PSEN1 S290_S319delinsC G>A (ΔE9)

Other Names: ΔE9, Δ9, c.869-1G>A


Pathogenicity: Alzheimer's Disease : Pathogenic
ACMG/AMP Pathogenicity Criteria: PS1, PS3, PS4, PM1, PM2, PP1, PP3
Clinical Phenotype: Alzheimer's Disease, Spastic Paraparesis
Reference Assembly: GRCh37/hg19
Position: Chr14:73673093 G>A
dbSNP ID: rs63750219
Coding/Non-Coding: Both
DNA Change: Substitution
Expected RNA Consequence: Splicing Alteration
Expected Protein Consequence: Deletion-Insertion
Genomic Region: Intron 8, Exon 9


This point mutation at a splice site in intron 8 results in the exclusion of exon 9 from mRNA transcripts. It is one of several known mutations that result in exon 9 exclusion, which are known as ΔE9, delE9, E9, or deltaE9. This specific mutation (G>A) has been detected in four families with very  different ancestries. A similar point mutation (G>T) at the same position has also been reported in two families and appears to have a similar effect on splicing.

The G>A mutation was first reported in a large Japanese pedigree known as TK-1 (Sato et al., 1998). The reported pedigree shows 11 affected family members over five generations. The mean age of onset in this family was reported as 47.50 ± 3.29 and the mean age at death was 54.62 ± 4.37. Symptoms included classic features of AD (e.g., memory impairment, lack of spontaneity, disorientation), but also some extrapyramidal signs and a progressive form of spastic paralysis with rigidity which started in the lower limbs.

The mutation appeared to segregate with disease in TK-1. Of the 11 family members examined, the mutation was present in the proband and in four asymptomatic individuals under the mean age of onset for the family. The mutation was absent in six unaffected family members and in 98 healthy Japanese controls.

The second pedigree, an Australian family known as EOFAD-2, were of Anglo-Celtic origin (Brooks et al., 2003). The reported pedigree shows 14 affected individuals over four generations. The clinical phenotype consisted of progressive cognitive decline with some individuals displaying symptoms of spastic paraparesis (spasticity of the lower limbs, gait disturbance, etc.). The mean onset age was 44.9 years (range: 36 to 52 years) with a trend toward those individuals with spasticity displaying a slightly later onset. A diagnosis of AD was confirmed by autopsy in four individuals. The G>A splice acceptor mutation was found in the proband and test results from 11 other members of the EOFAD-2 family were consistent with segregation of the mutation with the disease phenotype (dementia, spastic paraparesis, or both) in an autosomal-dominant manner.

The mutation was also found in a U.K. genetic screen of patients with dementia (Koriath et al., 2018). The family of the mutation carrier had at least three members, including a first-degree relative, diagnosed with AD across two generations. The carrier’s AD symptoms emerged at age 57.

In addition, the mutation was identified in two male siblings of a Turkish family including 39 members spanning four generations with nine affected individuals (Doğan et al., 2022). The carriers' first clinical symptom was memory impairment, surfacing at ages 40 and 38 years. Both men also suffered from behavioral symptoms, delusions/hallucinations, spastic paraparesis, and myoclonus. 

This mutation was absent from genetic variant databases, including ExAC and gnomAD.


Two cases from the TK-1 family were examined neuropathologically (Tabira et al., 2002). The subjects were identical twin brothers with clinical histories typical of their family, including onset at age 45 and 46. One brother developed memory disturbances at age 45, followed by spastic paraparesis with muscular rigidity. He deteriorated gradually, becoming severely demented, with myoclonus and epilepsy, and died at age 64. The other brother first reported trembling and lower leg pain at age 46. His memory impairment became apparent later, developing over time into severe dementia. He also developed progressive spastic paraplegia with myoclonus and seizures. He died at age 61.

