Overview

Pathogenicity: Alzheimer's Disease : Pathogenic
ACMG/AMP Pathogenicity Criteria: PS3, PM1, PM2, PP1, PP2, PP3, BS4
Clinical Phenotype: Alzheimer's Disease, Cerebral Amyloid Angiopathy
Position: (GRCh38/hg38):Chr21:25891858 C>G
Position: (GRCh37/hg19):Chr21:27264170 C>G
dbSNP ID: rs63750671
Coding/Non-Coding: Coding
DNA Change: Substitution
Expected RNA Consequence: Substitution
Expected Protein Consequence: Missense
Codon Change: GCA to GGA
Reference Isoform: APP Isoform APP770 (770 aa)
Genomic Region: Exon 17

Findings

This mutation has been reported in two families and two individuals of European ancestry. Of fifteen patients examined in the clinic—including two non-genotyped affected relatives from the two families—four were diagnosed with definite Alzheimer's disease (AD), four with possible/probable AD, five with uncharacterized progressive dementia, and five had at least one intracerebral hemorrhage (including two patients previously diagnosed with AD). Mean age at onset was 45.3 years, ranging between 35 and 54 (Sellal et al., 2017).

The mutation was first reported in a four-generation Flemish pedigree. Affected individuals were diagnosed with Alzheimer's disease or cerebral hemorrhage associated with cerebral amyloid angiopathy (CAA). The mean age at onset in this family was 46 years (Hendriks et al., 1992). The pedigree included five affected mutation carriers and four unaffected non-carriers indicating the mutation cosegregated with disease. However, there was an exception: a demented individual who did not carry the mutation. The survival of this individual until at least age 71, well past the carriers' range of ages at death (35-61 years), and their late age at onset (61 years) suggest their disease had a different etiology. Subsequent studies showed that, on average, first hemorrhages occurred when carriers were in their early 40s, with onset of dementia emerging in the late 40s, and death in the late 50s (Roks et al., 2000). In total, 19 affected individuals have been reported in this family, including eight mutation carriers (Cras et al., 1998, Roks et al., 2000, Sellal et al., 2017).

A second pedigree of three generations was reported with six affected individuals, including three mutation carriers (Brooks et al., 2004, Sellal et al., 2017). Dementia was the primary clinical feature in these patients. The proband also had a cerebral hemorrhage, but other affected family members did not. Neuropathologic examination confirmed AD, congophilic angiopathy, and hemorrhagic infarction. In this family, dementia onset ranged from 39 to 54 years of age (Brooks et al., 2004).

Two individual carriers, one living in the UK and another of Portuguese ancestry, have also been described. The first was diagnosed with probable AD and had increased white matter hyperintensities as assessed by MRI (Ryan et al., 2015). The second had CAA and progressive cognitive impairment, including memory loss starting at age 45 (Sellal et al., 2017). Two members of this carrier’s family were affected, but not genotyped.

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

Neuropathology

The Flemish mutation is associated with variable pathology, but generally involves amyloid deposition in the blood vessels of the brain. Four autopsied carriers were diagnosed with severe CAA and definite AD (Sellal et al., 2017). Many plaques were described as containing large amyloid cores, often more than 30 microns in diameter and surrounded by dystrophic neurites (Cras et al., 1998). Also, in brain tissues from three carriers, nearly 70 percent of neuritic senile plaques enclosed a vessel, while the remainder were associated with vascular walls (Kumar-Singh et al., 2002). The deposits contained primarily Aβ40.

Of note, MRI scans of presymptomatic carriers showed an increase in the number of periventricular and subcortical white matter lesions at a young age (mean age 26.4 years) (Roks et al., 2000).

Biological Effect

The A692G mutation falls within the Aβ region of APP. It is also called A21G because it affects the 21st amino acid in the Aβ sequence. The substitution exchanges a neutral amino acid with another neutral amino acid involving the removal of a single methyl group (Yang et al., 2018). In smooth muscle cells isolated from human cerebral microvessels or the aorta, A21G induced little or no toxicity (Wang et al., 2000). Moreover, in human embryonic kidney (HEK) cells, the mutation did not affect APP localization to the cis-Golgi, early endosomes, or the cell surface, nor did it affect APP synaptogenic activity as assessed in a co-culture of HEK cells and mouse primary cortical neurons (Schilling et al., 2023). However, multiple studies in cultured cells and using isolated proteins have shown the Flemish mutation alters both APP processing and Aβ oligomerization and aggregation.

