ClinVar Genomic variation as it relates to human health
NM_000484.4(APP):c.2149G>A (p.Val717Ile)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000484.4(APP):c.2149G>A (p.Val717Ile)
Variation ID: 18088 Accession: VCV000018088.33
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 21q21.3 21: 25891784 (GRCh38) [ NCBI UCSC ] 21: 27264096 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline May 3, 2013 Apr 15, 2024 Feb 22, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000484.4:c.2149G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000475.1:p.Val717Ile missense NM_001136016.3:c.2077G>A NP_001129488.1:p.Val693Ile missense NM_001136129.3:c.1756G>A NP_001129601.1:p.Val586Ile missense NM_001136130.3:c.1981G>A NP_001129602.1:p.Val661Ile missense NM_001136131.3:c.1819G>A NP_001129603.1:p.Val607Ile missense NM_001204301.2:c.2095G>A NP_001191230.1:p.Val699Ile missense NM_001204302.2:c.2038G>A NP_001191231.1:p.Val680Ile missense NM_001204303.2:c.1870G>A NP_001191232.1:p.Val624Ile missense NM_001385253.1:c.1981G>A NP_001372182.1:p.Val661Ile missense NM_201413.3:c.2092G>A NP_958816.1:p.Val698Ile missense NM_201414.3:c.1924G>A NP_958817.1:p.Val642Ile missense NC_000021.9:g.25891784C>T NC_000021.8:g.27264096C>T NG_007376.2:g.284345G>A P05067:p.Val717Ile - Protein change
- V717I, V607I, V624I, V661I, V642I, V680I, V693I, V698I, V699I, V586I
- Other names
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- Canonical SPDI
- NC_000021.9:25891783:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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APP | No evidence available | Some evidence for dosage pathogenicity |
GRCh38 GRCh37 |
444 | 552 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Feb 2, 2022 | RCV000019714.37 | |
Pathogenic (2) |
criteria provided, single submitter
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Nov 11, 2023 | RCV000020308.12 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Dec 16, 2021 | RCV000084575.19 | |
Pathogenic (1) |
criteria provided, single submitter
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Dec 10, 2021 | RCV002496421.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Feb 22, 2024 | RCV003993747.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Feb 02, 2022)
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criteria provided, single submitter
Method: clinical testing
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Alzheimer disease type 1
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002557779.1
First in ClinVar: Aug 08, 2022 Last updated: Aug 08, 2022 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Toxic gain of function is a known … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Toxic gain of function is a known mechanism of disease in this gene and is associated with Alzheimer disease 1, familial (MIM#104300) (PMID: 24524897). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance. p.(Ala713Thr) has been reported to exhibit reduced penetrance (PMID: 28350801). (I) 0115 - Variants in this gene are known to have variable expressivity. Age of onset and disease progression can vary (GeneReviews; PMID: 24650794). (I) 0200 - Variant is predicted to result in a missense amino acid change from valine to isoleucine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants within the transmembrane domain (DECIPHER; PMID: 24524897). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in more than ten unrelated families with Alzheimer disease. Asymptomatic carriers were noted in some; however, their ages were not provided to rule out reduced penetrance. Finally, this variant has been classified as pathogenic by diagnostic laboratories in ClinVar (PMID: 24650794, 25138979, 27838006, 28350801). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Dec 16, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics Inc
Accession: SCV002771849.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
Comment:
This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). This variant has been identified in … (more)
This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). This variant has been identified in multiple unrelated individuals with clinical features associated with this gene. This variant segregates with disease in at least one family. Assessment of experimental evidence suggests this variant results in abnormal protein function. Experiments show this variant results in an increased ratio of amyloid-beta-42 to amyloid-beta-40 (PMID: 8886002, 9328472, 11487570, 19281847). This variant is located in a region that is considered important for protein function and/or structure. (less)
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Pathogenic
(Dec 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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Alzheimer disease type 1
Cerebral amyloid angiopathy, APP-related
