Mutations

APOE L167del

Mature Protein Numbering: L149del

Overview

Clinical Phenotype: Multiple Conditions
Reference Assembly: GRCh37/hg19
Transcript: NM_000041; ENSG00000130203
dbSNP ID: NA
Coding/Non-Coding: Coding
DNA Change: Deletion
Expected RNA Consequence: Deletion
Expected Protein Consequence: Deletion
Codon Change: CTC to -
Reference Isoform: APOE Isoform 1
Genomic Region: Exon 4

Findings

This mutation is an in-frame deletion resulting in loss of a leucine codon within ApoE’s receptor binding region. Most carriers develop a condition indistinguishable from hyperlipoproteinemia type IIa (HLPP2a), also known as autosomal dominant hypercholesterolemia, which can lead to cardiovascular disease at an early age (e.g., Awan et al., 2013, Pirillo et al., 2017, Bea et al., 2019, Khalil et al., 2022, Bea et al., 2023). Mutations in genes involved in lipid metabolism, LDLR, APOB, and PCSK9, have long been implicated in HLPP2a, but APOE’s association with this disease is relatively recent (see Di Taranto et al., 2020 and Civeira et al., 2024 for reviews).

Interestingly, L167del was first identified in individuals with sea-blue histiocytosis, a condition characterized by an enlarged spleen and a low platelet count in blood. The original report described two unrelated probands of French-Canadian ancestry with a moderate elevation of blood triglycerides that worsened after spleen removal (Nguyen et al., 2000). Subsequent studies, including two members of a French family (Faivre et al., 2005), an individual of Japanese and British ancestry (Rahalkar et al., 2008), and an American man (Okorodudu et al., 2013), also reported carriers who suffered from spleen enlargement and platelet deficiency. However, studies including larger numbers of carriers suggested that, in fact, these alterations occur only in a minority of L167del carriers. Marduel and colleagues, for example, observed no such phenotypes in 12 carriers (Marduel et al., 2013), nor did Solanas-Barca and co-workers in three families with 11 affected individuals (Solanas-Barca et al., 2012). Even in the earlier studies, the authors reported that some family members did not express the sea-blue histiocytosis phenotype (Faivre et al., 2005, Okorodudu et al., 2013). A 2016 report concluded that of the 38 carriers studied up to that date, only seven had enlarged spleens (Cenarro et al., 2016).

In contrast, 29 of the 38 carriers had a phenotype consistent with HLPP2a or, in some cases, hyperlipoproteinemia type IIb (HLPP2b), a condition characterized by elevated levels of both cholesterol and triglycerides (Solanas-Barca et al., 2012, Cenarro et al., 2016). The autosomal dominant inheritance of hypercholesterolemia was perhaps most clearly established in a study of a family including 27 members spanning three generations, with 14 affected individuals (Marduel et al., 2013). Consistent with these findings, in a subsequent study, L167del was found to segregate with hypercholesterolemia in 30 subjects from eight families (Cenarro et al., 2016). In this latter study, 18 of 19 carriers had levels of low-density lipoprotein (LDL) cholesterol above the 90th percentile and all had normal, or in three cases, only slightly elevated, levels of triglycerides. The authors noted that the clinical phenotype of the carriers in their study appeared to be milder than that associated with mutations in the LDLR gene, with L167del carriers lacking lipid deposits in tendons and having a lower prevalence of cardiovascular disease.

L167del has been identified in individuals with severe phenotypes in some cases, however. For example, it was found in a middle-aged Caucasian woman with extremely high levels of LDL cholesterol and severe nonalcoholic fatty liver disease (Vilar-Gomez et al., 2020). It was also reported in a 10-year-old Iranian girl whose high cholesterol levels were detected at age 3 (Noorian et al., 2022). 

At least in some cases, it is likely the associated phenotype depends on multiple genetic factors. For example, of 14 carriers with HLPP2a in one study, six had a strong probability of their condition being due to variants in multiple genes (weighted polygenic risk scores in deciles > VII; Abou Khalil et al., 2022).