This mutation affects APP processing. In cellular assays, it increased levels of secreted Aβ42 and Aβ40—approximately two- to fourfold (Haass et al., 1994; De Jonghe et al., 1998, Nilsberth et al., 2001, Van Nostrand et al., 2001, Schilling et al., 2023); although the Aβ42/Aβ40 ratio was similar to that of wildtype (Kwart et al., 2019, Schilling et al., 2023) or only slightly increased (Nilsberth et al., 2001). The increase in Aβ peptide production may be at least partially due to the location of the mutation in the amino acid sequence LVFFAED, which, when deleted, increased the relative production of Aβ40 10-fold (Tian et al., 2010). The mutation appears to alter the secondary structure of this inhibitory region (Tang et al., 2014). Also, resistance to cleavage by neprisylin may contribute to increased Aβ levels (Tsubuki et al., 2003, Betts et al., 2008). 

Analyses of APP peptides and peptide fragments suggest additional alterations in APP processing. For example, the mutant was shown to promote the accumulation of APP β-C-terminal fragments which disrupt endosomes (Kwart et al., 2019, Aug 2019 news). Also, some findings suggest decreased proteolysis by α-secretase, whose cleavage site is in close proximity to the mutation (Haass et al., 1994). Moreover, a relative decrease in Aβ1-19 and an increase in Aβ5-40 were reported (Schilling et al., 2023). Increased production of N-terminally truncated Aβ peptides starting at position 5 was associated with several APP mutations and the authors suggested it may contribute to AD pathogenesis.

Although Aβ peptides carrying the Flemish mutation have relatively low aggregation propensity and a decreased extension rate in vitro, including dimerization (De Jonghe et al., 1998, Van Nostrand et al., 2001, Murakami et al., 2002; Meinhardt et al., 2007; Huet et al., 2006, Betts et al., 2008, Illes-Toh et al., 2021), their unique aggregation properties may contribute to their pathogenicity.

The A21G substitution appears to preserve the basic structure of the wildtype Aβ monomer, yet affects oligomerization (Gessel et al., 2012, Bitan 2003, Yang 2018). Two studies have suggested A21G blocks Aβ42 oligomerization at the hexamer level, with these small oligomers adopting an open, rather than cyclic, conformation, which reduces fibril formation. This reduction results in increased solubility which could facilitate diffusion or transport into cerebral blood vessels (Gessel et al., 2012, Bitan 2003). Other studies have indicated fibril formation can be promoted through interaction with gangliosides in the vascular wall, which may partly explain the propensity of Flemish Aβ to deposit in the vasculature (Yamamoto et al., 2005; Yagi-Utsumi and Dobson 2015).

This variant's PHRED-scaled CADD score, which integrates diverse information in silico, was above 20, suggesting a deleterious effect (CADD v.1.6, Oct 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.