In both cases senile plaques were numerous in the hippocampus, frontal, temporal, and parietal cortices, moderate in the occipital cortex, and mild in the cerebellar cortex and the inferior olive. Some plaques had an amyloid core, and mild neuritic changes were observed. Neurofibrillary tangles were likewise abundant and amyloid angiopathy was scattered. Cotton-wool plaques could be seen by hematoxylin and eosin staining. The neuropathology of one of these cases was further investigated in the context of comparison to other mutations that involve exon 9 exclusion (Mann et al., 2001).

Neuropathological findings are also available from four cases within the EOFAD-2 kindred (Brooks et al., 2003). All four cases were affected by early onset dementia, but none had reported symptoms of spasticity. The neuropathology in all four was sufficient to meet NIA-Reagan criteria for Alzheimer's disease, with numerous neurofibrillary tangles and plaques in the hippocampus and cerebral cortex, and neuronal loss throughout the cortex. The plaques were both of the large, cotton-wool type and the neuritic type. Congophilic angiopathy was also noted as being present in all four brains.

Magnetic resonance imaging of the brains of the two Turkish carriers revealed atrophy in the parahippocampal gyrus (Doğan et al., 2022).

Biological Effect

This point mutation occurs at a splice acceptor site in intron 8 and causes aberrant splicing leading to the generation of PSEN1 mRNA lacking exon 9 and proteins that lack 28 amino acid residues (291-319). The mutation also causes an amino acid change (S290C) at the splice junction of exons 8 and 10. Koriath and colleagues reported a CADD score of 26.7, predicted to be amongst the top one percent of deleterious variants in the human genome (Koriath et al., 2018), and Xiao and colleagues reported multiple in silico algorithms predicted the mutation was damaging (Xiao et al., 2021). 

The following summary refers to studies of PSEN1 mutants that result in the exclusion of exon 9 (denoted here as PSEN1ΔE9). Multiple in vitro and in vivo assays have shown that PSEN1ΔE9 impairs endoproteolytic processing of PSEN1 (Thinakaran et al., 1996, Lee et al., 1997) and alters the production of Aβ42 and Aβ40 peptides resulting in an increased Aβ42/Aβ40 ratio (Borchelt et al., 1996, Steiner et al., 1999, Dumanchin et al., 2006; Kumar-Singh et al., 2006, Bentahir et al., 2006, Woodruff et al., 2013, Cacquevel et al., 2012, Sun et al., 2017). Moreover, studies surveying the production of Aβ peptides of different lengths have indicated that these mutations result in increased levels of longer Aβ peptides, and decreased levels of shorter peptides (Chávez-Gutiérrez et al., 2012; Svedružić et al., 2012; Kakuda et al., 2021). Chávez-Gutiérrez and colleagues proposed this is the result of impairment of the fourth γ-secretase cleavage in the two Aβ production lines that sequentially digest Aβ49 and Aβ48 into shorter peptides (Chávez-Gutiérrez et al., 2012).

Consistent with these findings, three more recent studies revealed PSEN1ΔE9 mutants decrease the Aβ (37 + 38 + 40) / (42 + 43) ratio and the Aβ37/Aβ42 ratio, both of which reflect γ-processivity, compared with cells expressing wildtype PSEN1 (Apr 2022 news; Petit et al., 2022; Liu et al., 2022). The two ratios were reported to outperform the Aβ42/Aβ40 ratio as indicators of AD pathogenicity, with the former correlating with AD age at onset. Moreover, a follow-up study reported in a preprint, combined the Aβ (37 + 38 + 40) / (42 + 43) ratio with the commonly used Aβ42/Aβ40 ratio (a measure of the relative production of aggregation-prone Aβ) to yield a composite measure which reflects γ-secretase function as a percentage of wildtype activity (Schulz et al., 2023). This composite score (36.87 for PSEN1ΔE9) was strongly associated, not only with age at onset, but with biomarker and cognitive trajectories.

Exon 9 deletion mutations may also affect PSEN1 transcription. In a bacterial artificial chromosome (BAC)-based expression model, PSEN1ΔE9-expressing cells exhibited reduced PSEN1 gene expression and partial loss of function relative to cells expressing wild-type PSEN1 (Ahmadi et al., 2014).