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002807780.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Nov 11, 2023)
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criteria provided, single submitter
Method: clinical testing
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Alzheimer disease
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000935808.6
First in ClinVar: Aug 14, 2019 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 717 of the APP protein (p.Val717Ile). … (more)
This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 717 of the APP protein (p.Val717Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with early-onset Alzheimer's disease (EOAD) (PMID: 24650794, 25138979, 27838006). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 18088). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt APP protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects APP function (PMID: 11978821, 19281847, 24524897). This variant disrupts the p.Val717 amino acid residue in APP. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 1925564, 15776278). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Feb 22, 2024)
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criteria provided, single submitter
Method: clinical testing
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Cerebral amyloid angiopathy, APP-related
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004813609.1
First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024 |
Comment:
Variant summary: APP c.2149G>A (p.Val717Ile) results in a conservative amino acid change located in the Beta-amyloid precursor protein C-terminal domain (IPR019543) of the encoded protein … (more)
Variant summary: APP c.2149G>A (p.Val717Ile) results in a conservative amino acid change located in the Beta-amyloid precursor protein C-terminal domain (IPR019543) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251364 control chromosomes (gnomAD). c.2149G>A has been reported in the literature in multiple individuals affected with early-onset Alzheimer's disease (EOAD) (examples: Noroozian_2014 and Zhang_2017). These data indicate that the variant is very likely to be associated with disease. Other variant(s) that disrupt this residue have been classified pathogenic in ClinVar. The following publications have been ascertained in the context of this evaluation (PMID: 27838006, 25138979). ClinVar contains an entry for this variant (Variation ID: 18088). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Alzheimer disease type 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV004048033.1
First in ClinVar: Oct 28, 2023 Last updated: Oct 28, 2023 |
Comment:
The missense c.2149G>A(p.Val717Ile) variant in APP gene has been reported in heterozygous state in individuals affected with Alzheimer's disease (Jiao, Bin et al.,2014). It has … (more)
The missense c.2149G>A(p.Val717Ile) variant in APP gene has been reported in heterozygous state in individuals affected with Alzheimer's disease (Jiao, Bin et al.,2014). It has also been observed to segregate with disease in related individuals. Experimental studies have shown that this missense change affects APP function (Herl, Lauren et al., 2009 ). The variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. It has been submitted to ClinVar as Pathogenic. The amino acid Val at position 717 is changed to a Ile changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Val717Ile in APP is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. (less)
Clinical Features:
Parkinsonian disorder (present) , Neurodegeneration (present)
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Pathogenic
(Jun 01, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001250462.20
First in ClinVar: May 12, 2020 Last updated: Apr 15, 2024 |
Number of individuals with the variant: 1
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Pathogenic
(Oct 23, 1996)
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no assertion criteria provided
Method: literature only
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ALZHEIMER DISEASE, FAMILIAL, 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000040012.6
First in ClinVar: Apr 04, 2013 Last updated: Feb 17, 2019 |
Comment on evidence:
In affected members of 2 families with early-onset Alzheimer disease-1 (104300), Goate et al. (1991) identified a heterozygous 2149C-T transition in exon 17 of the … (more)
