ABCA1
Chr 9ADARATP binding cassette subfamily A member 1
Also known as: ABC-1, ABC1, CERP, HDLCQTL13, HDLDT1, HPALP1, TGD
This protein catalyzes the ATP-dependent translocation of phospholipids across cell membranes and participates in cholesterol efflux to form nascent high-density lipoproteins. Mutations cause familial HDL deficiency and Tangier disease, which are inherited in autosomal recessive patterns, though some variants may act in an autosomal dominant manner. The gene is highly intolerant to loss-of-function variants, indicating that complete loss of protein function has severe consequences.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Mild missense constraint
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Literature Evidence
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
500 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 14 | 0 | 1 | 0 | 15 |
Likely Pathogenic | 8 | 1 | 0 | 0 | 9 |
VUS | 0 | 210 | 6 | 1 | 217 |
Likely Benign | 0 | 17 | 46 | 134 | 197 |
Benign | 0 | 1 | 3 | 0 | 4 |
Conflicting | — | 1 | |||
| Total | 22 | 229 | 56 | 135 | 443 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
ABCA1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Phenotypic and Molecular Characterisation of Cerebral Amyloid Angiopathy
RECRUITINGStudy of the Effect of Innate on the Inflammatory Response to Endotoxin
RECRUITINGExternal Resources
Links to major genomics databases and tools