Mutations

PSEN1 A79V

Overview

Pathogenicity: Alzheimer's Disease : Pathogenic
Clinical Phenotype: Alzheimer's Disease
Reference Assembly: GRCh37 (105)
Position: Chr14:73637653 C>T
dbSNP ID: rs63749824
Coding/Non-Coding: Coding
Mutation Type: Point, Missense
Codon Change: GCC to GTC
Reference Isoform: PSEN1 isoform 1 (467 aa)
Genomic Region: Exon 4

Findings

This mutation was first identified in three Alzheimer’s disease patients from the Netherlands. The patients (1005, 1061, and 1087) were not known to be related, but genetic markers flanking PSEN1 suggested a relatively recent common ancestor. All three patients met NINCDS-ADRDA criteria for probable AD and had a family history of dementia. The ages at onset were 53, 55, and 58, consistent with early onset AD. The mutation was absent in the 118 control individuals screened (Cruts et al., 1998).

Two years later, the A79V mutation was reported in a German individual with AD, known as patient 1. Like the previously reported Dutch cases, her symptoms began at age 58. The disease course was initially mild, but ultimately culminated in severe dementia more than 10 years after symptom onset. A similar age at onset and a 10-year disease duration were reported for this patient's mother (Finckh et al., 2000).

This mutation was described as most likely having reduced penetrance, however, with an allele count of four, and a frequency of 0.0014 percent in the gnomAD variant database (Koriath et al., 2018), and it is associated with a variable age at onset. A fifth family was identified with a later age at onset than observed previously, with greater variability within the family as well (mean age at onset of 69 years; range: 55 to 78 years) (Kauwe et al., 2007). The mutation segregated with disease in this family, with the exception of one affected individual who did not carry the mutation and was thought to have sporadic AD (age at onset: 78 years).

Three additional AD patients carrying this mutation have been identified (Rogaeva et al., 2001; Miravalle et al., 2002), and more recently the A79V mutation was detected in a screen of 439 families with a history of late-onset AD (onset at age 65 or later) (Cruchaga et al., 2012). The mutation was found in four of these families, including in one individual from a previously reported family (Kauwe et al., 2007). The sequenced individual from this family had autopsy-confirmed AD and an age of onset of 76 years. A79V was found also in a sporadic AD case (out of 1,806 screened), but not in 1,346 unrelated controls. In addition, the mutation was identified in 10 of 22 members of a family of European ancestry who developed AD symptoms in their 70s and 80s (Day et al., 2016). Overall, their phenotypes were similar to those of patients with late-onset AD (LOAD), including onset age, duration of dementia, rate of progression, and associated symptoms and comorbidities. However, the early emergence of hallucinations and delusions was more frequent in this family than in sporadic LOAD. Age at onset was not influenced by APOE allele carrier status.

The A79V mutation also has been linked to other neurodegenerative diseases. In a cohort including 490 PD patients, three individuals carried the mutation: an early onset case (44 years old at onset) and two late-onset cases (75 and 64 years old at onset). None of these carriers reported PD or AD family history. Neurological evaluation at 46, 86, and 82 years of age revealed no evidence of dementia after two, 11, and 18 years of disease onset, respectively (Ibanez et al., 2018). In addition, a 72-year-old carrier of the mutation, who suffered primarily from progressive memory loss, was diagnosed with probable dementia with Lewy bodies (Meeus et al., 2012).

 

Neuropathology

Autopsies from six mutation carriers have revealed neuropathology consistent with AD (Cruchaga et al., 2012; Day et al., 2016). In the five cases reported by Day and colleagues, Aβ plaques and neurofibrillary tangles were prominent in cortical association areas including the medial temporal lobe, and less abundant in deep gray nuclei. Mild to moderate cerebral amyloid angiopathy was reported. Lewy bodies limited to the substantia nigra pars compacta were present in one case, and arteriolosclerosis with lacunar infarcts was present in two cases. Of note, CSF Aβ42 and Aβ42/Aβ40 concentrations were found to be very high in one nondemented mutation carrier (Kauwe et al., 2007).

