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dbSNP Short Genetic Variations

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs63751039

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr21:25891855 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
APP : Missense Variant
Publications
6 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 21 NC_000021.9:g.25891855T>C
GRCh37.p13 chr 21 NC_000021.8:g.27264167T>C
APP RefSeqGene NG_007376.1:g.283966A>G
Gene: APP, amyloid beta precursor protein (minus strand)
Molecule type Change Amino acid[Codon] SO Term
APP transcript variant 6 NM_001136130.2:c.1910A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform f precursor NP_001129602.1:p.Glu637Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant 5 NM_001136129.2:c.1685A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform e precursor NP_001129601.1:p.Glu562Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant 1 NM_000484.3:c.2078A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform a precursor NP_000475.1:p.Glu693Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant 2 NM_201413.2:c.2021A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform b precursor NP_958816.1:p.Glu674Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant 3 NM_201414.2:c.1853A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform c precursor NP_958817.1:p.Glu618Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant 9 NM_001204302.1:c.1967A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform i precursor NP_001191231.1:p.Glu656Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant 8 NM_001204301.1:c.2024A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform h precursor NP_001191230.1:p.Glu675Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant 10 NM_001204303.1:c.1799A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform j precursor NP_001191232.1:p.Glu600Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant 4 NM_001136016.3:c.2006A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform d NP_001129488.1:p.Glu669Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant 7 NM_001136131.2:c.1748A>G E [GAA] > G [GGA] Coding Sequence Variant
amyloid-beta precursor protein isoform g NP_001129603.1:p.Glu583Gly E (Glu) > G (Gly) Missense Variant
APP transcript variant X1 XM_024452075.1:c. N/A Genic Downstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: C (allele ID: 33137 )
ClinVar Accession Disease Names Clinical Significance
RCV000019725.27 Alzheimer disease, type 1 Pathogenic
RCV000019726.27 Cerebral amyloid angiopathy, APP-related Pathogenic
RCV000020307.2 Alzheimer's disease Pathogenic
RCV000084563.1 not provided Not-Provided
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

None
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement T= C Note
GRCh38.p12 chr 21 NC_000021.9:g.25891855T= NC_000021.9:g.25891855T>C
GRCh37.p13 chr 21 NC_000021.8:g.27264167T= NC_000021.8:g.27264167T>C
APP RefSeqGene NG_007376.1:g.283966A= NG_007376.1:g.283966A>G
APP transcript variant 1 NM_000484.3:c.2078A= NM_000484.3:c.2078A>G
APP transcript variant 4 NM_001136016.3:c.2006A= NM_001136016.3:c.2006A>G
APP transcript variant 2 NM_201413.2:c.2021A= NM_201413.2:c.2021A>G
APP transcript variant 6 NM_001136130.2:c.1910A= NM_001136130.2:c.1910A>G
APP transcript variant 3 NM_201414.2:c.1853A= NM_201414.2:c.1853A>G
APP transcript variant 7 NM_001136131.2:c.1748A= NM_001136131.2:c.1748A>G
APP transcript variant 5 NM_001136129.2:c.1685A= NM_001136129.2:c.1685A>G
APP transcript variant 8 NM_001204301.1:c.2024A= NM_001204301.1:c.2024A>G
APP transcript variant 9 NM_001204302.1:c.1967A= NM_001204302.1:c.1967A>G
APP transcript variant 10 NM_001204303.1:c.1799A= NM_001204303.1:c.1799A>G
amyloid-beta precursor protein isoform a precursor NP_000475.1:p.Glu693= NP_000475.1:p.Glu693Gly
amyloid-beta precursor protein isoform d NP_001129488.1:p.Glu669= NP_001129488.1:p.Glu669Gly
amyloid-beta precursor protein isoform b precursor NP_958816.1:p.Glu674= NP_958816.1:p.Glu674Gly
amyloid-beta precursor protein isoform f precursor NP_001129602.1:p.Glu637= NP_001129602.1:p.Glu637Gly
amyloid-beta precursor protein isoform c precursor NP_958817.1:p.Glu618= NP_958817.1:p.Glu618Gly
amyloid-beta precursor protein isoform g NP_001129603.1:p.Glu583= NP_001129603.1:p.Glu583Gly
amyloid-beta precursor protein isoform e precursor NP_001129601.1:p.Glu562= NP_001129601.1:p.Glu562Gly
amyloid-beta precursor protein isoform h precursor NP_001191230.1:p.Glu675= NP_001191230.1:p.Glu675Gly
amyloid-beta precursor protein isoform i precursor NP_001191231.1:p.Glu656= NP_001191231.1:p.Glu656Gly
amyloid-beta precursor protein isoform j precursor NP_001191232.1:p.Glu600= NP_001191232.1:p.Glu600Gly
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

4 SubSNP, 4 ClinVar submissions
No Submitter Submission ID Date (Build)
1 VIB_MOLGEN_ADFTDMDB ss95215955 Feb 13, 2013 (137)
2 GENEREVIEWS ss158188431 Nov 16, 2012 (137)
3 OMIM-CURATED-RECORDS ss475871881 Nov 28, 2011 (136)
4 ILLUMINA ss3625794433 Oct 12, 2018 (152)
5 ClinVar RCV000019725.27 Oct 12, 2018 (152)
6 ClinVar RCV000019726.27 Oct 12, 2018 (152)
7 ClinVar RCV000020307.2 Oct 12, 2018 (152)
8 ClinVar RCV000084563.1 Oct 12, 2018 (152)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3625794433 NC_000021.8:27264166:T:C NC_000021.9:25891854:T:C
RCV000019725.27, RCV000019726.27, RCV000020307.2, RCV000084563.1, ss95215955, ss158188431, ss475871881 NC_000021.9:25891854:T:C NC_000021.9:25891854:T:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

6 citations for rs63751039
PMID Title Author Year Journal
1415269 Linkage and mutational analysis of familial Alzheimer disease kindreds for the APP gene region. Kamino K et al. 1992 American journal of human genetics
10821838 Substitutions at codon 22 of Alzheimer's abeta peptide induce diverse conformational changes and apoptotic effects in human cerebral endothelial cells. Miravalle L et al. 2000 The Journal of biological chemistry
11528419 The 'Arctic' APP mutation (E693G) causes Alzheimer's disease by enhanced Abeta protofibril formation. Nilsberth C et al. 2001 Nature neuroscience
15502844 Aggressive amyloidosis in mice expressing human amyloid peptides with the Arctic mutation. Cheng IH et al. 2004 Nature medicine
18413473 Clinical and neuropathological features of the arctic APP gene mutation causing early-onset Alzheimer disease. Basun H et al. 2008 Archives of neurology
20301414 Early-Onset Familial Alzheimer Disease Bird TD et al. 1993 GeneReviews®

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post104+4a6ee9c