LCAT deficiency: genes and variants
LCAT deficiency is linked to 1 analyzed protein (LCAT). 10 DNA variants are known to cause it; 4 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to LCAT deficiency
LCAT: Phosphatidylcholine-sterol acyltransferase
It esterifies free cholesterol on circulating lipoproteins, allowing HDL particles to mature and participate in reverse cholesterol transport. Biallelic loss-of-function variants cause familial LCAT deficiency or fish-eye disease, with very low HDL and variable corneal, renal, and hematologic manifestations.
10 disease-causing and 4 uncertain variants in LCAT are linked to LCAT deficiency.
Known disease-causing variants in LCAT deficiency
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| LCAT R123C | 123 | Disease-causing (★★) | |
| LCAT V333M | 333 | Disease-causing (★) | |
| LCAT M404V | 404 | Disease-causing (★) | |
| LCAT L233P | 233 | Disease-causing | |
| LCAT M276K | 276 | Disease-causing | |
| LCAT M317I | 317 | Disease-causing | |
| LCAT W170R | 170 | Disease-causing | |
| LCAT N252K | 252 | Disease-causing | |
| LCAT A117T | 117 | Disease-causing | |
| LCAT R182C | 182 | Disease-causing |
Which prediction tools work for LCAT deficiency
How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).
- SIFT: 100 out of 100
- CATVariant: 96 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- PolyPhen-2: 95 out of 100 (learned from overlapping clinical labels, so this is optimistic)
Same protein, different disease
- Fish-eye disease is also caused by LCAT variants; they fall mostly in different places as the LCAT deficiency variants (7 disease-causing).
- Norum disease is also caused by LCAT variants; they fall mostly in different places as the LCAT deficiency variants (7 disease-causing).
Diseases related to LCAT deficiency
- Fish-eye disease, also linked to LCAT
- Norum disease, also linked to LCAT
Frequently asked questions
Which genes are linked to LCAT deficiency?
In CATVariant, LCAT deficiency is linked to 1 analyzed protein: LCAT (Phosphatidylcholine-sterol acyltransferase).
How many genetic variants are linked to LCAT deficiency?
26 variants: 10 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 4 are of uncertain significance or have conflicting reports.
Which uncertain variants in LCAT 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 LCAT deficiency?
Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 1.00, based on 10 disease-causing and 8 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