The absence of exon 9 may impair Notch processing as well. Although one study found no effect of the mutation on this substrate (Chávez-Gutiérrez et al., 2012), others have reported impaired Notch S3 cleavage and corresponding alterations in the differentiation and self-renewal of neural progenitor cells in the adult mouse brain (Bentahir et al., 2006; Veeraraghavalu et al., 2010; May 2010 news).

PSEN1ΔE9 mutations have also been implicated in the disruption of several intracellular functions. For example, by lowering PIP2 levels, PSEN1ΔE9 appears to block a cation channel that mediates capacitive calcium entry (Landman et al., 2006; Dec 2006 news). In addition, impairments in endocytosis, cholesterol homeostasis, autophagy, and APP intracellular localization have been reported (Woodruff et al., 2016; Oct 2016 news; Cho et al., 2019; Oh and Chung, 2017). In addition, alterations in tight and adherens junction protein expression, as well as in efflux properties, were found in iPSC-derived brain endothelial cells, a model of blood-brain barrier function (Oikari et al., 2020).

Interestingly, PSEN1 was reported to play a key role in ApoE secretion and cytoplasmic localization. In experiments with PSEN-deficient fibroblasts, PSEN1ΔE9 transfection was less able to rescue these functions compared with transfection of wildtype PSEN1 (Islam et al., 2022).

PSEN1ΔE9 had little effect on microglia, a cell type that normally expresses very low levels of PSEN1, although it appeared to weaken the cells’ inflammatory response (Konttinen et al., 2019, Sep 2019 news).


Alzheimer's Disease : Pathogenic

This variant fulfilled the following criteria based on the ACMG/AMP guidelines. See a full list of the criteria in the Methods page.


Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.


Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. S290_S319delinsC G>A : Functional data derive from assays involving exon 9 deletion mutants, not necessarily this specific variant.


The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. S290_S319delinsC G>A : The variant was reported in 3 or more unrelated patients with the same phenotype, and absent from controls.


Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.


Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. *Alzforum uses the gnomAD variant database.


Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease: *Alzforum requires at least one affected carrier and one unaffected non-carrier from the same family to fulfill this criterion. S290_S319delinsC G>A : Cosegregation demonstrated in >1 family.


Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). *In most cases, Alzforum applies this criterion when the variant’s PHRED-scaled CADD score is greater than or equal to 20.

Pathogenic (PS, PM, PP) Benign (BA, BS, BP)
Criteria Weighting Strong (-S) Moderate (-M) Supporting (-P) Supporting (-P) Strong (-S) Strongest (BA)

Research Models

Multiple mouse models that express PSEN1 lacking exon 9 have been developed. One line, referred to as S-9 (Lee et al., 1997), was subsequently bred to an APP-transgenic mouse to generate a double-transgenic (APPSwe/PSEN1dE9), which has a more severe phenotype than either of the parental lines. Another double-transgenic model was made by co-injecting vectors expressing PSEN1ΔE9 and APP with the Swedish mutation (APPswe/PSEN1dE9 (Borchelt mice)). Although cotton-wool plaques are sometimes prominent in the brains of AD patients with ΔE9 mutations, this pathology has not been observed in ΔE9 mouse models.

In addition, induced pluripotent stem cell lines derived from patients have been used to generate neurons (Woodruff et al., 2013) astrocytes (Oksanen et al., 2017), and brain endothelial cells (Oikari et al., 2020) which display several features of AD pathology.

