Overview

Pathogenicity: Alzheimer's Disease : Not Classified
ACMG/AMP Pathogenicity Criteria: PS3, PM1, PM2, PP2, PP3
Clinical Phenotype: Alzheimer's Disease
Position: (GRCh38/hg38):Chr21:25897619 C>T
Position: (GRCh37/hg19):Chr21:27269931 C>T
dbSNP ID: NA
Coding/Non-Coding: Coding
DNA Change: Substitution
Expected RNA Consequence: Substitution
Expected Protein Consequence: Missense
Codon Change: GCA to GTA
Reference Isoform: APP Isoform APP770 (770 aa)
Genomic Region: Exon 16

Findings

The A673V mutation in APP is unusual in that it appears to be recessive rather than autosomal-dominant.

It was detected as a homozygous allele in two Italian siblings with symptoms of Alzheimer’s disease. Genetic testing of multiple relatives revealed many heterozygous carriers who were not affected by AD. The proband presented with behavioral changes and cognitive deficits at the age of 36, and he was diagnosed with early onset Alzheimer's disease. His symptoms evolved into severe dementia with spastic tetraparesis (spasticity affecting all four limbs), and he died at 46 years old. The proband’s younger sister had mild cognitive impairment at the time the report was published.

Genotyping of relatives from both the maternal and paternal branches of the family revealed six heterozygous carriers who were unaffected by AD. The siblings’ parents were deceased and therefore could not be genotyped, but they are presumed to be heterozygous carriers and did not have AD at the time of their deaths (both at 60-plus). In addition to screening the APP gene, PSEN1, PSEN2, MAPT, and progranulin (PGRN) were interrogated, but no additional mutations were found (Di Fede et al., 2009).

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

Neuropathology

Autopsy of the proband confirmed a diagnosis of definite AD by CERAD criteria. Extensive Aβ and tau pathology were noted (stage VI of Braak and Braak). Aβ plaques and cerebral amyloid angiopathy were abundant throughout the cerebral cortex, but largely spared the neostriatum. Plaques were unusually perfuse in the cerebellum and brainstem, and were frequently perivascular. Plaques contained abundant Aβ40, and were noted to be unusually large, with few preamyloid deposits. A detailed neuropathological analysis of the proband’s brain is reported in Giaccone et al., 2010.

Biological Effect

The A673 residue of APP lies very near the primary β-secretase site, and after cleavage the residue becomes part of the Aβ peptide. In vitro studies suggest that the A673V mutation contributes to AD pathology not only by increasing total Aβ production, but also by enhancing Aβ aggregation and toxicity.

The A673V mutation makes APP a more favorable substrate for β-secretase, shifting APP processing toward the amyloidogenic pathway. When overexpressed in CHO, COS-7, and N2a cells, mutant APP produced higher levels of Aβ40 peptides than wild-type APP (Di Fede et al., 2009, Kimura et al., 2016). Additional β-secretase cleavage products, e.g., sAPPβ and CTFβ/C99, were likewise increased. While in CHO and COS-7 cells the ratio of Aβ40 to Aβ42 was unchanged because the levels of both peptides increased similarly (Di Fede et al., 2009), in the N2a experiments, the increase in Aβ42 was slight and did not reach significance (Kimura et al., 2016). Elevated Aβ production was also confirmed in primary mouse neurons expressing human APP (isoform 695) with A673V (Benilova et al., 2014; Maloney et al., 2014), and in iPSC-derived human neurons (Maloney et al., 2014).  A detailed study of the cleavage pattern of A673V in N2a cells suggested the mutation decreases β′-site cleavage of APP, while increasing β-site cleavage, resulting in higher levels of Aβ40 and only a slight increase in Aβ42 levels (Kimura et al., 2016). Interestingly, a substitution at the same site but which confers protection against AD, A653T (Icelandic), appears to do the opposite, increasing β′-site cleavage.

Several studies, although not all, have found that the A673V mutation also accelerates Aβ aggregation. The mutant Aβ, called A2V because the A673V mutation occurs at position 2 of Aβ, appears to be more aggregation-prone than wild-type Aβ (see Di Fede et al., 2009; Benilova et al., 2014; Maloney et al., 2014, Hatami et al., 2017). A study of the Aβ40 mutant peptide revealed a decrease in the lag time and an increase in the rate of aggregation, resulting in abundant fibrils of at least two different morphologies as well as globular aggregates (Hatami et al., 2017).  Structural characterization of Aβ42 AV2 assemblies revealed the mutation alters oligomerization, promoting the formation of a polymer-like network with hydrophobic residues exposed on the external surface (Messa et al., 2014). 

Notably, given that this mutation appears to be pathogenic only in the homozygous state, a mixture of wild-type and mutant Aβ peptides aggregated more slowly than either peptide alone, likely due to less stable intermolecular interactions, and generated assemblies similar to those produced by the wildtype peptide alone (Messa et al., 2014). Furthermore, in cultured neuroblastoma cells, a mixture of mutant and wild-type Aβ42 was less toxic than either peptide alone, suggesting that in heterozygous carriers, a single mutant allele may actually protect against AD by reducing Aβ aggregation and toxicity (Di Fede et al., 2009; Di Fede et al., 2012). Even as a pure peptide, A2V Aβ may only be mildly toxic to neurons, requiring a high concentration (10 µM) to reduce viability (Maloney et al., 2014). Moreover, a yeast cell-based assay indicated decreased, rather than increased, nucleation of A2V peptides compared with wildtype Aβ (Seuma et al., 2022, suppl 3).

