chr20:4680251:A>G Detail (hg19) (PRNP)

Information

Genome

Assembly Position
hg19 chr20:4,680,251-4,680,251
hg38 chr20:4,699,605-4,699,605 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000311.3:c.385A>G NP_000302.1:p.Met129Val
NM_001080121.1:c.385A>G NP_001073590.1:p.Met129Val
NM_001080122.1:c.385A>G NP_001073591.1:p.Met129Val
Summary

MGeND

Clinical significance Pathogenic Uncertain significance
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.040
ToMMo:0.039
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.024

Prediction

ClinVar

Clinical Significance Benign Likely 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 tgv62971343 TogoVar
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
Uncertain significance other unknown MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2009-11-19 no assertion criteria provided Prion disease, susceptibility to germline Detail
risk factor 2009-11-19 no assertion criteria provided Alzheimer disease, early-onset, susceptibility to germline Detail
risk factor 2009-11-19 no assertion criteria provided Aphasia, primary progressive, susceptibility to germline Detail
Pathogenic 2008-11-26 no assertion criteria provided Inherited Creutzfeldt-Jakob disease germline Detail
Pathogenic 2008-11-26 no assertion criteria provided fatal familial insomnia germline Detail
Benign 2017-04-27 criteria provided, single submitter Inherited prion disease germline Detail
Benign Likely benign no assertion criteria provided not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Huntington disease-like 1 germline unknown Detail
Likely benign 2019-01-01 criteria provided, single submitter Inherited Creutzfeldt-Jakob disease unknown Detail
Benign 2023-11-29 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2021-07-22 criteria provided, single submitter fatal familial insomnia,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to,Gerstmann-Straussler-Scheinker syndrome unknown Detail
Benign 2021-07-22 criteria provided, single submitter fatal familial insomnia,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to,Gerstmann-Straussler-Scheinker syndrome unknown Detail
Benign 2021-07-22 criteria provided, single submitter fatal familial insomnia,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to,Gerstmann-Straussler-Scheinker syndrome unknown Detail
Benign 2021-07-22 criteria provided, single submitter fatal familial insomnia,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to,Gerstmann-Straussler-Scheinker syndrome unknown Detail
Benign 2021-07-22 criteria provided, single submitter fatal familial insomnia,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to,Gerstmann-Straussler-Scheinker syndrome unknown Detail
Benign 2021-07-22 criteria provided, single submitter fatal familial insomnia,Spongiform encephalopathy with neuropsychiatric features,Huntington disease-like 1,Inherited Creutzfeldt-Jakob disease,Kuru, susceptibility to,Gerstmann-Straussler-Scheinker syndrome unknown Detail
Uncertain significance 2023-07-28 no assertion criteria provided autism spectrum disorder unknown Detail
Benign criteria provided, single submitter fatal familial insomnia germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.481 Prion Diseases NA CLINVAR Detail
0.859 Creutzfeldt-Jakob disease A similar association was found in a small sample of patients with iatrogenic CJ... GWASCAT 19081515 Detail
0.177 Alzheimer's disease [The findings support the association of several loci with AD, and suggest how i... GAD 20574532 Detail
0.128 Hepatolenticular Degeneration This study shows for the first time, to our knowledge, that the human PrP polymo... BeFree 16831968 Detail
0.859 Creutzfeldt-Jakob disease FFI and a familial type of Creutzfeldt-Jakob disease (CJD178), share the D178N m... BeFree 8647879 Detail
0.010 Plaque, Amyloid The amount of PrP deposition including florid/amyloid plaques in the brain also ... BeFree 23792955 Detail
0.859 Creutzfeldt-Jakob disease A total of 616 chromosomes from control individuals of all major continental gro... BeFree 12815603 Detail
0.001 colorectal carcinoma Prion protein expression and the M129V polymorphism of the PRNP gene in patients... BeFree 20564346 Detail
0.481 Prion Diseases Genome-wide association study in multiple human prion diseases suggests genetic ... GWASCAT 22210626 Detail
0.859 Creutzfeldt-Jakob disease [A similar association was found in a small sample of patients with iatrogenic C... GAD 19081515 Detail
0.024 Creutzfeldt-Jakob Disease, Sporadic We provide a detailed analysis on clinical presentation and first diagnosis in a... BeFree 25022936 Detail
0.011 Epilepsy, Temporal Lobe Association between the M129V variant allele of PRNP gene and mild temporal lobe... BeFree 17092648 Detail
