chr20:4680404:G>A Detail (hg19) (PRNP)

Information

Genome

Assembly Position
hg19 chr20:4,680,404-4,680,404
hg38 chr20:4,699,758-4,699,758 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000311.3:c.538G>A NP_000302.1:p.Val180Ile
NM_001080121.1:c.538G>A NP_001073590.1:p.Val180Ile
NM_001080122.1:c.538G>A NP_001073591.1:p.Val180Ile
Summary

MGeND

Clinical significance Benign Pathogenic
Variant entry 3
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.004
ToMMo:0.005
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic low penetrance
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 tgv62971385 TogoVar
COSMIC COSM3758611 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other unknown MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
Pathogenic other germline MGS000073
(TMGS000167) 		Kenjiro Kosaki
 Keio University
IRUD
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely pathogenic 2016-03-18 criteria provided, single submitter Inherited Creutzfeldt-Jakob disease germline Detail
Pathogenic 2019-04-05 criteria provided, single submitter Inherited prion disease germline Detail
Pathogenic low penetrance 2023-12-11 criteria provided, single submitter Huntington disease-like 1 germline Detail
Likely pathogenic 2022-01-03 criteria provided, single submitter Gerstmann-Straussler-Scheinker syndrome germline Detail
Pathogenic 2021-11-24 criteria provided, single submitter fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to unknown Detail
Pathogenic 2021-11-24 criteria provided, single submitter fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to unknown Detail
Pathogenic 2021-11-24 criteria provided, single submitter fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to unknown Detail
Pathogenic 2021-11-24 criteria provided, single submitter fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to unknown Detail
Pathogenic 2021-11-24 criteria provided, single submitter fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to unknown Detail
Pathogenic 2021-11-24 criteria provided, single submitter fatal familial insomnia,Gerstmann-Straussler-Scheinker syndrome,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.481 Prion Diseases NA CLINVAR Detail
0.859 Creutzfeldt-Jakob disease NA CLINVAR Detail
0.859 Creutzfeldt-Jakob disease An autopsied case of V180I Creutzfeldt-Jakob disease presenting with panencephal... BeFree 21269331 Detail
0.859 Creutzfeldt-Jakob disease An autopsy case of Creutzfeldt-Jakob disease with a V180I mutation of the PrP ge... BeFree 19703264 Detail
0.859 Creutzfeldt-Jakob disease Rare V180I mutation in PRNP gene of a Chinese patient with Creutzfeldt-Jakob dis... BeFree 25482600 Detail
0.859 Creutzfeldt-Jakob disease The present study reported DWI results in cases of familial CJD with a V180I mut... BeFree 20051687 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND Inherited Creutzfeldt-Jakob disease ClinVar Detail
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND Inherited prion disease ClinVar Detail
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND Huntington disease-like 1 ClinVar Detail
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND Gerstmann-Straussler-Scheinker syndrome ClinVar Detail
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.538G>A (p.Val180Ile) AND multiple conditions ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
An autopsied case of V180I Creutzfeldt-Jakob disease presenting with panencephalopathic-type patholo... DisGeNET Detail
An autopsy case of Creutzfeldt-Jakob disease with a V180I mutation of the PrP gene and Alzheimer-typ... DisGeNET Detail
Rare V180I mutation in PRNP gene of a Chinese patient with Creutzfeldt-Jakob disease. DisGeNET Detail
The present study reported DWI results in cases of familial CJD with a V180I mutation (CJD180) in th... 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
rs74315408 dbSNP
Genome
hg19
Position
chr20:4,680,404-4,680,404
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
203.75
Standard deviation of sample read depth (HGVD)
94.16
Number of reference allele (HGVD)
2411
Number of alternative allele (HGVD)
9
Allele Frequency (HGVD)
0.00371900826446281
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))
rs74315408
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0047
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
79
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
3
East Asian Heterozygous Counts (ExAC)
3
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
3.4666050381326557E-4
Chromosome Counts in All Race (ExAC)
121398
Allele Counts in All Race (ExAC)
6
Heterozygous Counts in All Race (ExAC)
6
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
4.942420797706717E-5
Genome browser