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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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ABCA3
ATP binding cassette subfamily A member 3
Chromosome 16 Β· 16p13.3
NCBI Gene: 21Ensembl: ENSG00000167972.15HGNC: HGNC:33UniProt: Q99758
121PubMed Papers
21Diseases
0Drugs
135Pathogenic Variants
FUNCTIONAL ROLE
Transporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
phosphatidylcholine transfer activityxenobiotic export from cellGO:0005615positive regulation of phospholipid transportNeonatal acute respiratory distress with surfactant metabolism deficiencyCongenital pulmonary alveolar proteinosishereditary pulmonary alveolar proteinosisnewborn respiratory distress syndrome
✦AI Summary

ABCA3 is an ATP-dependent phospholipid transporter predominantly expressed in alveolar type II cells that catalyzes the transport of phosphatidylcholine and phosphoglycerol from the cytoplasm into lamellar bodies, critical organelles for pulmonary surfactant synthesis and storage 1. The protein preferentially transports phosphatidylcholine with short acyl chains and also functions as an efflux transporter of free cholesterol and miltefosine, protecting cells from cholesterol toxicity 2. ABCA3 is essential for normal lamellar body biogenesis and surfactant homeostasis, with expression developmentally regulated and peaking before birth 1. Biallelic ABCA3 mutations represent the most frequent genetic cause of congenital surfactant deficiency and childhood interstitial lung disease (chILD), producing disease ranging from neonatal respiratory distress to chr16 diffuse parenchymal lung disease 1. Over 200 mutations have been identified, predominantly unique to families 1. Mutations affecting the first extracellular loop and second nucleotide-binding domain account for much phenotypic diversity through defective glycosylation, trafficking defects, and impaired ATP binding 1. Null mutations (frameshift/nonsense) predict neonatal presentation and poor prognosis, while missense and splice-site mutations show variable age-of-onset and clinical course 3. Recent iPSC-derived models demonstrate that ABCA3-mutant alveolar epithelial cells exhibit diminished surfactant secretion, reduced progenitor potential, and increased pro-inflammatory signaling 4. Currently, no proven therapy exists, though hydroxychloroquine response appears variant-dependent 5.

Sources cited
1
ABCA3 is a phospholipid transporter critical for surfactant synthesis, lamellar body formation, and developmental expression; biallelic mutations are the most frequent cause of congenital surfactant deficiency
PMID: 26517903
2
ABCA3 functions as a lipid transporter regulating surfactant homeostasis; mutations cause inherited pulmonary diseases with variable presentations from neonatal respiratory failure to childhood diffuse parenchymal lung disease
PMID: 28025703
3
Null ABCA3 mutations (frameshift/nonsense) predict neonatal respiratory failure and poor outcome by age 1, while missense and splice-site mutations show more variable presentation
PMID: 24871971
4
ABCA3-mutant alveolar type II cells derived from patient iPSCs show decreased surfactant secretion, diminished progenitor potential, increased NFΞΊB signaling, and perturbed lamellar body morphology
PMID: 38226623
5
ABCA3 deficiency causes chILD; hydroxychloroquine response is variant-specific with in vitro ABCA3 functional assays predicting clinical treatment outcomes
PMID: 37175887
Disease Associationsβ“˜21
Neonatal acute respiratory distress with surfactant metabolism deficiencyOpen Targets
0.85Strong
Congenital pulmonary alveolar proteinosisOpen Targets
0.84Strong
hereditary pulmonary alveolar proteinosisOpen Targets
0.56Moderate
newborn respiratory distress syndromeOpen Targets
0.48Moderate
Primary interstitial lung disease specific to childhood due to pulmonary surfactant protein anomaliesOpen Targets
0.45Moderate
neurodegenerative diseaseOpen Targets
0.42Moderate
interstitial lung diseaseOpen Targets
0.40Moderate
idiopathic pulmonary fibrosisOpen Targets
0.40Moderate
carbamoyl phosphate synthetase I deficiency diseaseOpen Targets
0.27Weak
Loeys-Dietz syndromeOpen Targets
0.27Weak
surfactant metabolism dysfunction, pulmonary, 1Open Targets
0.13Weak
lung diseaseOpen Targets
0.13Weak
respiratory failureOpen Targets
0.12Weak
Abnormal pulmonary interstitial morphologyOpen Targets
0.12Weak
prostate cancerOpen Targets
0.11Weak
chromosome 22q11.2 deletion syndrome, distalOpen Targets
0.11Weak
Familial prostate cancerOpen Targets
0.11Weak
lung adenocarcinomaOpen Targets
0.08Suggestive
neoplasmOpen Targets
0.07Suggestive
surfactant metabolism dysfunction, pulmonary, 2Open Targets
0.06Suggestive
Pulmonary surfactant metabolism dysfunction 3UniProt
