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NM_000447.3(PSEN2):c.954C>T (p.Pro318=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 19, 2020
Accession:
VCV000295994.4
Variation ID:
295994
Description:
single nucleotide variant
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NM_000447.3(PSEN2):c.954C>T (p.Pro318=)

Allele ID
279393
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q42.13
Genomic location
1: 226891345 (GRCh38) GRCh38 UCSC
1: 227079046 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.11:g.226891345C>T
NG_007381.1:g.25774C>T
NG_007381.2:g.26162C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:226891344:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00019
Trans-Omics for Precision Medicine (TOPMed) 0.00021
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
Trans-Omics for Precision Medicine (TOPMed) 0.00023
Exome Aggregation Consortium (ExAC) 0.00044
The Genome Aggregation Database (gnomAD) 0.00022
The Genome Aggregation Database (gnomAD), exomes 0.00041
Links
ClinGen: CA1424716
dbSNP: rs199587016
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Oct 19, 2020 RCV000403224.3
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV000338629.2
Benign 1 criteria provided, single submitter Mar 21, 2017 RCV000516572.1
Likely benign 1 criteria provided, single submitter Aug 22, 2018 RCV000860935.1
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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
170 203

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 21, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000614838.1
Submitted: (Aug 17, 2017)
Evidence details
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Dilated cardiomyopathy 1V
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000355189.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Alzheimer disease, type 4
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000355190.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Aug 22, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001001121.1
Submitted: (Mar 14, 2019)
Evidence details
Likely benign
(Oct 19, 2020)
criteria provided, single submitter
Method: clinical testing
Alzheimer disease, type 4
Allele origin: germline
Invitae
Accession: SCV001688058.1
Submitted: (Jan 07, 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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs199587016...

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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 Nov 27, 2021