Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_000311.5(PRNP):c.655G>A (p.Glu219Lys)

Help
Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Aug 24, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000013409.9
Variation ID:
13409
Description:
single nucleotide variant
Help

NM_000311.5(PRNP):c.655G>A (p.Glu219Lys)

Allele ID
28448
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
20p13
Genomic location
20: 4699875 (GRCh38) GRCh38 UCSC
20: 4680521 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000020.10:g.4680521G>A
NC_000020.11:g.4699875G>A
NM_000311.5:c.655G>A MANE Select NP_000302.1:p.Glu219Lys missense
... more HGVS
Protein change
E219K
Other names
-
Canonical SPDI
NC_000020.11:4699874:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.01617 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00802
Exome Aggregation Consortium (ExAC) 0.00873
Trans-Omics for Precision Medicine (TOPMed) 0.00299
The Genome Aggregation Database (gnomAD) 0.00185
1000 Genomes Project 0.01617
Links
ClinGen: CA123094
UniProtKB: P04156#VAR_006477
OMIM: 176640.0019
dbSNP: rs1800014
Varsome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Mar 6, 2018 RCV000020257.5
Benign 1 criteria provided, single submitter Dec 4, 2020 RCV000873683.3
Benign 1 criteria provided, single submitter Apr 3, 2020 RCV001287480.1
Protection against Creutzfeldt-Jakob disease
Uncertain significance 1 no assertion criteria provided Feb 1, 2012 RCV000014350.8
Likely benign 2 no assertion criteria provided - RCV001573203.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PRNP - - GRCh38
GRCh37
98 130

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Mar 06, 2018)
criteria provided, single submitter
Method: clinical testing
Genetic prion diseases
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000434232.3
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)
Benign
(Apr 03, 2020)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001474173.1
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Huntington disease-like 1
Allele origin: germline
Invitae
Accession: SCV001015725.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001807093.1
Submitted: (Aug 24, 2021)
Evidence details
Uncertain significance
(Feb 01, 2012)
no assertion criteria provided
Method: literature only
RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE
Allele origin: germline
OMIM
Accession: SCV000034599.7
Submitted: (Aug 23, 2016)
Evidence details
Publications
PubMed (6)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001798698.1
Submitted: (Aug 19, 2021)
Evidence details

Functional evidence

Help
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

Help
Title Author Journal Year Link
Prion protein gene M232R variation is probably an uncommon polymorphism rather than a pathogenic mutation. Beck J Brain : a journal of neurology 2012 PMID: 22108575
Heterozygosity at polymorphic codon 219 in variant creutzfeldt-jakob disease. Lukic A Archives of neurology 2010 PMID: 20697057
Association of sporadic Creutzfeldt-Jakob disease with homozygous genotypes at PRNP codons 129 and 219 in the Korean population. Jeong BH Neurogenetics 2005 PMID: 16217673
Creutzfeldt-Jakob disease with a novel insertion and codon 219 Lys/Lys polymorphism in PRNP. Nishida Y Neurology 2004 PMID: 15557533
Prion susceptibility and protective alleles exhibit marked geographic differences. Soldevila M Human mutation 2003 PMID: 12815603
Protective prion protein polymorphisms against sporadic Creutzfeldt-Jakob disease. Shibuya S Lancet (London, England) 1998 PMID: 9482303

Text-mined citations for rs1800014...

Help
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 Aug 25, 2021