Pathogenic Variants135
NM_001089.3(ABCA3):c.875A>T (p.Glu292Val)Pathogenic
Interstitial lung disease due to ABCA3 deficiency|not provided|Primary interstitial lung disease specific to childhood due to pulmonary surfactant protein anomalies;Diffuse interstitial pulmonary fibrosis|Interstitial lung disease 2|Hereditary pulmonary alveolar proteinosis|Sarcoma|Ovarian serous cystadenocarcinoma|Malignant tumor of urinary bladder|Cervical cancer
β˜…β˜…β˜†β˜†2026β†’ Residue 292
NM_001089.3(ABCA3):c.3600CTT[3] (p.Phe1203del)Pathogenic
Interstitial lung disease due to ABCA3 deficiency|Hereditary pulmonary alveolar proteinosis|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 1203
NM_001089.3(ABCA3):c.1474dup (p.Tyr492fs)Pathogenic
not provided|Hereditary pulmonary alveolar proteinosis|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2026β†’ Residue 492
NM_001089.3(ABCA3):c.3208G>A (p.Ala1070Thr)Likely pathogenic
not provided|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 1070
NM_001089.3(ABCA3):c.2890G>A (p.Gly964Ser)Pathogenic
not provided|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 964
NM_001089.3(ABCA3):c.3863-98C>TPathogenic
not provided|Interstitial lung disease due to ABCA3 deficiency|ABCA3-related disorder|Hereditary pulmonary alveolar proteinosis
β˜…β˜…β˜†β˜†2025
NM_001089.3(ABCA3):c.622C>T (p.Arg208Trp)Pathogenic
not provided|Interstitial lung disease due to ABCA3 deficiency|Surfactant metabolism dysfunction, pulmonary, 1
β˜…β˜…β˜†β˜†2025β†’ Residue 208
NM_001089.3(ABCA3):c.737C>T (p.Pro246Leu)Pathogenic
not provided|Hereditary pulmonary alveolar proteinosis
β˜…β˜…β˜†β˜†2025β†’ Residue 246
NM_001089.3(ABCA3):c.4195G>A (p.Val1399Met)Pathogenic
Hereditary pulmonary alveolar proteinosis|Interstitial lung disease due to ABCA3 deficiency|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1399
NM_001089.3(ABCA3):c.1112-20G>ALikely pathogenic
not provided|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025
NM_001089.3(ABCA3):c.4090G>A (p.Glu1364Lys)Pathogenic
Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 1364
NM_001089.3(ABCA3):c.3145T>C (p.Ser1049Pro)Likely pathogenic
not provided|Congenital hyperammonemia, type I|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 1049
NM_001089.3(ABCA3):c.557C>T (p.Pro186Leu)Likely pathogenic
Hereditary pulmonary alveolar proteinosis|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 186
NM_001089.3(ABCA3):c.4261G>A (p.Gly1421Arg)Likely pathogenic
Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 1421
NM_001089.3(ABCA3):c.604G>A (p.Gly202Arg)Pathogenic
not provided|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 202
NM_001089.3(ABCA3):c.614-2A>GLikely pathogenic
not provided|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025
NM_001089.3(ABCA3):c.537G>C (p.Trp179Cys)Pathogenic
not provided|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2025β†’ Residue 179
NM_001089.3(ABCA3):c.1890C>A (p.Tyr630Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 630
NM_001089.3(ABCA3):c.4376G>A (p.Gly1459Asp)Likely pathogenic
Hereditary pulmonary alveolar proteinosis|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 1459
NM_001089.3(ABCA3):c.1303C>T (p.Arg435Ter)Pathogenic
not provided|Interstitial lung disease due to ABCA3 deficiency
β˜…β˜…β˜†β˜†2024β†’ Residue 435
View on ClinVar β†—
Related Genes
SFTPBProtein interaction96%SFTPCProtein interaction90%CSF2RAProtein interaction81%SFTPA1Protein interaction71%ABCA8Shared pathway18%CETPShared pathway16%
Tissue Expression6 tissues
Lung
100%
Brain
40%
Heart
13%
Ovary
6%
Bone Marrow
3%
Liver
2%
Gene Interaction Network
Click a node to explore
ABCA3SFTPBSFTPCCSF2RASFTPA1ABCA8CETP
PROTEIN STRUCTURE
Preparing viewer…
PDB7W01 Β· 3.30 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.61LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.51 [0.43–0.61]
RankingsWhere ABCA3 stands among ~20K protein-coding genes
  • #3,871of 20,598
    Most Researched121 Β· top quartile
  • #571of 5,498
    Most Pathogenic Variants135 Β· top quartile
  • #4,253of 17,882
    Most Constrained (LOEUF)0.61 Β· top quartile
Genes detectedABCA3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
The biology, function, and applications of exosomes in cancer.
PMID: 34589397
Acta Pharm Sin B Β· 2021
1.00
2
Genotype-phenotype correlations for infants and children with ABCA3 deficiency.
PMID: 24871971
Am J Respir Crit Care Med Β· 2014
0.90
3
European protocols for the diagnosis and initial treatment of interstitial lung disease in children.
PMID: 26135832
Thorax Β· 2015
0.80
4
Farewell, king coal!
PMID: 26856364
Thorax Β· 2016
0.70
5
Human pluripotent stem cell modeling of alveolar type 2 cell dysfunction caused by ABCA3 mutations.
PMID: 38226623
J Clin Invest Β· 2024
0.60