGSafety and Efficacy of PMT Therapy of hPAP
NCT01511068PHASE2COMPLETEDInhaled Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF) in Hereditary Pulmonary Alveolar Proteinosis (PAP)

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
SARGRAMOSTIM41