This variant's PHRED-scaled CADD score was above 20, suggesting a damaging effect (CADD v1.6, 2021). 

Pathogenicity

Alzheimer's Disease : Not Classified*

*This variant fulfilled some ACMG-AMP criteria, but it is not classified because it was reported as likely being recessive with only 1 affected homozygote reported, and the variant is absent, or very rare, in the gnomAD database.

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

Comments

1. • Miguel Rodríguez-Manotas
     
   • Posted: 02 Mar 2011
   • Paper: A recessive mutation in the APP gene with dominant-negative effect on amyloidogenesis.

   There may be a reversible formation of dimers in the APP molecule, before being cleaved by γ-secretase and the subsequent formation of Aβ dimers, thus preserving the molecule for cleavage by α-secretase.

   Data provided by this extraordinary article based on a mutation of the amino-terminal region of Aβ in its precursor molecule APP (changes in its primary sequence trigger peptide assembly and fibril formation) point to this possibility, since the relationship between the carboxy-terminal fragments generated by β- and α-secretase (1.9 ± 0.2 increase in C99: C83 ratio in patient's fibroblasts) implies double the rate of β product versus α in the mutant APP.

   View all comments by Miguel Rodríguez-Manotas

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References

Mutations Citations

1. APP A673T (Icelandic)

Paper Citations

1. Di Fede G, Catania M, Morbin M, Rossi G, Suardi S, Mazzoleni G, Merlin M, Giovagnoli AR, Prioni S, Erbetta A, Falcone C, Gobbi M, Colombo L, Bastone A, Beeg M, Manzoni C, Francescucci B, Spagnoli A, Cantù L, Del Favero E, Levy E, Salmona M, Tagliavini F. A recessive mutation in the APP gene with dominant-negative effect on amyloidogenesis. Science. 2009 Mar 13;323(5920):1473-7. PubMed.
2. Giaccone G, Morbin M, Moda F, Botta M, Mazzoleni G, Uggetti A, Catania M, Moro ML, Redaelli V, Spagnoli A, Rossi RS, Salmona M, Di Fede G, Tagliavini F. Neuropathology of the recessive A673V APP mutation: Alzheimer disease with distinctive features. Acta Neuropathol. 2010 Dec;120(6):803-12. PubMed.
3. Kimura A, Hata S, Suzuki T. Alternative Selection of β-Site APP-Cleaving Enzyme 1 (BACE1) Cleavage Sites in Amyloid β-Protein Precursor (APP) Harboring Protective and Pathogenic Mutations within the Aβ Sequence. J Biol Chem. 2016 Nov 11;291(46):24041-24053. Epub 2016 Sep 29 PubMed.
4. Benilova I, Gallardo R, Ungureanu AA, Castillo Cano V, Snellinx A, Ramakers M, Bartic C, Rousseau F, Schymkowitz J, De Strooper B. The Alzheimer disease protective mutation A2T modulates kinetic and thermodynamic properties of amyloid-β (Aβ) aggregation. J Biol Chem. 2014 Nov 7;289(45):30977-89. Epub 2014 Sep 24 PubMed.
5. Maloney JA, Bainbridge T, Gustafson A, Zhang S, Kyauk R, Steiner P, van der Brug M, Liu Y, Ernst JA, Watts RJ, Atwal JK. Molecular mechanisms of Alzheimer disease protection by the A673T allele of amyloid precursor protein. J Biol Chem. 2014 Nov 7;289(45):30990-1000. Epub 2014 Sep 24 PubMed.
6. Hatami A, Monjazeb S, Milton S, Glabe CG. Familial Alzheimer's Disease Mutations within the Amyloid Precursor Protein Alter the Aggregation and Conformation of the Amyloid-β Peptide. J Biol Chem. 2017 Feb 24;292(8):3172-3185. Epub 2017 Jan 3 PubMed.
7. Messa M, Colombo L, del Favero E, Cantù L, Stoilova T, Cagnotto A, Rossi A, Morbin M, Di Fede G, Tagliavini F, Salmona M. The peculiar role of the A2V mutation in amyloid-β (Aβ) 1-42 molecular assembly. J Biol Chem. 2014 Aug 29;289(35):24143-52. Epub 2014 Jul 18 PubMed.
8. Di Fede G, Catania M, Morbin M, Giaccone G, Moro ML, Ghidoni R, Colombo L, Messa M, Cagnotto A, Romeo M, Stravalaci M, Diomede L, Gobbi M, Salmona M, Tagliavini F. Good gene, bad gene: New APP variant may be both. Prog Neurobiol. 2012 Jun 19; PubMed.
9. Seuma M, Lehner B, Bolognesi B. An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation. Nat Commun. 2022 Nov 18;13(1):7084. PubMed.

Other Citations

1. Maloney et al., 2014

Further Reading