Although L167del is rare, reported in only three individuals in the gnomAD variant database (v2.1.1, May 2022), it appears to be enriched in cohorts of patients with primary dyslipidemias without LDLR, APOB, and PCSK9 mutations. For example, in a French cohort its frequency was 0.0016, including 14 HLPP2a and four HLPP2b cases (Abou Khalil et al., 2022). It may be even more prevalent in Spain, where, in one study, it was found in approximately 3 percent of HLPP1 cases in one study (Cenarro et al., 2016) and in 0.5 percent of all subjects with hyperlipidemia in another (Bea et al., 2023). In the latter study, L167del was the most frequent APOE mutation in patients with any form of hyperlipidemia who also carried an APOE mutation (16 of 55). All the families examined in the two studies came from northeastern Spain, although they were not known to be related. In contrast, the L167del mutation was absent from 125 HLPP1 patients in the U.K. (Futema et al., 2014).

Biological effect

L167del, located in ApoE’s receptor-binding site, appears to act as a gain-of-function mutation, enhancing receptor interaction and consequently downregulating receptor expression. In their initial study, Nguyen and colleagues were unable to detect an effect on receptor binding in a competitive binding assay pitting lipid-loaded ApoE isolated from very low-density lipoprotein (VLDL) particles of a mutation carrier against LDL isolated from controls (Nguyen et al., 2000). However, they also reported that mutant VLDL induced mouse macrophages to accumulate cholesteryl esters to a greater extent than VLDL from APOE3/3 or APOE2/2 individuals, suggesting the mutant protein enabled increased VLDL uptake. Of note, this may explain the spleen pathology seen in some mutation carriers since, in addition to hepatocytes, macrophages in bone marrow and spleen play a role in clearing lipoprotein particles from circulation.

Subsequently, more detailed studies showed that mutant VLDL particles are taken up more efficiently by human hepatoma and monocytic cell lines than those isolated from non-mutation carriers with either homozygous APOE3 or APOE2 genotypes, and this enhanced uptake is followed by downregulation of LDL receptor expression (Cenarro et al., 2016). Consistent with these observations, VLDL uptake decreased when hepatoma cells were preincubated with L167del-containing VLDL particles. It is thus suspected that the elevated LDL cholesterol levels observed in patients are due to reduced receptor levels.

Although two in silico studies suggested L167del might impair receptor binding (Marduel et al., 2013, Wintjens et al., 2016), a third study indicated the opposite, consistent with the experimental findings above (Rashidi et al., 2017). Rashidi and co-workers noted that the stronger association mediated by the mutant protein might hinder LDL receptor recycling.

It has also been observed that L167del carriers have fewer ApoE proteins in their LDL and VLDL particles resulting in a reduced ApoE:ApoB ratio (Marduel et al., 2013, Cenarro et al., 2016). How this lower ratio might mediate stronger receptor binding is unclear, but Cenarro and colleagues proposed it might accelerate multi-valent binding of VLDL to LDL receptors (Cenarro et al., 2016, Martínez-Oliván et al., 2014). 

L167del might also affect lipoprotein catabolism. Marduel and colleagues reported decreased LDL catabolism based on kinetic measurements in one mutation carrier (Marduel et al., 2013).  In addition, Bea and co-workers more recently proposed that elevated catabolism of small and medium VLDL might explain the heightened responses of L167del carriers to treatment with statins, medications that reduce VLDL synthesis and increase receptor expression (Bea et al., 2019). The authors also noted that L167del might alter ApoE’s lipolytic activity. 

L167 is not evolutionarily conserved, but it is the fourth residue in a motif that is six amino acids long where positions 1, 2, 3 and 6 are highly conserved from frogs to humans (Marduel et al., 2013). Moreover, L167’s position in the fourth helix of the N-terminal domain has been predicted to be important for stabilizing interactions between ApoE’s four N-terminal helices.

