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NM_000447.3(PSEN2):c.184C>T (p.Arg62Cys)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Sep 1, 2021)
Last evaluated:
Jun 10, 2020
Accession:
VCV000567646.7
Variation ID:
567646
Description:
single nucleotide variant
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NM_000447.3(PSEN2):c.184C>T (p.Arg62Cys)

Allele ID
556792
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q42.13
Genomic location
1: 226883747 (GRCh38) GRCh38 UCSC
1: 227071448 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_225t1:c.184C>T LRG_225p1:p.Arg62Cys
NC_000001.10:g.227071448C>T
NC_000001.11:g.226883747C>T
... more HGVS
Protein change
R62C
Other names
-
Canonical SPDI
NC_000001.11:226883746:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Exome Aggregation Consortium (ExAC) 0.00017
Trans-Omics for Precision Medicine (TOPMed) 0.00020
The Genome Aggregation Database (gnomAD), exomes 0.00021
The Genome Aggregation Database (gnomAD) 0.00029
Links
dbSNP: rs150400387
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Jun 10, 2020 RCV000687794.4
Uncertain significance 1 criteria provided, single submitter Dec 16, 2019 RCV001584558.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PSEN2 - - GRCh38
GRCh37
164 197

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 10, 2020)
criteria provided, single submitter
Method: clinical testing
Alzheimer disease, type 4
Allele origin: germline
Invitae
Accession: SCV000815381.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (8)
Comment:
This sequence change replaces arginine with cysteine at codon 62 of the PSEN2 protein (p.Arg62Cys). The arginine residue is moderately conserved and there is a … (more)
Uncertain significance
(Dec 16, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001820246.1
Submitted: (Sep 01, 2021)
Evidence details
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the … (more)

Functional evidence

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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 this variant

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Title Author Journal Year Link
Predictors for a dementia gene mutation based on gene-panel next-generation sequencing of a large dementia referral series. Koriath C Molecular psychiatry 2020 PMID: 30279455
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
A case of possibly pathogenic <i>PSEN2</i> R62C mutation in a patient with probable early-onset Alzheimer's dementia supported by structure prediction. Park KW Clinical interventions in aging 2017 PMID: 28243073
Pathogenic variant burden in the ExAC database: an empirical approach to evaluating population data for clinical variant interpretation. Kobayashi Y Genome medicine 2017 PMID: 28166811
A genetic screen of the mutations in the Korean patients with early-onset Alzheimer's disease. An SS Clinical interventions in aging 2016 PMID: 28008242
On the identification of low allele frequency mosaic mutations in the brains of Alzheimer's disease patients. Sala Frigerio C Alzheimer's & dementia : the journal of the Alzheimer's Association 2015 PMID: 25937274
Familial clustering and genetic risk for dementia in a genetically isolated Dutch population. Sleegers K Brain : a journal of neurology 2004 PMID: 15130954
- - - - PMID: 225104557

Text-mined citations for rs150400387...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 29, 2021