APOE E98fs

Mature Protein Numbering: E80fs

Other Names: E97fs


Clinical Phenotype: Alzheimer's Disease, Cardiovascular Disease, Hyperlipoproteinemia Type III
Reference Assembly: GRCh37/hg19
Position: Chr19:45411844 G>-
Transcript: NM_000041; ENSG00000130203
dbSNP ID: rs527236160
Coding/Non-Coding: Coding
DNA Change: Deletion
Expected RNA Consequence: Deletion
Expected Protein Consequence: Frame Shift
Codon Change: GAA to AAC
Reference Isoform: APOE Isoform 1
Genomic Region: Exon 4


In homozygous form, this variant results in the ablation of ApoE protein. It is a single-nucleotide deletion that causes a frameshift leading to a truncated protein that is rapidly degraded (Mak et al., 2014). Although the literature includes other descriptions of patients with ApoE loss, the report of this variant is the only one that included the examination of neurological features and involved complete ablation due to homozygosity.

Ee98Nfs was identified by whole-exome sequencing of the DNA of a 40-year-old African American man with a severe form of the lipid metabolism disease hyperlipoproteinemia type III (HLPP3), a.k.a. familial dysbetalipoproteinemia. The man was homozygous for the mutation and had no detectable ApoE in blood. Surprisingly, the authors found no abnormalities in the man’s vision, cognition, neurological profile, retinal function, brain MRI, or cerebrospinal fluid levels of biomarkers for Alzheimer’s disease (AD) Aβ42, total tau, and phospho-tau 181.

Of note, although the patient’s neuropsychological performance was essentially normal, he was reported as having a learning disability, possibly dyslexia. In addition, his global score on the Mini-Mental State Examination was within the normal range, but he had deficits in subdomain tests of memory, language, visuospatial abilities, and executive function. Unlike progressive neurodegenerative deficits, however, these impairments appeared to be stable, and the authors noted in a subsequent communication that the patient had a profoundly disadvantaged childhood which could have contributed to his deficiencies (Malloy et al., 2015).

Several researchers have commented on the implications of these findings for AD. It has been noted that the proband is still relatively young and neurological alterations caused by the ApoE deficiency might emerge later (Lane-Donovan and Herz, 2014; Belloy et al., 2020). Whether the mutation is responsible for some or all of the cognitive deficits of the proband and, if so, whether these deficits arose from neurodevelopmental alterations or from non-amyloid, prodromal AD pathology have also been noted as important, unresolved questions (Belloy et al., 2020; Cullum and Weiner, 2015). In addition, it has been suggested that the mutation may have induced developmental changes that compensate for the negative consequences of ApoE deficiency (Laskowitz and Kernagis, 2014). It is also possible that the proband’s genetic ancestry may mitigate the negative effects of ApoE reduction as it has been suggested to reduce AD risk conferred by the APOE4 allele (Belloy et al., 2020).

Importantly, partial loss of ApoE seems to be tolerated in heterozygote carriers of other loss-of-function APOE variants, with carriers remaining cognitively healthy beyond age 75 (Chemparathy et al., 2024, see APOE W5Ter).  Moreover, when these loss-of-function variants were present on the same chromosome as the major AD risk variant C130R (APOE4), they appeared to decrease AD risk supporting the safety and potential efficacy of therapies that aim to reduce ApoE in APOE4 carriers.

Non-neurological Effects 

The proband lacked clear symptoms of cardiovascular disease, except for a hint of myocardial ischemia on treadmill testing and mild atherosclerosis (Mak et al., 2014). However, he had multiple, large lipid deposits under his skin known as xanthomas, and his blood lipid profile was severely abnormal. He had extremely high cholesterol levels and a high ratio of cholesterol to triglycerides in very low-density lipoproteins (VLDL), with elevated levels of small diameter high-density lipoproteins (HDL). Also, his intermediate-density lipoproteins (IDL), LDL, and VLDL contained elevated levels of ApoA-I and ApoA-IV. ApoC-III and ApoC-IV levels were decreased in VLDL. Consistent with these findings, other patients with ApoE deficiency have been diagnosed with HLPP3, with similar alterations of their blood lipid and lipoprotein profiles (see c.237-1A>G, A227_E230del, and W228Ter; also, Mabuchi et al., 1989; Kurosaka et al., 1991).

