Pathogenicity: Alzheimer's Disease : Not Classified
Clinical Phenotype: Alzheimer's Disease
Reference Assembly: GRCh37/hg19
Position: Chr14:73640411 A>T
dbSNP ID: rs778630379
Coding/Non-Coding: Coding
Mutation Type: Point, Missense
Codon Change: TAT to TTT
Reference Isoform: PSEN1 Isoform 1 (467 aa)
Genomic Region: Exon 5


This mutation was found in a woman whose family included four members, spanning three generations, affected by early onset dementia (Kerchner and Holbrook, 2012). At 43 years of age, the proband presented with short-term memory loss that began six months earlier. A neuropsychological assessment revealed severe impairments in episodic memory, visuoconstructional ability, language, and executive function. She also had mild depression, but no changes in personality, behavior, or motor skills. The proband’s mother and a maternal uncle developed dementia in their early 50s, and her maternal grandmother showed signs of dementia at 68. The mutation was detected in both the proband and her affected uncle. The proband was homozygous for the APOE3 allele and had no mutations in APP, PSEN2, or other regions of the PSEN1 gene.

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


Neuropathological data are unavailable, but levels of AD biomarkers in the cerebrospinal fluid of the proband, including Aβ42, total tau, and 181-phosphorylated tau, were suggestive of an AD diagnosis. A brain MRI scan failed to reveal any abnormalities.

Biological Effect

The biological effect of the mutation is unknown, but it is in a region that is evolutionarily conserved between mouse and human. Moreover, a cryo-electron microscopy study of the atomic structure of γ-secretase bound to an APP fragment, showed that Y159 appears to help stabilize the hybrid β-sheet that forms between PSEN1 and APP in preparation for cleavage (Zhou et al., 2019; Jan 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).

Last Updated: 10 Sep 2021


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News Citations

  1. CryoEM γ-Secretase Structures Nail APP, Notch Binding

Paper Citations

  1. . Novel presenilin-1 Y159F sequence variant associated with early-onset Alzheimer's disease. Neurosci Lett. 2012 Dec 7;531(2):142-4. PubMed.
  2. . Recognition of the amyloid precursor protein by human γ-secretase. Science. 2019 Feb 15;363(6428) Epub 2019 Jan 10 PubMed.
  3. . 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.

External Citations

  1. gnomAD v2.1.1

Further Reading

No Available Further Reading

Protein Diagram

Primary Papers

  1. . Novel presenilin-1 Y159F sequence variant associated with early-onset Alzheimer's disease. Neurosci Lett. 2012 Dec 7;531(2):142-4. PubMed.

Other mutations at this position

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