Hypoalphalipoproteinemia, primary, 1: genes and variants
Hypoalphalipoproteinemia, primary, 1 is linked to 2 analyzed proteins (APOA1 and ABCA1). 6 DNA variants are known to cause it; 93 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Also known as: hypoalphalipoproteinemia, primary, 2
Genes linked to Hypoalphalipoproteinemia, primary, 1
APOA1: Apolipoprotein A-I
It is the principal protein scaffold of HDL and activates LCAT, supporting cholesterol efflux from peripheral tissues and reverse cholesterol transport. Pathogenic variants can cause very low HDL cholesterol, familial amyloidosis in some alleles, or altered cardiovascular risk.
4 disease-causing and 26 uncertain variants in APOA1 are linked to Hypoalphalipoproteinemia, primary, 1.
ABCA1: Phospholipid-transporting ATPase ABCA1
It transfers cellular cholesterol and phospholipids to lipid-poor apolipoproteins, especially ApoA-I, initiating HDL formation and reverse cholesterol transport. Severe loss of function causes Tangier disease, while partial impairment can markedly lower HDL cholesterol.
2 disease-causing and 67 uncertain variants in ABCA1 are linked to Hypoalphalipoproteinemia, primary, 1.
Known disease-causing variants in Hypoalphalipoproteinemia, primary, 1
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| ABCA1 N1800H | 1800 | Disease-causing (★★) | |
| APOA1 L99P | 99 | 2 | Disease-causing (★★) |
| APOA1 G50R | 50 | Disease-causing (★★) | |
| APOA1 D181G | 181 | 6 | Disease-causing (★) |
| ABCA1 F2009S | 2009 | ABC transporter 2 | Disease-causing |
| APOA1 V180E | 180 | 6 | Disease-causing |
Same protein, different disease
- Familial amyloid polyneuropathy, Iowa type is also caused by APOA1 variants; they fall mostly in different places as the Hypoalphalipoproteinemia, primary, 1 variants (5 disease-causing).
- Tangier disease is also caused by ABCA1 variants; they fall mostly in different places as the Hypoalphalipoproteinemia, primary, 1 variants (5 disease-causing).
Diseases related to Hypoalphalipoproteinemia, primary, 1
- Tangier disease, also linked to ABCA1
- Familial amyloid polyneuropathy, Iowa type, also linked to APOA1
- Familial visceral amyloidosis, Ostertag type, also linked to APOA1
- Hypoalphalipoproteinemia, primary, 2, intermediate, also linked to APOA1
Frequently asked questions
Which genes are linked to Hypoalphalipoproteinemia, primary, 1?
In CATVariant, Hypoalphalipoproteinemia, primary, 1 is linked to 2 analyzed proteins: APOA1 (Apolipoprotein A-I) and ABCA1 (Phospholipid-transporting ATPase ABCA1).
How many genetic variants are linked to Hypoalphalipoproteinemia, primary, 1?
132 variants: 6 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 93 are of uncertain significance or have conflicting reports.
Which uncertain variants in Hypoalphalipoproteinemia, primary, 1 look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
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.
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