Overview

Pathogenicity: Alzheimer's Disease : Not Classified
ACMG/AMP Pathogenicity Criteria: PS3, PM2, PP3
Clinical Phenotype: Alzheimer's Disease
Position: (GRCh37/hg19):Chr1:227073241 T>G
Position: (GRCh38/hg38):Chr1:226885540 T>G
dbSNP ID: NA
Coding/Non-Coding: Coding
DNA Change: Substitution
Expected RNA Consequence: Substitution
Expected Protein Consequence: Missense
Codon Change: ATC to AGC
Reference Isoform: PSEN2 Isoform 1 (448 aa)
Genomic Region: Exon 6

Findings

Detailed information on carriers of this variant is unavailable. However, it was classified as “Likely Pathogenic” for Alzheimer’s disease (AD) and eligible for inclusion in clinical trials organized by the Dominantly Inherited Alzheimer Network Trials Unit (DIAN-TU) to test disease-modifying treatments for Alzheimer’s disease (Liu et al., 2025). Data used to determine DIAN-TU eligibility include family history suggesting an autosomal dominant pattern of inheritance, documentation of amnestic-predominant, progressive cognitive impairment leading to AD dementia (preferably with AD biomarkers and/or neuropathological confirmation of AD in at least one family member), low frequency of the variant in a large population database such as the gnomAD, evidence of co-segregation with disease within a family, and assessment of Aβ42 and Aβ40 levels in a cell-based assay. Additional supportive criteria include conservation of the affected amino acid between PSEN1 and PSEN2, presence of other AD pathogenic variants at the same amino acid site, and in silico prediction of damaging effects.

This variant was absent from the gnomAD variant database (gnomAD v4.1.0).

Neuropathology
Neuropathological data are unavailable.

Biological Effect
In a cell-based assay, this variant slightly increased Aβ42 levels, but did not alter the Aβ42/Aβ40 ratio significantly compared to wildtype PSEN2 (Marsh et al., 2025). This variant’s PHRED-scaled CADD score, which integrates diverse information in silico.

Pathogenicity

Alzheimer's Disease : Not Classified*

*Carriers of this variant are eligible for inclusion in clinical trials organized by the Dominantly Inherited Alzheimer Network Trials Unit (DIAN-TU) to test disease-modifying treatments for Alzheimer’s disease (Liu et al., 2025). Alzforum has not yet classified this variant because carrier data are not yet published.

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

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References

Paper Citations

1. Liu H, Marsh TW, Shi X, Renton AE, Bowling KM, Ziegemeier E, Wang G, Cao Y, Aristel A, Li J, Dickson A, Perrin RJ, Goate AM, Fernández V, Day GS, Doering M, Daniels A, Gordon BA, Benzinger TL, Hassenstab J, Ibanez L, Supnet-Bell C, Xiong C, Allegri R, Berman SB, Fox NC, Ryan N, Huey ED, Vöglein J, Noble JM, Roh JH, Jucker M, Laske C, Ikeuchi T, Sanchez-Valle R, Schofield PR, Chrem Mendez P, Chhatwal JP, Farlow M, Lee JH, Levey AI, Levin J, Lopera F, Martins R, Niimi Y, Rosa-Neto P, Morris JC, Bateman RJ, Karch CM, Cruchaga C, McDade E, Llibre-Guerra JJ. The landscape of autosomal-dominant Alzheimer's disease: global distribution and age of onset. Brain. 2025 Feb 4; Epub 2025 Feb 4 PubMed.
2. Marsh JA, Huang G, Bowling K, Renton AE, Ziegemeier E, Ball T, Pottier C, Cruchaga C, Day GS, Bateman RJ, Llibre-Guerra JJ, McDade E, Karch CM. Evaluating pathogenicity of variants of unknown significance in APP, PSEN1, and PSEN2. Neurotherapeutics. 2025 Jan 27;:e00527. Epub 2025 Jan 27 PubMed.

Further Reading

No Available Further Reading