Interstitial lung disease due to ABCA3 deficiency: genes and variants

Genes linked to Interstitial lung disease due to ABCA3 deficiency

• ABCA3: Phospholipid-transporting ATPase ABCA3

  It transports phospholipids into lamellar bodies of alveolar type II cells, supporting pulmonary surfactant assembly and normal gas exchange. Biallelic loss-of-function variants can cause neonatal respiratory failure or childhood interstitial lung disease.

  30 disease-causing and 106 uncertain variants in ABCA3 are linked to Interstitial lung disease due to ABCA3 deficiency.

Known disease-causing variants in Interstitial lung disease due to ABCA3 deficiency

Which prediction tools work for Interstitial lung disease due to ABCA3 deficiency

How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).

• MetaLR: 100 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• phyloP: 98 out of 100
• CATVariant: 98 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• CADD: 97 out of 100
• PolyPhen-2: 96 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 95 out of 100
• REVEL: 95 out of 100 (learned from overlapping clinical labels, so this is optimistic)

Same protein, different disease

• Hereditary pulmonary alveolar proteinosis is also caused by ABCA3 variants; they fall mostly in different places as the Interstitial lung disease due to ABCA3 deficiency variants (12 disease-causing).

Diseases related to Interstitial lung disease due to ABCA3 deficiency

• Loeys-Dietz syndrome, also linked to ABCA3
• Hereditary pulmonary alveolar proteinosis, also linked to ABCA3
• Surfactant metabolism dysfunction, pulmonary, 1, also linked to ABCA3
• Interstitial lung disease, also linked to ABCA3

Frequently asked questions

Which genes are linked to Interstitial lung disease due to ABCA3 deficiency?

In CATVariant, Interstitial lung disease due to ABCA3 deficiency is linked to 1 analyzed protein: ABCA3 (Phospholipid-transporting ATPase ABCA3).

How many genetic variants are linked to Interstitial lung disease due to ABCA3 deficiency?

141 variants: 30 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 106 are of uncertain significance or have conflicting reports.

Which uncertain variants in Interstitial lung disease due to ABCA3 deficiency look disease-causing?

None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.

Which variant effect predictor works best for Interstitial lung disease due to ABCA3 deficiency?

Among tools not trained on clinical labels, phyloP separates this disease's known disease-causing variants from harmless ones best (AUROC 0.98, based on 23 disease-causing and 22 harmless variants).

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.

Download every variant as CSV · Browse all diseases · Methods · About the Center