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References

News Citations

1. Familial AD Mutations, β-CTF, Spell Trouble for Endosomes 16 Aug 2019

Paper Citations

1. Sellal F, Wallon D, Martinez-Almoyna L, Marelli C, Dhar A, Oesterlé H, Rovelet-Lecrux A, Rousseau S, Kourkoulis CE, Rosand J, DiPucchio ZY, Frosch M, Gombert C, Audoin B, Miné M, Riant F, Frebourg T, Hannequin D, Campion D, Greenberg SM, Tournier-Lasserve E, Nicolas G. APP Mutations in Cerebral Amyloid Angiopathy with or without Cortical Calcifications: Report of Three Families and a Literature Review. J Alzheimers Dis. 2017;56(1):37-46. PubMed.
2. Hendriks L, van Duijn CM, Cras P, Cruts M, Van Hul W, van Harskamp F, Warren A, McInnis MG, Antonarakis SE, Martin JJ. Presenile dementia and cerebral haemorrhage linked to a mutation at codon 692 of the beta-amyloid precursor protein gene. Nat Genet. 1992 Jun;1(3):218-21. PubMed.
3. Roks G, Van Harskamp F, De Koning I, Cruts M, De Jonghe C, Kumar-Singh S, Tibben A, Tanghe H, Niermeijer MF, Hofman A, Van Swieten JC, Van Broeckhoven C, Van Duijn CM. Presentation of amyloidosis in carriers of the codon 692 mutation in the amyloid precursor protein gene (APP692). Brain. 2000 Oct;123 ( Pt 10):2130-40. PubMed.
4. Cras P, van Harskamp F, Hendriks L, Ceuterick C, van Duijn CM, Stefanko SZ, Hofman A, Kros JM, Van Broeckhoven C, Martin JJ. Presenile Alzheimer dementia characterized by amyloid angiopathy and large amyloid core type senile plaques in the APP 692Ala-->Gly mutation. Acta Neuropathol. 1998 Sep;96(3):253-60. PubMed.
5. Brooks WS, Kwok JB, Halliday GM, Godbolt AK, Rossor MN, Creasey H, Jones AO, Schofield PR. Hemorrhage is uncommon in new Alzheimer family with Flemish amyloid precursor protein mutation. Neurology. 2004 Nov 9;63(9):1613-7. PubMed.
6. Ryan NS, Biessels GJ, Kim L, Nicholas JM, Barber PA, Walsh P, Gami P, Morris HR, Bastos-Leite AJ, Schott JM, Beck J, Mead S, Chavez-Gutierrez L, de Strooper B, Rossor MN, Revesz T, Lashley T, Fox NC. Genetic determinants of white matter hyperintensities and amyloid angiopathy in familial Alzheimer's disease. Neurobiol Aging. 2015 Dec;36(12):3140-3151. Epub 2015 Sep 4 PubMed.
7. Kumar-Singh S, Cras P, Wang R, Kros JM, van Swieten J, Lübke U, Ceuterick C, Serneels S, Vennekens K, Timmermans JP, Van Marck E, Martin JJ, van Duijn CM, Van Broeckhoven C. Dense-core senile plaques in the Flemish variant of Alzheimer's disease are vasocentric. Am J Pathol. 2002 Aug;161(2):507-20. PubMed.
8. Yang X, Meisl G, Frohm B, Thulin E, Knowles TP, Linse S. On the role of sidechain size and charge in the aggregation of Aβ42 with familial mutations. Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):E5849-E5858. Epub 2018 Jun 12 PubMed.
9. Wang Z, Natté R, Berliner JA, van Duinen SG, Vinters HV. Toxicity of Dutch (E22Q) and Flemish (A21G) mutant amyloid beta proteins to human cerebral microvessel and aortic smooth muscle cells. Stroke. 2000 Feb;31(2):534-8. PubMed.
10. Schilling S, Pradhan A, Heesch A, Helbig A, Blennow K, Koch C, Bertgen L, Koo EH, Brinkmalm G, Zetterberg H, Kins S, Eggert S. Differential effects of familial Alzheimer's disease-causing mutations on amyloid precursor protein (APP) trafficking, proteolytic conversion, and synaptogenic activity. Acta Neuropathol Commun. 2023 Jun 1;11(1):87. PubMed.
11. Haass C, Hung AY, Selkoe DJ, Teplow DB. Mutations associated with a locus for familial Alzheimer's disease result in alternative processing of amyloid beta-protein precursor. J Biol Chem. 1994 Jul 1;269(26):17741-8. PubMed.
12. De Jonghe C, Zehr C, Yager D, Prada CM, Younkin S, Hendriks L, Van Broeckhoven C, Eckman CB. Flemish and Dutch mutations in amyloid beta precursor protein have different effects on amyloid beta secretion. Neurobiol Dis. 1998 Oct;5(4):281-6. PubMed.
