chr20:4680561:T>G Detail (hg19) (PRNP)

Information

Genome

Assembly Position
hg19 chr20:4,680,561-4,680,561
hg38 chr20:4,699,915-4,699,915 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000311.3:c.695T>G NP_000302.1:p.Met232Arg
NM_001080121.1:c.695T>G NP_001073590.1:p.Met232Arg
NM_001080122.1:c.695T>G NP_001073591.1:p.Met232Arg
Summary

MGeND

Clinical significance Benign Likely pathogenic
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.006
ToMMo:0.007
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.001

Prediction

ClinVar

Clinical Significance Uncertain significance
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 tgv62971427 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
Likely pathogenic other unknown 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 Inherited Creutzfeldt-Jakob disease germline Detail
Uncertain significance 2023-11-01 criteria provided, multiple submitters, no conflicts Huntington disease-like 1 germline unknown Detail
Uncertain significance 2021-12-02 criteria provided, single submitter Kuru, susceptibility to,Huntington disease-like 1,fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Inherited Creutzfeldt-Jakob disease,Spongiform encephalopathy with neuropsychiatric features unknown Detail
Uncertain significance 2021-12-02 criteria provided, single submitter Kuru, susceptibility to,Huntington disease-like 1,fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Inherited Creutzfeldt-Jakob disease,Spongiform encephalopathy with neuropsychiatric features unknown Detail
Uncertain significance 2021-12-02 criteria provided, single submitter Kuru, susceptibility to,Huntington disease-like 1,fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Inherited Creutzfeldt-Jakob disease,Spongiform encephalopathy with neuropsychiatric features unknown Detail
Uncertain significance 2021-12-02 criteria provided, single submitter Kuru, susceptibility to,Huntington disease-like 1,fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Inherited Creutzfeldt-Jakob disease,Spongiform encephalopathy with neuropsychiatric features unknown Detail
Uncertain significance 2021-12-02 criteria provided, single submitter Kuru, susceptibility to,Huntington disease-like 1,fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Inherited Creutzfeldt-Jakob disease,Spongiform encephalopathy with neuropsychiatric features unknown Detail
Uncertain significance 2021-12-02 criteria provided, single submitter Kuru, susceptibility to,Huntington disease-like 1,fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Inherited Creutzfeldt-Jakob disease,Spongiform encephalopathy with neuropsychiatric features unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.481 Prion Diseases NA CLINVAR Detail
<0.001 Creutzfeldt-Jakob Disease, Familial Point mutations M232R (PrP(232R)), M232T (PrP(232T)), and P238S (PrP(238S)) in t... BeFree 18325785 Detail
0.012 Creutzfeldt-Jakob Disease, Familial Point mutations M232R (PrP(232R)), M232T (PrP(232T)), and P238S (PrP(238S)) in t... BeFree 18325785 Detail
0.859 Creutzfeldt-Jakob disease Point mutations M232R (PrP(232R)), M232T (PrP(232T)), and P238S (PrP(238S)) in t... BeFree 18325785 Detail
0.859 Creutzfeldt-Jakob disease NA CLINVAR Detail
0.859 Creutzfeldt-Jakob disease Patients with genetic Creutzfeldt-Jakob disease in which arginine is substituted... BeFree 19422537 Detail
0.859 Creutzfeldt-Jakob disease Creutzfeldt-Jakob disease with the M232R mutation in the prion protein gene in t... BeFree 21983261 Detail
0.481 Prion Diseases Based on these findings, together with the results in previous CJD cases with M2... BeFree 21983261 Detail
0.859 Creutzfeldt-Jakob disease To describe the clinical features of Creutzfeldt-Jakob disease with a substituti... BeFree 17965961 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000311.5(PRNP):c.695T>G (p.Met232Arg) AND Inherited Creutzfeldt-Jakob disease ClinVar Detail
NM_000311.5(PRNP):c.695T>G (p.Met232Arg) AND Huntington disease-like 1 ClinVar Detail
NM_000311.5(PRNP):c.695T>G (p.Met232Arg) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.695T>G (p.Met232Arg) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.695T>G (p.Met232Arg) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.695T>G (p.Met232Arg) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.695T>G (p.Met232Arg) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.695T>G (p.Met232Arg) AND multiple conditions ClinVar Detail
NA DisGeNET Detail
Point mutations M232R (PrP(232R)), M232T (PrP(232T)), and P238S (PrP(238S)) in the glycosylphosphati... DisGeNET Detail
Point mutations M232R (PrP(232R)), M232T (PrP(232T)), and P238S (PrP(238S)) in the glycosylphosphati... DisGeNET Detail
Point mutations M232R (PrP(232R)), M232T (PrP(232T)), and P238S (PrP(238S)) in the glycosylphosphati... DisGeNET Detail
NA DisGeNET Detail
Patients with genetic Creutzfeldt-Jakob disease in which arginine is substituted for methionine at c... DisGeNET Detail
Creutzfeldt-Jakob disease with the M232R mutation in the prion protein gene in two cases showing dif... DisGeNET Detail
Based on these findings, together with the results in previous CJD cases with M232R, we noted the po... DisGeNET Detail
To describe the clinical features of Creutzfeldt-Jakob disease with a substitution of arginine for m... 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
rs74315409 dbSNP
Genome
hg19
Position
chr20:4,680,561-4,680,561
Variant Type
snv
Reference Allele
T
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
54.61
Standard deviation of sample read depth (HGVD)
26.39
Number of reference allele (HGVD)
2404
Number of alternative allele (HGVD)
14
Allele Frequency (HGVD)
0.005789909015715467
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))
rs74315409
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.007
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
117
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8478
East Asian Allele Counts (ExAC)
10
East Asian Heterozygous Counts (ExAC)
10
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0011795234725171032
Chromosome Counts in All Race (ExAC)
117352
Allele Counts in All Race (ExAC)
10
Heterozygous Counts in All Race (ExAC)
10
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
8.521371599972732E-5
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