The authors also detected in the proband’s DNA 645 rare and deleterious variants, nine mapping to genes in lipid metabolism pathways (Mak et al., 2014). They noted that two of the variants, a homozygous variant in the multi-drug resistance transport gene ABCC2 and a heterozygous variant in the hepatic lipase gene LIPC, may affect phenotype severity. The LIPC variant might contribute to the severity of the patient’s HLPP3, and both variants might facilitate the formation of abnormal lamellar particles observed in electron micrographs of the proband’s IDL and LDL.

The E98fs mutation was also found in heterozygous form in DNA samples from the proband’s mother and two daughters. As expected, these individuals had ApoE levels that were approximately half those of controls and their blood lipid profiles were altered, but not as dramatically as those of the proband. In all cases, the mutation was on an APOE3 background.

This variant is absent from the gnomAD variant database (v2.1.1, Apr 2022).

Biological effect

This variant is a deletion of the third nucleotide in the codon for glutamic acid 97, predicting a change of glutamic acid 98 to asparagine followed by a stop codon (Mak et al., 2014). The resulting truncated protein, lacking both the receptor- and lipid-binding regions of ApoE, was undetectable in carriers’ blood samples.

Although the effect of this variant on the central nervous system is unknown, one might expect that in homozygous form, it could have a substantial impact given ApoE’s involvement in multiple brain functions (for reviews see Koutsodendris et al., 2021; Raulin et al., 2022). Under physiological conditions, ApoE is produced and secreted primarily by astrocytes and activated microglia and expressed at low levels in neurons. It plays key roles in metabolizing and transporting lipids to neurons, and facilitates synaptogenesis, axonal regeneration, as well as neural stem cell maintenance and differentiation.

How much a loss or reduction of ApoE function might affect or contribute to the pathology of AD has been an important question in the field (see e.g. Belloy et al., 2019). As noted above, the cognitive health of several aged, heterozygous carriers of this variant suggests a 50 percent loss is benign and perhaps protective when in phase with APOE4 (Chemparathy et al., 2024; Vance et al., 2024). Data from mouse models are mixed. In general, reducing or eliminating ApoE in mouse models of amyloid deposition appears to reduce amyloid accumulation, but selectively reducing ApoE in astrocytes, microglia, neurons, or brain endothelial cells suggests cell type-specific effects that can be beneficial, neutral, or harmful (for more information, see APOE Loss of Function Variants).

Last Updated: 26 Mar 2024


  1. The recent report by Mak et al. is a thorough examination of an individual lacking ApoE. This case report is remarkable for its examination of neurological function and cognition, which appears entirely normal. The dyslipidemia observed in this individual is in line with previous reports of the effect of inactivation of APOE genes.

    While the report has elicited considerable attention, it is generally consistent with phenotypes observed in ApoE knockout mice. The ApoE null mice do not exhibit cognitive or other behavioral deficits. In the brain, ApoE is the principal apolipoprotein and is responsible for trafficking cholesterol and phospholipids throughout the brain. However, other apolipoproteins are found in the CSF of normal and diseased men and mice, most prominently ApoA1. The origin of the CSF ApoA1 remains controversial, but could functionally compensate for ApoE. It would be of interest to examine CSF to determine the abundance and lipidation status of other apoplipoproteins in this individual. While much has been made about the relevance of this case report to AD risk, it is not clear to me that it provides much additional insight into disease pathogenesis. 

    View all comments by Gary Landreth
  2. This recent paper by Mak et al., describes the effects of ApoE deficiency in a 40-year-old human patient. The results revealed that, despite complete absence of ApoE, the patient had normal vision, exhibited normal cognitive neurological and retinal function, and had normal magnetic resonance in the brain and normal CSF tau and Aβ42 levels. In contrast, ApoE deficiency had a profound effect on the levels and composition of serum lipoproteins. In their concluding remarks the authors suggest that “functions of apoE in the brain and eye are not essential … and that targeted knockdown of ApoE might be a therapeutic modality.”

    Animal model studies revealed that the pathological effects of ApoE deficiency are accentuated following brain insults such as head trauma (Chen et al., 1997). Accordingly, as the patient studied was in his 40s, it is likely that under challenging conditions, such as AD or aging, lack of ApoE will have pronounced effects that are not observed at a relatively young age.

