Overview

Clinical Phenotype: Alzheimer's Disease
Position: (GRCh38/hg38):Chr11:121604306 G>A
Position: (GRCh37/hg19):Chr11:121475015 G>A
dbSNP ID: NA
Coding/Non-Coding: Coding
DNA Change: Substitution
Expected Protein Consequence: Missense
Codon Change: GAT to AAT
Reference Isoform: SORL1 Isoform 1 (2214 aa)
Genomic Region: Exon 33

Findings

The D1545N variant was found in one of 1383 Alzheimer’s cases from the Centre National de Référence - Malades Alzheimer Jeunes (CNR-MAJ), the French national reference center for young Alzheimer patients (Rovelet-Lecrux et al., 2021).

In a study that included 15,808 Alzheimer’s cases and 16,097 control subjects from multiple European and American cohorts, including CNR-MAJ, this allele was observed once among the AD cases (Holstege et al., 2022).

Functional Consequences

The SORL1 protein contains 11 complement-type repeats (CRs). A majority of known SORL1 ligands, including APP, bind to the CR cluster, and ligand binding is Ca²⁺-dependent. In proteins with CR domains, each CR contains four amino acids whose acidic side chains, together with the backbone carbonyls of two additional residues, form an octahedral Ca²⁺ cage critical for proper folding of the domain. Residue 1545 is a component of the Ca²⁺ cage in CR11.

Andersen and colleagues predicted that variants affecting residues that contribute their acidic side chains to the Ca²⁺ cages are highly likely to increase AD risk (Andersen et al., 2023). Domain mapping of disease mutations revealed that several variants associated with medical conditions—in genes including LDLR (familial hypercholesterolemia), LRP2 (intellectual disability, Stickler syndrome), LRP5 (exudative vitreoretinopathy 4), TMPRSS3 (deafness), and TMPRSS6 (iron-refractory iron deficiency anemia)—occur in Ca²⁺-cage residues. Furthermore, analysis of data from the Alzheimer’s Disease Sequencing Project and the Alzheimer Disease European Sequencing consortium showed that SORL1 Ca²⁺-cage variants significantly increased the risk of AD (OR = infinity), leading to the suggestion that these variants be considered causative for AD (Andersen et al., 2023).

The following Ca²⁺-cage variants are listed in the Alzforum database: D1108N, D1182N, D1219G, D1261G, D1267N, D1267E, D1345N, D1439N, D1502G, D1535N, D1545N, D1545G, D1545E. With the exception of D1267E, all carriers of these variants were Alzheimer’s cases.

This variant was predicted to be deleterious by SIFT, Mutation Taster, and PolyPhen-2 (Rovelet-Lecrux et al., 2021).

In a study investigating the effects of SORL1 missense mutations on protein processing, the D1545N variant did not affect the maturation (glycosylation) of SORL1 overexpressed in HEK293 cells (Rovelet-Lecrux et al., 2021).

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References

Paper Citations

1. Rovelet-Lecrux A, Feuillette S, Miguel L, Schramm C, Pernet S, Quenez O, Ségalas-Milazzo I, Guilhaudis L, Rousseau S, Riou G, Frébourg T, Campion D, Nicolas G, Lecourtois M. Impaired SorLA maturation and trafficking as a new mechanism for SORL1 missense variants in Alzheimer disease. Acta Neuropathol Commun. 2021 Dec 18;9(1):196. PubMed.
2. Holstege H, Hulsman M, Charbonnier C, Grenier-Boley B, Quenez O, Grozeva D, van Rooij JG, Sims R, Ahmad S, Amin N, Norsworthy PJ, Dols-Icardo O, Hummerich H, Kawalia A, Amouyel P, Beecham GW, Berr C, Bis JC, Boland A, Bossù P, Bouwman F, Bras J, Campion D, Cochran JN, Daniele A, Dartigues JF, Debette S, Deleuze JF, Denning N, DeStefano AL, Farrer LA, Fernández MV, Fox NC, Galimberti D, Genin E, Gille JJ, Le Guen Y, Guerreiro R, Haines JL, Holmes C, Ikram MA, Ikram MK, Jansen IE, Kraaij R, Lathrop M, Lemstra AW, Lleó A, Luckcuck L, Mannens MM, Marshall R, Martin ER, Masullo C, Mayeux R, Mecocci P, Meggy A, Mol MO, Morgan K, Myers RM, Nacmias B, Naj AC, Napolioni V, Pasquier F, Pastor P, Pericak-Vance MA, Raybould R, Redon R, Reinders MJ, Richard AC, Riedel-Heller SG, Rivadeneira F, Rousseau S, Ryan NS, Saad S, Sanchez-Juan P, Schellenberg GD, Scheltens P, Schott JM, Seripa D, Seshadri S, Sie D, Sistermans EA, Sorbi S, van Spaendonk R, Spalletta G, Tesi N, Tijms B, Uitterlinden AG, van der Lee SJ, Visser PJ, Wagner M, Wallon D, Wang LS, Zarea A, Clarimon J, van Swieten JC, Greicius MD, Yokoyama JS, Cruchaga C, Hardy J, Ramirez A, Mead S, van der Flier WM, van Duijn CM, Williams J, Nicolas G, Bellenguez C, Lambert JC. Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer's disease. Nat Genet. 2022 Dec;54(12):1786-1794. Epub 2022 Nov 21 PubMed.
3. Andersen OM, Monti G, Jensen AM, deWaal M, Hulsman M, Olsen JG, Holstege H. Relying on the relationship with known disease-causing variants in homologous proteins to predict pathogenicity of SORL1 variants in Alzheimer's disease. 2023 Feb 27 10.1101/2023.02.27.524103 (version 1) bioRxiv.

Further Reading

No Available Further Reading