Last Updated: 14 Oct 2023


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News Citations

  1. Ratio of Short to Long Aβ Peptides: Better Handle on Alzheimer's than Aβ42/40?
  2. Notch Your Average Joe—Grounds for PS1 Neurogenesis Inhibition?
  3. Beyond γ-Secretase: FAD Mutations Affect Calcium Channel via Lipid Messenger
  4. Cholesterol Trafficking Takes a Hit in Alzheimer’s Neurons
  5. Among AD Mutations, Only ApoE4 Seems to Hobble Microglia

Paper Citations

  1. . Hyperaccumulation of FAD-linked presenilin 1 variants in vivo. Nat Med. 1997 Jul;3(7):756-60. PubMed.
  2. . Defective Transcytosis of APP and Lipoproteins in Human iPSC-Derived Neurons with Familial Alzheimer's Disease Mutations. Cell Rep. 2016 Oct 11;17(3):759-773. PubMed.
  3. . PSEN1 Mutant iPSC-Derived Model Reveals Severe Astrocyte Pathology in Alzheimer's Disease. Stem Cell Reports. 2017 Dec 12;9(6):1885-1897. Epub 2017 Nov 16 PubMed.
  4. . Altered Brain Endothelial Cell Phenotype from a Familial Alzheimer Mutation and Its Potential Implications for Amyloid Clearance and Drug Delivery. Stem Cell Reports. 2020 May 12;14(5):924-939. Epub 2020 Apr 9 PubMed.
  5. . Splicing mutation of presenilin-1 gene for early-onset familial Alzheimer's disease. Hum Mutat. 1998;Suppl 1:S91-4. PubMed.
  6. . Alzheimer's disease with spastic paraparesis and 'cotton wool' plaques: two pedigrees with PS-1 exon 9 deletions. Brain. 2003 Apr;126(Pt 4):783-91. PubMed.
  7. . Predictors for a dementia gene mutation based on gene-panel next-generation sequencing of a large dementia referral series. Mol Psychiatry. 2018 Oct 2; PubMed.
  8. . Clinical and Molecular Findings in a Turkish Family Who Had a (c.869- 1G>A) Splicing Variant in PSEN1 Gene with A Rare Condition: The Variant Alzheimer's Disease with Spastic Paraparesis. Curr Alzheimer Res. 2022;19(3):223-235. PubMed.
  9. . Alzheimer's disease with spastic paresis and cotton wool type plaques. J Neurosci Res. 2002 Nov 1;70(3):367-72. PubMed.
  10. . Cases of Alzheimer's disease due to deletion of exon 9 of the presenilin-1 gene show an unusual but characteristic beta-amyloid pathology known as 'cotton wool' plaques. Neuropathol Appl Neurobiol. 2001 Jun;27(3):189-96. PubMed.
  11. . APP, PSEN1, and PSEN2 Variants in Alzheimer's Disease: Systematic Re-evaluation According to ACMG Guidelines. Front Aging Neurosci. 2021;13:695808. Epub 2021 Jun 18 PubMed.
  12. . Endoproteolysis of presenilin 1 and accumulation of processed derivatives in vivo. Neuron. 1996 Jul;17(1):181-90. PubMed.
  13. . Familial Alzheimer's disease-linked presenilin 1 variants elevate Abeta1-42/1-40 ratio in vitro and in vivo. Neuron. 1996 Nov;17(5):1005-13. PubMed.
  14. . The biological and pathological function of the presenilin-1 Deltaexon 9 mutation is independent of its defect to undergo proteolytic processing. J Biol Chem. 1999 Mar 19;274(12):7615-8. PubMed.
  15. . Biological effects of four PSEN1 gene mutations causing Alzheimer disease with spastic paraparesis and cotton wool plaques. Hum Mutat. 2006 Oct;27(10):1063. PubMed.
  16. . Mean age-of-onset of familial alzheimer disease caused by presenilin mutations correlates with both increased Abeta42 and decreased Abeta40. Hum Mutat. 2006 Jul;27(7):686-95. PubMed.
  17. . Presenilin clinical mutations can affect gamma-secretase activity by different mechanisms. J Neurochem. 2006 Feb;96(3):732-42. PubMed.