13. Nilsberth C, Westlind-Danielsson A, Eckman CB, Condron MM, Axelman K, Forsell C, Stenh C, Luthman J, Teplow DB, Younkin SG, Näslund J, Lannfelt L. The 'Arctic' APP mutation (E693G) causes Alzheimer's disease by enhanced Abeta protofibril formation. Nat Neurosci. 2001 Sep;4(9):887-93. PubMed.
14. Van Nostrand WE, Melchor JP, Cho HS, Greenberg SM, Rebeck GW. Pathogenic effects of D23N Iowa mutant amyloid beta -protein. J Biol Chem. 2001 Aug 31;276(35):32860-6. Epub 2001 Jul 5 PubMed.
15. Kwart D, Gregg A, Scheckel C, Murphy EA, Paquet D, Duffield M, Fak J, Olsen O, Darnell RB, Tessier-Lavigne M. A Large Panel of Isogenic APP and PSEN1 Mutant Human iPSC Neurons Reveals Shared Endosomal Abnormalities Mediated by APP β-CTFs, Not Aβ. Neuron. 2019 Oct 23;104(2):256-270.e5. Epub 2019 Aug 12 PubMed.
16. Tian Y, Bassit B, Chau D, Li YM. An APP inhibitory domain containing the Flemish mutation residue modulates gamma-secretase activity for Abeta production. Nat Struct Mol Biol. 2010 Feb;17(2):151-8. PubMed.
17. Tang TC, Hu Y, Kienlen-Campard P, El Haylani L, Decock M, Van Hees J, Fu Z, Octave JN, Constantinescu SN, Smith SO. Conformational changes induced by the A21G Flemish mutation in the amyloid precursor protein lead to increased Aβ production. Structure. 2014 Mar 4;22(3):387-96. Epub 2014 Jan 23 PubMed.
18. Tsubuki S, Takaki Y, Saido TC. Dutch, Flemish, Italian, and Arctic mutations of APP and resistance of Abeta to physiologically relevant proteolytic degradation. Lancet. 2003 Jun 7;361(9373):1957-8. PubMed.
19. Betts V, Leissring MA, Dolios G, Wang R, Selkoe DJ, Walsh DM. Aggregation and catabolism of disease-associated intra-Abeta mutations: reduced proteolysis of AbetaA21G by neprilysin. Neurobiol Dis. 2008 Sep;31(3):442-50. Epub 2008 Jun 17 PubMed.
20. Murakami K, Irie K, Morimoto A, Ohigashi H, Shindo M, Nagao M, Shimizu T, Shirasawa T. Synthesis, aggregation, neurotoxicity, and secondary structure of various A beta 1-42 mutants of familial Alzheimer's disease at positions 21-23. Biochem Biophys Res Commun. 2002 May 31;294(1):5-10. PubMed.
21. Meinhardt J, Tartaglia GG, Pawar A, Christopeit T, Hortschansky P, Schroeckh V, Dobson CM, Vendruscolo M, Fändrich M. Similarities in the thermodynamics and kinetics of aggregation of disease-related Abeta(1-40) peptides. Protein Sci. 2007 Jun;16(6):1214-22. PubMed.
22. Huet A, Derreumaux P. Impact of the mutation A21G (Flemish variant) on Alzheimer's beta-amyloid dimers by molecular dynamics simulations. Biophys J. 2006 Nov 15;91(10):3829-40. PubMed.
23. Illes-Toth E, Meisl G, Rempel DL, Knowles TP, Gross ML. Pulsed Hydrogen-Deuterium Exchange Reveals Altered Structures and Mechanisms in the Aggregation of Familial Alzheimer's Disease Mutants. ACS Chem Neurosci. 2021 Jun 2;12(11):1972-1982. Epub 2021 May 14 PubMed.
24. Gessel MM, Bernstein S, Kemper M, Teplow DB, Bowers MT. Familial Alzheimer's disease mutations differentially alter amyloid β-protein oligomerization. ACS Chem Neurosci. 2012 Nov 21;3(11):909-18. Epub 2012 Jun 26 PubMed.
25. Bitan G, Vollers SS, Teplow DB. Elucidation of primary structure elements controlling early amyloid beta-protein oligomerization. J Biol Chem. 2003 Sep 12;278(37):34882-9. Epub 2003 Jul 2 PubMed.
26. Yamamoto N, Hirabayashi Y, Amari M, Yamaguchi H, Romanov G, Van Nostrand WE, Yanagisawa K. Assembly of hereditary amyloid beta-protein variants in the presence of favorable gangliosides. FEBS Lett. 2005 Apr 11;579(10):2185-90. PubMed.
27. Yagi-Utsumi M, Dobson CM. Conformational Effects of the A21G Flemish Mutation on the Aggregation of Amyloid β Peptide. Biol Pharm Bull. 2015;38(10):1668-72. PubMed.

Further Reading