NM_000447.3(PSEN2):c.211C>T (p.Arg71Trp) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely benign (4 submissions)
Last evaluated:: Sep 18, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000861064.8

Allele description

NM_000447.3(PSEN2):c.211C>T (p.Arg71Trp)

Gene:

PSEN2:presenilin 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q42.13

Genomic location:

Preferred name:

NM_000447.3(PSEN2):c.211C>T (p.Arg71Trp)

HGVS:

NC_000001.11:g.226883774C>T
NG_007381.2:g.18591C>T
NM_000447.3:c.211C>TMANE SELECT
NM_012486.3:c.211C>T
NP_000438.2:p.Arg71Trp
NP_036618.2:p.Arg71Trp
LRG_225t1:c.211C>T
LRG_225:g.18591C>T
LRG_225p1:p.Arg71Trp
NC_000001.10:g.227071475C>T
NG_007381.1:g.18203C>T
NM_000447.2:c.211C>T
P49810:p.Arg71Trp

Protein change:

R71W

Links:

UniProtKB: P49810#VAR_070027; dbSNP: rs140501902

NCBI 1000 Genomes Browser:

rs140501902

Molecular consequence:

NM_000447.3:c.211C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_012486.3:c.211C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000614831	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely benign (Nov 8, 2018)	germline	clinical testing	PubMed (14) [See all records that cite these PMIDs] 23990795, 15130954, 16474849, 18667258, 21544564, 21959359, 22312439, 22503161, 22118943, 22475797, 25604855, 26242991, 22753229, 26467025
SCV001807919	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001927747	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV004563098	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Likely benign (Sep 18, 2023)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The PSEN1, p.E318G variant increases the risk of Alzheimer's disease in APOE-ε4 carriers.

Benitez BA, Karch CM, Cai Y, Jin SC, Cooper B, Carrell D, Bertelsen S, Chibnik L, Schneider JA, Bennett DA; Alzheimer's Disease Neuroimaging Initiative.; Genetic and Environmental Risk for Alzheimer's Disease Consortium GERAD., Fagan AM, Holtzman D, Morris JC, Goate AM, Cruchaga C.

PLoS Genet. 2013;9(8):e1003685. doi: 10.1371/journal.pgen.1003685. Epub 2013 Aug 22.

PubMed [citation]

PMID:: 23990795
PMCID:: PMC3750021

Familial clustering and genetic risk for dementia in a genetically isolated Dutch population.

Sleegers K, Roks G, Theuns J, Aulchenko YS, Rademakers R, Cruts M, van Gool WA, Van Broeckhoven C, Heutink P, Oostra BA, van Swieten JC, van Duijn CM.

Brain. 2004 Jul;127(Pt 7):1641-9. Epub 2004 May 6.

PubMed [citation]

PMID:: 15130954

See all PubMed Citations (14)

Details of each submission

From Athena Diagnostics, SCV000614831.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (14)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001807919.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001927747.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV004563098.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 7, 2024

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