chr20:4699875:G>A Detail (hg38) (PRNP)

Information

Genome

Assembly Position
hg19 chr20:4,680,521-4,680,521 View the variant detail on this assembly version.
hg38 chr20:4,699,875-4,699,875

HGVS

Type Transcript Protein
RefSeq NM_000311.3:c.655G>A NP_000302.1:p.Glu219Lys
NM_001080121.1:c.655G>A NP_001073590.1:p.Glu219Lys
NM_001080122.1:c.655G>A NP_001073591.1:p.Glu219Lys
Summary

MGeND

Clinical significance Benign
Variant entry 4
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.053
ToMMo:0.065
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.040

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 176640 OMIM
HGNC 9449 HGNC
Ensembl ENSG00000171867 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62971417 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
Benign either cerebellar ataxia without significant cognitive impairments germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
Benign progressive dementia with mild dystonia germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
Benign ataxia germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2012-02-01 no assertion criteria provided Protection against Creutzfeldt-Jakob disease germline Detail
Benign 2018-03-06 criteria provided, single submitter Inherited prion disease germline Detail
Benign 2024-01-19 criteria provided, single submitter Huntington disease-like 1 germline Detail
Benign 2022-02-05 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.859 Creutzfeldt-Jakob disease A total of 616 chromosomes from control individuals of all major continental gro... BeFree 12815603 Detail
0.588 fatal familial insomnia A total of 616 chromosomes from control individuals of all major continental gro... BeFree 12815603 Detail
0.600 Gerstmann-Straussler-Scheinker Disease A new variant of Gerstmann-Sträussler-Scheinker disease (GSS) was reported, whic... BeFree 9153600 Detail
0.024 Creutzfeldt-Jakob Disease, Sporadic Prion protein gene (PRNP) E219K is a human polymorphism commonly occurring in As... BeFree 19074151 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000311.5(PRNP):c.655G>A (p.Glu219Lys) AND Protection against Creutzfeldt-Jakob disease ClinVar Detail
NM_000311.5(PRNP):c.655G>A (p.Glu219Lys) AND Inherited prion disease ClinVar Detail
NM_000311.5(PRNP):c.655G>A (p.Glu219Lys) AND Huntington disease-like 1 ClinVar Detail
NM_000311.5(PRNP):c.655G>A (p.Glu219Lys) AND not provided ClinVar Detail
A total of 616 chromosomes from control individuals of all major continental groups, and six individ... DisGeNET Detail
A total of 616 chromosomes from control individuals of all major continental groups, and six individ... DisGeNET Detail
A new variant of Gerstmann-Sträussler-Scheinker disease (GSS) was reported, which had a substitution... DisGeNET Detail
Prion protein gene (PRNP) E219K is a human polymorphism commonly occurring in Asian populations but ... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1800014 dbSNP
Genome
hg38
Position
chr20:4,699,875-4,699,875
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
75.98
Standard deviation of sample read depth (HGVD)
36.20
Number of reference allele (HGVD)
2289
Number of alternative allele (HGVD)
129
Allele Frequency (HGVD)
0.05334987593052109
Gene Symbol (HGVD)
PRNP
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1800014
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0648
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1086
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
348
East Asian Heterozygous Counts (ExAC)
334
East Asian Homozygous Counts (ExAC)
7
East Asian Allele Frequency (ExAC)
0.040268456375838924
Chromosome Counts in All Race (ExAC)
121214
Allele Counts in All Race (ExAC)
1058
Heterozygous Counts in All Race (ExAC)
1010
Homozygous Counts in All Race (ExAC)
24
Allele Frequency in All Race (ExAC)
0.00872836471034699
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