Last Updated: 22 Apr 2024

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References

Paper Citations

  1. . APOE p.Leu167del mutation in familial hypercholesterolemia. Atherosclerosis. 2013 Dec;231(2):218-22. Epub 2013 Sep 19 PubMed.
  2. . Spectrum of mutations in Italian patients with familial hypercholesterolemia: New results from the LIPIGEN study. Atheroscler Suppl. 2017 Oct;29:17-24. PubMed.
  3. . Lipid-lowering response in subjects with the p.(Leu167del) mutation in the APOE gene. Atherosclerosis. 2019 Mar;282:143-147. Epub 2019 Jan 29 PubMed.
  4. . APOE Molecular Spectrum in a French Cohort with Primary Dyslipidemia. Int J Mol Sci. 2022 May 21;23(10) PubMed.
  5. . Contribution of APOE Genetic Variants to Dyslipidemia. Arterioscler Thromb Vasc Biol. 2023 Jun;43(6):1066-1077. Epub 2023 Apr 13 PubMed.
  6. . Familial hypercholesterolemia: A complex genetic disease with variable phenotypes. Eur J Med Genet. 2020 Apr;63(4):103831. Epub 2019 Dec 25 PubMed.
  7. . APOE and familial hypercholesterolemia. Curr Opin Lipidol. 2024 Apr 17; PubMed.
  8. . Familial splenomegaly: macrophage hypercatabolism of lipoproteins associated with apolipoprotein E mutation [apolipoprotein E (delta149 Leu)]. J Clin Endocrinol Metab. 2000 Nov;85(11):4354-8. PubMed.
  9. . Variable expressivity of the clinical and biochemical phenotype associated with the apolipoprotein E p.Leu149del mutation. Eur J Hum Genet. 2005 Nov;13(11):1186-91. PubMed.
  10. . An unusual case of severe hypertriglyceridemia and splenomegaly. Clin Chem. 2008 Mar;54(3):606-10; discussion 610-1. PubMed.
  11. . Inherited lipemic splenomegaly and the spectrum of apolipoprotein E p.Leu167del mutation phenotypic variation. J Clin Lipidol. 2013 Nov-Dec;7(6):566-72. Epub 2013 Sep 18 PubMed.
  12. . Description of a large family with autosomal dominant hypercholesterolemia associated with the APOE p.Leu167del mutation. Hum Mutat. 2013 Jan;34(1):83-7. Epub 2012 Oct 11 PubMed.
  13. . Apolipoprotein E gene mutations in subjects with mixed hyperlipidemia and a clinical diagnosis of familial combined hyperlipidemia. Atherosclerosis. 2012 Jun;222(2):449-55. Epub 2012 Mar 16 PubMed.
  14. . The p.Leu167del Mutation in APOE Gene Causes Autosomal Dominant Hypercholesterolemia by Down-regulation of LDL Receptor Expression in Hepatocytes. J Clin Endocrinol Metab. 2016 May;101(5):2113-21. Epub 2016 Mar 25 PubMed.
  15. . Interrogation of selected genes influencing serum LDL-Cholesterol levels in patients with well characterized NAFLD. J Clin Lipidol. 2021 Mar-Apr;15(2):275-291. Epub 2020 Dec 27 PubMed.
  16. . Familial hypercholesterolemia in an Iranian family due to a mutation in the APOE gene (first case report). J Diabetes Metab Disord. 2022 Jun;21(1):1201-1205. Epub 2022 Mar 10 PubMed.
  17. . Whole exome sequencing of familial hypercholesterolaemia patients negative for LDLR/APOB/PCSK9 mutations. J Med Genet. 2014 Aug;51(8):537-44. Epub 2014 Jul 1 PubMed.
  18. . Global molecular analysis and APOE mutations in a cohort of autosomal dominant hypercholesterolemia patients in France. J Lipid Res. 2016 Mar;57(3):482-91. Epub 2016 Jan 22 PubMed.
  19. . Interpreting the Mechanism of APOE (p.Leu167del) Mutation in the Incidence of Familial Hypercholesterolemia; An In-silico Approach. Open Cardiovasc Med J. 2017;11:84-93. Epub 2017 Sep 14 PubMed.
  20. . LDL receptor/lipoprotein recognition: endosomal weakening of ApoB and ApoE binding to the convex face of the LR5 repeat. FEBS J. 2014 Mar;281(6):1534-46. Epub 2014 Feb 6 PubMed.

Further Reading

No Available Further Reading

Protein Diagram

Primary Papers

  1. . Familial splenomegaly: macrophage hypercatabolism of lipoproteins associated with apolipoprotein E mutation [apolipoprotein E (delta149 Leu)]. J Clin Endocrinol Metab. 2000 Nov;85(11):4354-8. PubMed.

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