    There is a growing body of evidence based on animal models that the pathological effects of ApoE4 may be due to both loss-of-function and gain-of-toxic-function mechanisms (for review, see Michaelson 2014). Examples of the loss-of-function effect are the findings that ApoE4 is hypolipidated in targeted replacement mice and that correction of this impairment reverses key pathological effects in ApoE4 mice (Boehm-Cagan and Michaelson, 2014). A counterexample of a gain-of-toxicity mechanism is the finding that ApoE4 stimulates the accumulation of Aβ into hippocampal neurons following activation of the amyloid cascade and that this effect is significantly more pronounced than in either apoE3 mice or ApoE deficient mice (Zepa et al., 2011). 

    In view of this, we believe that it is important that the therapeutic focus remain on apoE4 versus apoE3 and not shift to targeted knockdown of ApoE.


    . Motor and cognitive deficits in apolipoprotein E-deficient mice after closed head injury. Neuroscience. 1997 Oct;80(4):1255-62. PubMed.

    . Reversal of apoE4-driven brain pathology and behavioral deficits by bexarotene. J Neurosci. 2014 May 21;34(21):7293-301. PubMed.

    . ApoE4-Driven Accumulation of Intraneuronal Oligomerized Aβ42 following Activation of the Amyloid Cascade In Vivo Is Mediated by a Gain of Function. Int J Alzheimers Dis. 2011 Feb 15;2011:792070. PubMed.

    . APOE ε4: the most prevalent yet understudied risk factor for Alzheimer's disease. Alzheimers Dement. 2014 Nov;10(6):861-8. Epub 2014 Sep 10 PubMed.

    View all comments by Daniel Michaelson

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Mutations Citations

  1. APOE C130R (ApoE4)
  2. APOE W5Ter
  3. APOE c.237-1A>G
  4. APOE A227_E230del
  5. APOE W228Ter

Mutation Data Table Citations

  1. APOE Loss of Function Variants

Paper Citations

  1. . Effects of the absence of apolipoprotein e on lipoproteins, neurocognitive function, and retinal function. JAMA Neurol. 2014 Oct;71(10):1228-36. PubMed.
  2. . Apolipoprotein E and neurocognitive function--in reply. JAMA Neurol. 2015 Apr;72(4):479. PubMed.
  3. . Is apolipoprotein e required for cognitive function in humans?: implications for Alzheimer drug development. JAMA Neurol. 2014 Oct;71(10):1213-5. PubMed.
  4. . A Quarter Century of APOE and Alzheimer's Disease: Progress to Date and the Path Forward. Neuron. 2019 Mar 6;101(5):820-838. PubMed.
  5. . Apolipoprotein E and neurocognitive function. JAMA Neurol. 2015 Apr;72(4):478. PubMed.
  6. . Congenital absence of apolipoprotein E and neurological function. JAMA Neurol. 2014 Dec;71(12):1578-9. PubMed.
  7. . APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer's disease pathology. Neuron. 2024 Apr 3;112(7):1110-1116.e5. Epub 2024 Jan 31 PubMed.
  8. . A young type III hyperlipoproteinemic patient associated with apolipoprotein E deficiency. Metabolism. 1989 Feb;38(2):115-9. PubMed.
  9. . Apolipoprotein E deficiency with a depressed mRNA of normal size. Atherosclerosis. 1991 May;88(1):15-20. PubMed.
  10. . Apolipoprotein E and Alzheimer's Disease: Findings, Hypotheses, and Potential Mechanisms. Annu Rev Pathol. 2022 Jan 24;17:73-99. Epub 2021 Aug 30 PubMed.
  11. . Lipoproteins in the Central Nervous System: From Biology to Pathobiology. Annu Rev Biochem. 2022 Jun 21;91:731-759. Epub 2022 Mar 18 PubMed.
  12. . Report of the APOE4 National Institute on Aging/Alzheimer Disease Sequencing Project Consortium Working Group: Reducing APOE4 in Carriers is a Therapeutic Goal for Alzheimer's Disease. Ann Neurol. 2024 Jan 5; PubMed.

Further Reading

No Available Further Reading

Protein Diagram

Primary Papers

  1. . Effects of the absence of apolipoprotein e on lipoproteins, neurocognitive function, and retinal function. JAMA Neurol. 2014 Oct;71(10):1228-36. PubMed.

APOE Loss of Function Variants

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