  18. . The presenilin-1 ΔE9 mutation results in reduced γ-secretase activity, but not total loss of PS1 function, in isogenic human stem cells. Cell Rep. 2013 Nov 27;5(4):974-85. Epub 2013 Nov 14 PubMed.
  19. . Alzheimer's disease-linked mutations in presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. PLoS One. 2012;7(4):e35133. PubMed.
  20. . Analysis of 138 pathogenic mutations in presenilin-1 on the in vitro production of Aβ42 and Aβ40 peptides by γ-secretase. Proc Natl Acad Sci U S A. 2017 Jan 24;114(4):E476-E485. Epub 2016 Dec 5 PubMed.
  21. . The mechanism of γ-Secretase dysfunction in familial Alzheimer disease. EMBO J. 2012 May 16;31(10):2261-74. Epub 2012 Apr 13 PubMed.
  22. . Modulation of γ-secretase activity by multiple enzyme-substrate interactions: implications in pathogenesis of Alzheimer's disease. PLoS One. 2012;7(3):e32293. PubMed.
  23. . Switched Aβ43 generation in familial Alzheimer's disease with presenilin 1 mutation. Transl Psychiatry. 2021 Nov 3;11(1):558. PubMed.
  24. . Aβ profiles generated by Alzheimer's disease causing PSEN1 variants determine the pathogenicity of the mutation and predict age at disease onset. Mol Psychiatry. 2022 Jun;27(6):2821-2832. Epub 2022 Apr 1 PubMed.
  25. . Identification of the Aβ37/42 peptide ratio in CSF as an improved Aβ biomarker for Alzheimer's disease. Alzheimers Dement. 2022 Mar 12; PubMed.
  26. . Functional variations in gamma-secretase activity are critical determinants of the clinical, biomarker, and cognitive progression of autosomal dominant Alzheimer's disease. 2023 Jul 25 10.1101/2023.07.04.547688 (version 2) bioRxiv.
  27. . Familial Alzheimer's disease coding mutations reduce Presenilin-1 expression in a novel genomic locus reporter model. Neurobiol Aging. 2014 Feb;35(2):443.e5-443.e16. PubMed.
  28. . Presenilin 1 mutants impair the self-renewal and differentiation of adult murine subventricular zone-neuronal progenitors via cell-autonomous mechanisms involving notch signaling. J Neurosci. 2010 May 19;30(20):6903-15. PubMed.
  29. . Presenilin mutations linked to familial Alzheimer's disease cause an imbalance in phosphatidylinositol 4,5-bisphosphate metabolism. Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19524-9. PubMed.
  30. . Elevated cellular cholesterol in Familial Alzheimer's presenilin 1 mutation is associated with lipid raft localization of β-amyloid precursor protein. PLoS One. 2019;14(1):e0210535. Epub 2019 Jan 25 PubMed.
  31. . Activation of transient receptor potential melastatin 7 (TRPM7) channel increases basal autophagy and reduces amyloid β-peptide. Biochem Biophys Res Commun. 2017 Nov 4;493(1):494-499. Epub 2017 Sep 1 PubMed.
  32. . Presenilin Is Essential for ApoE Secretion, a Novel Role of Presenilin Involved in Alzheimer's Disease Pathogenesis. J Neurosci. 2022 Feb 23;42(8):1574-1586. Epub 2022 Jan 5 PubMed.
  33. . PSEN1ΔE9, APPswe, and APOE4 Confer Disparate Phenotypes in Human iPSC-Derived Microglia. Stem Cell Reports. 2019 Oct 8;13(4):669-683. Epub 2019 Sep 12 PubMed.

Other Citations

  1. APPSwe/PSEN1dE9

Further Reading


  1. . Variable presentation of Alzheimer's disease and/or spastic paraparesis phenotypes in pedigrees with a novel PS-1 exon 9 gene deletion or exon 9 splice acceptor mutations. Neurobiol Aging. 2000 May-Jun; 21(Supp1):25.

Protein Diagram

Primary Papers

  1. . Splicing mutation of presenilin-1 gene for early-onset familial Alzheimer's disease. Hum Mutat. 1998;Suppl 1:S91-4. PubMed.

Other mutations at this position


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