In affected members of 2 families with early-onset Alzheimer disease-1 (104300), Goate et al. (1991) identified a heterozygous 2149C-T transition in exon 17 of the APP gene, resulting in a val717-to-ile (V717I) substitution. The mutation may have involved a CpG dinucleotide. The substitution created a BclI restriction site which allowed detection of the corresponding change within the PCR product. Naruse et al. (1991) identified the V717I mutation in 2 unrelated Japanese patients with familial early-onset Alzheimer disease, and Yoshioka et al. (1991) identified it in a third Japanese family. Failing to find the V717I mutation in 100 patients with early-onset AD, van Duijn et al. (1991) concluded that it accounts for less than 3.6% of all cases with early-onset AD. Schellenberg et al. (1991) did not identify the V717I mutation in 76 families with familial Alzheimer disease, 127 subjects with presumably sporadic Alzheimer disease, 16 patients with Down syndrome, or 256 normal controls. Karlinsky et al. (1992) reported an AD family from Toronto with the V717I mutation. The family immigrated to Canada from the British Isles in the 18th century. Relationship to one or both of the pedigrees reported by Goate et al. (1991) could not be excluded. In a follow-up report of the family reported by Karlinsky et al. (1992), St. George-Hyslop et al. (1994) noted that 1 family member with the V717I mutation remained clinically healthy with no sign of disease on neurologic or neuropsychologic tests or on brain imaging. The authors suggested that this might be due to the fact that this individual lacked the E4 allele at the APOE locus (107741), his genotype being E2/E3. All 3 living clinically affected family members with the V717I mutation were considerably younger and had the E3/E4 genotype. St. George-Hyslop et al. (1994) suggested that there is an interaction between the development of Alzheimer disease due to mutations in the APP gene and the E4 allele. In contrast, they observed no relationship between the APOE genotype and age of onset or other clinical features in affected members of a large pedigree in which familial AD was linked to chromosome 14 (AD3; 607822). Maruyama et al. (1996) explored the significance of the fact that 3 mutations in the val717 residue of APP (V717I; V717F; 104760.0003, and V717G; 104760.0004) had been found in patients with familial Alzheimer disease and that these mutations resulted in increased secretion of A-beta-42(43). Functional expression studies showed that the FAD-linked mutations at residue 717 increased the levels or ratios of A-beta-42(43), whereas the secretion of A-beta-40 was decreased. Mutations at residue 717 irrelevant to FAD, except V717K, had little effect on the ratio of beta-42(43). V717K decreased the secretion of beta-42. Overall, the results suggested a specific role of the val717 residue in APP processing and gamma-cleavage. (less)
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not provided
(-)
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no classification provided
Method: not provided
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not provided
Affected status: not provided
Allele origin:
not provided
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VIB Department of Molecular Genetics, University of Antwerp
Accession: SCV000116711.1
First in ClinVar: Feb 20, 2014 Last updated: Feb 20, 2014
Comment:
http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg18&id=ADM_90
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not provided
(-)
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no classification provided
Method: literature only
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Alzheimer disease
Affected status: not provided
Allele origin:
unknown
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GeneReviews
Accession: SCV000040683.3
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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APP, PSEN1, and PSEN2 mutations in early-onset Alzheimer disease: A genetic screening study of familial and sporadic cases. | Lanoiselée HM | PLoS medicine | 2017 | PMID: 28350801 |
Early-onset Alzheimer's disease in two Iranian families: a genetic study. | Noroozian M | Dementia and geriatric cognitive disorders | 2014 | PMID: 25138979 |
Mutational analysis in early-onset familial Alzheimer's disease in Mainland China. | Jiao B | Neurobiology of aging | 2014 | PMID: 24650794 |
The familial Alzheimer's disease APPV717I mutation alters APP processing and Tau expression in iPSC-derived neurons. | Muratore CR | Human molecular genetics | 2014 | PMID: 24524897 |
Early-Onset Familial Alzheimer Disease – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY. | Adam MP | - | 2012 | PMID: 20301414 |
Amyloid-β protein modulates the perivascular clearance of neuronal apolipoprotein E in mouse models of Alzheimer's disease. | Rolyan H | Journal of neural transmission (Vienna, Austria : 1996) | 2011 | PMID: 21210284 |
Mutations in amyloid precursor protein affect its interactions with presenilin/gamma-secretase. | Herl L | Molecular and cellular neurosciences | 2009 | PMID: 19281847 |
Genetic risk and transcriptional variability of amyloid precursor protein in Alzheimer's disease. | Brouwers N | Brain : a journal of neurology | 2006 | PMID: 16931535 |
