Mutations

PSEN1 L286V

Overview

Pathogenicity: Alzheimer's Disease : Pathogenic
ACMG/AMP Pathogenicity Criteria: PS3, PM1, PM2, PM5, PP1, PP2, PP3
Clinical Phenotype: Alzheimer's Disease
Reference Assembly: GRCh37/hg19
Position: Chr14:73664825 C>G
dbSNP ID: rs63751235
Coding/Non-Coding: Coding
Mutation Type: Point, Missense
Codon Change: CTC to GTC
Reference Isoform: PSEN1 Isoform 1 (467 aa)
Genomic Region: Exon 8
Research Models: 11

Findings

The L286V mutation was first identified in a German kindred in conjunction with the cloning of the PSEN1 gene in 1995 (Sherrington et al., 1995). The family, known as FAD2, was described previously to include 21 individuals affected by Alzheimer's disease, three with an autopsy-confirmed diagnosis. Six affected carriers and multiple unaffected non-carriers indicated segregation of the mutation with disease. Dementia was often accompanied by extrapyramidal features and myoclonus. Ancestors were traced through seven generations and the inheritance pattern was observed to be consistent with autosomal-dominant transmission (Frommelt et al., 1991).

More than a decade later, this mutation was reported in a Japanese individual with a family history of early onset dementia (Ikeuchi et al., 2008). The proband, P2712, experienced symptom onset at age 47. His pedigree included five affected individuals over three generations, all of whom displayed progressive memory impairment consistent with a clinical diagnosis of AD.

This variant was absent from the gnomAD variant database (gnomAD v2.1.1, July 2021).

Neuropathology

Neuropathology was consistent with AD in at least three affected members of the FAD2 pedigree (Frommelt et al., 1991).

Biological Effect

In HEK-293 cells transfected with APP with the Swedish mutation, the L286V mutation was found to increase the Aβ42/Aβ total ratio (Citron et al., 1997; Kulic et al., 2000). A similar effect was seen in COS-1 cells transfected with APP695—compared with cells expressing wild-type PSEN1, the L286V mutation increased the Aβ42/Aβ total ratio (Murayama et al., 1999). A subsequent cell-based study confirmed these findings and found increased production of the toxic peptide Aβ43 (Kakuda et al., 2021).

In vitro experiments with purified proteins revealed decreased Aβ40 and increased Aβ42 production (Sun et al., 2017). A cryo-electron microscopy study of the atomic structure of γ-secretase bound to an APP fragment indicated that, in wild-type PSEN1, L286 is apposed to the APP transmembrane helix, with its side-chain reaching towards the interior of the substrate-binding pore (Zhou et al., 2019; Jan 2019 news).

Although the mutation does not appear to affect Notch endoproteolysis (Kulic et al., 2000; Ikeuchi et al., 2008), it may have other effects beyond APP processing. In particular, the mutation has been reported to disrupt intracellular calcium dynamics (see Dec 2006 news; Landman et al., 2006; Oh et al., 2012; Yang et al., 2019).

Several in silico algorithms (SIFT, Polyphen-2, LRT, MutationTaster, MutationAssessor, FATHMM, PROVEAN, CADD, REVEL, and Reve in the VarCards database) predicted this variant is damaging (Xiao et al., 2021).

Pathogenicity

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.

PS3-S

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

PM1-S

Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation. L286V: Variant is in a mutational hot spot and cryo-EM data suggest residue is of functional importance.

PM2-M

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.

PM5-M

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

PP1-S

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. L286V: At least one family with >=3 affected carriers and >=1 unaffected noncarriers.

PP2-P

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

PP3-P

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

This pathogenic mutation is one of five introduced into the popular 5xFAD model of AD. The model also contains the PSEN1 mutation M146L (A>C) and three mutations in APP (Swedish, Florida, and London).

Last Updated: 07 Mar 2022

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References

News Citations

  1. CryoEM γ-Secretase Structures Nail APP, Notch Binding
  2. Beyond γ-Secretase: FAD Mutations Affect Calcium Channel via Lipid Messenger

Paper Citations

  1. . Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease. Nature. 1995 Jun 29;375(6534):754-60. PubMed.
  2. . Familial Alzheimer disease: a large, multigeneration German kindred. Alzheimer Dis Assoc Disord. 1991;5(1):36-43. PubMed.
  3. . Mutational analysis in early-onset familial dementia in the Japanese population. The role of PSEN1 and MAPT R406W mutations. Dement Geriatr Cogn Disord. 2008;26(1):43-9. Epub 2008 Jun 28 PubMed.
  4. . Mutant presenilins of Alzheimer's disease increase production of 42-residue amyloid beta-protein in both transfected cells and transgenic mice. Nat Med. 1997 Jan;3(1):67-72. PubMed.
  5. . Separation of presenilin function in amyloid beta-peptide generation and endoproteolysis of Notch. Proc Natl Acad Sci U S A. 2000 May 23;97(11):5913-8. PubMed.
  6. . Enhancement of amyloid beta 42 secretion by 28 different presenilin 1 mutations of familial Alzheimer's disease. Neurosci Lett. 1999 Apr 9;265(1):61-3. PubMed.
  7. . Switched Aβ43 generation in familial Alzheimer's disease with presenilin 1 mutation. Transl Psychiatry. 2021 Nov 3;11(1):558. PubMed.
  8. . 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.
  9. . Recognition of the amyloid precursor protein by human γ-secretase. Science. 2019 Feb 15;363(6428) Epub 2019 Jan 10 PubMed.
  10. . 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.
  11. . Modulation of transient receptor potential melastatin related 7 (TRPM7) channel by presenilins. Dev Neurobiol. 2011 Nov 18; PubMed.
  12. . Alzheimer's Disease Presenilin-1 Mutation Sensitizes Neurons to Impaired Autophagy Flux and Propofol Neurotoxicity: Role of Calcium Dysregulation. J Alzheimers Dis. 2019;67(1):137-147. PubMed.
  13. . 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.

Other Citations

  1. 5xFAD

External Citations

  1. gnomAD v2.1.

Further Reading

No Available Further Reading

Protein Diagram

Primary Papers

  1. . Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease. Nature. 1995 Jun 29;375(6534):754-60. PubMed.

Other mutations at this position

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