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NM_000447.3(PSEN2):c.415G>A (p.Val139Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Mar 31, 2018
Accession:
VCV000448149.8
Variation ID:
448149
Description:
single nucleotide variant
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NM_000447.3(PSEN2):c.415G>A (p.Val139Met)

Allele ID
440487
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q42.13
Genomic location
1: 226885596 (GRCh38) GRCh38 UCSC
1: 227073297 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.227073297G>A
NC_000001.11:g.226885596G>A
NM_000447.3:c.415G>A MANE Select NP_000438.2:p.Val139Met missense
... more HGVS
Protein change
V139M
Other names
-
Canonical SPDI
NC_000001.11:226885595:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00014
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA1424514
dbSNP: rs202178897
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Aug 8, 2017 RCV001099214.1
Benign 1 criteria provided, single submitter Aug 8, 2017 RCV001101216.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Mar 31, 2018 RCV000517898.3
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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
156 189

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Mar 31, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000614834.2
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (1)
Likely benign
(Aug 08, 2017)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1V
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001255649.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Aug 08, 2017)
criteria provided, single submitter
Method: clinical testing
Alzheimer disease, type 4
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001257809.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Feb 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001147699.6
Submitted: (Jul 04, 2021)
Evidence details

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
Alzheimer's disease phenotypes and genotypes associated with mutations in presenilin 2. Jayadev S Brain : a journal of neurology 2010 PMID: 20375137
Late onset familial Alzheimer's disease: novel presenilin 2 mutation and PS1 E318G polymorphism. Bernardi L Journal of neurology 2008 PMID: 18350357

Text-mined citations for rs202178897...

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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 Jul 10, 2021