Molecular diagnosis of autosomal dominant early onset Alzheimer's disease: an update. | Raux G | Journal of medical genetics | 2005 | PMID: 16033913 |
Novel mutations and repeated findings of mutations in familial Alzheimer disease. | Finckh U | Neurogenetics | 2005 | PMID: 15776278 |
Identification of new presenilin gene mutations in early-onset familial Alzheimer disease. | Tedde A | Archives of neurology | 2003 | PMID: 14623725 |
Early onset familial Alzheimer's disease: Mutation frequency in 31 families. | Janssen JC | Neurology | 2003 | PMID: 12552037 |
Neuronal deficiency of presenilin 1 inhibits amyloid plaque formation and corrects hippocampal long-term potentiation but not a cognitive defect of amyloid precursor protein [V717I] transgenic mice. | Dewachter I | The Journal of neuroscience : the official journal of the Society for Neuroscience | 2002 | PMID: 11978821 |
Pathogenic APP mutations near the gamma-secretase cleavage site differentially affect Abeta secretion and APP C-terminal fragment stability. | De Jonghe C | Human molecular genetics | 2001 | PMID: 11487570 |
High prevalence of pathogenic mutations in patients with early-onset dementia detected by sequence analyses of four different genes. | Finckh U | American journal of human genetics | 2000 | PMID: 10631141 |
Early-onset autosomal dominant Alzheimer disease: prevalence, genetic heterogeneity, and mutation spectrum. | Campion D | American journal of human genetics | 1999 | PMID: 10441572 |
A new pathogenic mutation in the APP gene (I716V) increases the relative proportion of A beta 42(43). | Eckman CB | Human molecular genetics | 1997 | PMID: 9328472 |
Familial Alzheimer's disease-linked mutations at Val717 of amyloid precursor protein are specific for the increased secretion of A beta 42(43). | Maruyama K | Biochemical and biophysical research communications | 1996 | PMID: 8886002 |
No founder effect in three novel Alzheimer's disease families with APP 717 Val-->Ile mutation. Clerget-darpoux. French Alzheimer's Disease Study Group. | Campion D | Journal of medical genetics | 1996 | PMID: 8863158 |
Japanese siblings with missense mutation (717Val --> Ile) in amyloid precursor protein of early-onset Alzheimer's disease. | Matsumura Y | Neurology | 1996 | PMID: 8649577 |
Epistatic effect of APP717 mutation and apolipoprotein E genotype in familial Alzheimer's disease. | Sorbi S | Annals of neurology | 1995 | PMID: 7611715 |
Alzheimer's disease and possible gene interaction. | St George-Hyslop P | Science (New York, N.Y.) | 1994 | PMID: 8290965 |
An increased percentage of long amyloid beta protein secreted by familial amyloid beta protein precursor (beta APP717) mutants. | Suzuki N | Science (New York, N.Y.) | 1994 | PMID: 8191290 |
APP717 and Alzheimer's disease in Italy. | Sorbi S | Nature genetics | 1993 | PMID: 8513318 |
Screening of the mis-sense mutation producing the 717Val-->Ile substitution in the amyloid precursor protein in Japanese familial and sporadic Alzheimer's disease. | Yoshizawa T | Journal of the neurological sciences | 1993 | PMID: 8410047 |
Molecular and prospective phenotypic characterization of a pedigree with familial Alzheimer's disease and a missense mutation in codon 717 of the beta-amyloid precursor protein gene. | Karlinsky H | Neurology | 1992 | PMID: 1520398 |
Screening for mutations in the open reading frame and promoter of the beta-amyloid precursor protein gene in familial Alzheimer's disease: identification of a further family with APP717 Val-->Ile. | Fidani L | Human molecular genetics | 1992 | PMID: 1303172 |
A mutation in the amyloid precursor protein associated with hereditary Alzheimer's disease. | Murrell J | Science (New York, N.Y.) | 1991 | PMID: 1925564 |
The 717Val----Ile substitution in amyloid precursor protein is associated with familial Alzheimer's disease regardless of ethnic groups. | Yoshioka K | Biochemical and biophysical research communications | 1991 | PMID: 1908231 |
APP717, APP693, and PRIP gene mutations are rare in Alzheimer disease. | Schellenberg GD | American journal of human genetics | 1991 | PMID: 1679288 |
Mis-sense mutation Val----Ile in exon 17 of amyloid precursor protein gene in Japanese familial Alzheimer's disease. | Naruse S | Lancet (London, England) | 1991 | PMID: 1678058 |
Amyloid precursor protein gene mutation in early-onset Alzheimer's disease. | van Duijn CM | Lancet (London, England) | 1991 | PMID: 1678057 |
Molecular classification of Alzheimer's disease. | - | Lancet (London, England) | 1991 | PMID: 1674311 |
Segregation of a missense mutation in the amyloid precursor protein gene with familial Alzheimer's disease. | Goate A | Nature | 1991 | PMID: 1671712 |
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Text-mined citations for rs63750264 ...
HelpRecord last updated Apr 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.