Biological Effect

Different experimental systems have yielded different results regarding the effects of this mutation on Aβ peptide production In HEK-293 cells expressing APP with the Swedish mutation, A79V increased the Aβ42/Aβ40 ratio by decreasing Aβ40. There was no change in Aβ42 compared to cells expressing wild-type PSEN1 (Kumar-Singh et al., 2006). In mouse embryonic fibroblasts lacking PSEN1 and PSEN2, however, expression of PSEN1 with the A79V mutation resulted in increased Aβ42 levels and an increased Aβ42/Aβ40 ratio in conditioned media compared with concentrations produced by cells expressing wild-type PSEN1. Aβ40 levels and total Aβ (combined Aβ40 and Aβ42) levels were not significantly different from wild-type controls (Kauwe et al., 2007). Moreover, in an in vitro assay using purified proteins to test this mutant's ability to cleave the APP-C99 substrate, Aβ42 levels were dramatically reduced compared with those produced by wildtype PSEN1, and Aβ40 was undetectable (Sun et al., 2017).

In silico, this mutation is predicted to be probably damaging by PolyPhen2 (Cruchaga et al., 2012).

Research Models

An iPSC cell line has been generated from skin fibroblasts of a 48-year-old presymptomatic woman carrying the mutation (Li et al., 2016). An isogenic control line, in which the mutation has been corrected, is also available (Pires et al., 2016).

Last Updated: 27 Aug 2019

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References

Paper Citations

  1. . Generation of induced pluripotent stem cells (iPSCs) from an Alzheimer's disease patient carrying an A79V mutation in PSEN1. Stem Cell Res. 2016 Mar;16(2):229-32. Epub 2016 Jan 14 PubMed.
  2. . Generation of a gene-corrected isogenic control cell line from an Alzheimer's disease patient iPSC line carrying a A79V mutation in PSEN1. Stem Cell Res. 2016 Sep;17(2):285-288. Epub 2016 Aug 7 PubMed.
  3. . Estimation of the genetic contribution of presenilin-1 and -2 mutations in a population-based study of presenile Alzheimer disease. Hum Mol Genet. 1998 Jan;7(1):43-51. PubMed.
  4. . High prevalence of pathogenic mutations in patients with early-onset dementia detected by sequence analyses of four different genes. Am J Hum Genet. 2000 Jan;66(1):110-7. PubMed.
  5. . 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.
  6. . Extreme cerebrospinal fluid amyloid beta levels identify family with late-onset Alzheimer's disease presenilin 1 mutation. Ann Neurol. 2007 May;61(5):446-53. PubMed.
  7. . Screening for PS1 mutations in a referral-based series of AD cases: 21 novel mutations. Neurology. 2001 Aug 28;57(4):621-5. PubMed.
  8. . Genetic mutations associated with presenile dementia. Neurobiol Aging. 2002 Jul-Aug; 23(S1):322.
  9. . Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer's disease families. PLoS One. 2012;7(2):e31039. PubMed.
  10. . Phenotypic Similarities Between Late-Onset Autosomal Dominant and Sporadic Alzheimer Disease: A Single-Family Case-Control Study. JAMA Neurol. 2016 Sep 1;73(9):1125-32. PubMed.
  11. . Pleiotropic Effects of Variants in Dementia Genes in Parkinson Disease. Front Neurosci. 2018;12:230. Epub 2018 Apr 10 PubMed.
  12. . DLB and PDD: a role for mutations in dementia and Parkinson disease genes?. Neurobiol Aging. 2012 Mar;33(3):629.e5-629.e18. PubMed.
  13. . 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.
  14. . 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.

Further Reading

Protein Diagram

Primary Papers

  1. . Estimation of the genetic contribution of presenilin-1 and -2 mutations in a population-based study of presenile Alzheimer disease. Hum Mol Genet. 1998 Jan;7(1):43-51. PubMed.

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