0.588 fatal familial insomnia A total of 616 chromosomes from control individuals of all major continental gro... BeFree 12815603 Detail
0.859 Creutzfeldt-Jakob disease An important determinant for CJD risk and phenotype is the M129V polymorphism of... BeFree 21600043 Detail
0.020 Neurodegenerative Disorders Moreover, the codon 129 polymorphism (M129V) of the PRNP gene (the PrP(C)-encodi... BeFree 20564346 Detail
0.177 Alzheimer's disease The association between the methionine/valine (M/V) polymorphism (rs1799990) in ... BeFree 23399523 Detail
0.859 Creutzfeldt-Jakob disease The polymorphism at codon 129 (M129V) of the human prion protein gene (PRNP) is ... BeFree 17202849 Detail
0.002 Impaired cognition The prion protein M129V polymorphism: longevity and cognitive impairment among P... BeFree 23406923 Detail
0.859 Creutzfeldt-Jakob disease Distribution of the M129V polymorphism of the prion protein gene in a Turkish po... BeFree 11840201 Detail
0.859 Creutzfeldt-Jakob disease Prion protein gene polymorphism M129V represents a known risk factor for Creutzf... BeFree 16897605 Detail
0.003 colorectal cancer Prion protein expression and the M129V polymorphism of the PRNP gene in patients... BeFree 20564346 Detail
<0.001 Psychotic Disorders M129V variation in the prion protein gene and psychotic disorders: relationship ... BeFree 16949098 Detail
<0.001 Migraine Disorders Prion protein gene M129V polymorphism and variability in age at migraine onset. BeFree 23405858 Detail
0.859 Creutzfeldt-Jakob disease The polymorphism at codon 129 (M129V) of the prion protein gene (PRNP) is a reco... BeFree 16324095 Detail
0.588 fatal familial insomnia NA CLINVAR Detail
0.859 Creutzfeldt-Jakob disease NA CLINVAR Detail
0.024 Creutzfeldt-Jakob Disease, Sporadic Significant association of a M129V independent polymorphism in the 5' UTR of the... BeFree 17047093 Detail
0.481 Prion Diseases In human prion diseases, the M129V prion protein polymorphism is known to confer... BeFree 22062631 Detail
0.008 Senile Plaques The amount of PrP deposition including florid/amyloid plaques in the brain also ... BeFree 23792955 Detail
0.012 New Variant Creutzfeldt-Jakob Disease So far, all clinical cases of new variant Creutzfeldt-Jakob disease (vCJD), thou... BeFree 19495414 Detail
0.481 Prion Diseases The genetic variant at codon 129 (M129V) of the prion protein gene (PRNP) is con... BeFree 20592456 Detail
0.859 Creutzfeldt-Jakob disease Our proband was MM homozygous for the M129V polymorphism within the prion protei... BeFree 18236005 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND Prion disease, susceptibility to ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND Alzheimer disease, early-onset, susceptibility to ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND Aphasia, primary progressive, susceptibility to ClinVar Detail
NM_000311.4(PRNP):c.[385A>G;532G>A] AND Inherited Creutzfeldt-Jakob disease ClinVar Detail
NM_000311.4(PRNP):c.[385A>G;532G>A] AND Fatal familial insomnia ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND Inherited prion disease ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND not specified ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND Huntington disease-like 1 ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND Inherited Creutzfeldt-Jakob disease ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND not provided ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND multiple conditions ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND Autism spectrum disorder ClinVar Detail
NM_000311.5(PRNP):c.385A>G (p.Met129Val) AND Fatal familial insomnia ClinVar Detail
NA DisGeNET Detail
A similar association was found in a small sample of patients with iatrogenic CJD (p=0.030) but not ... DisGeNET Detail
[The findings support the association of several loci with AD, and suggest how intermediate phenotyp... DisGeNET Detail
This study shows for the first time, to our knowledge, that the human PrP polymorphism M129V influen... DisGeNET Detail
FFI and a familial type of Creutzfeldt-Jakob disease (CJD178), share the D178N mutation in the PrP g... DisGeNET Detail
The amount of PrP deposition including florid/amyloid plaques in the brain also gradually decreased ... DisGeNET Detail
A total of 616 chromosomes from control individuals of all major continental groups, and six individ... DisGeNET Detail
Prion protein expression and the M129V polymorphism of the PRNP gene in patients with colorectal can... DisGeNET Detail
Genome-wide association study in multiple human prion diseases suggests genetic risk factors additio... DisGeNET Detail
[A similar association was found in a small sample of patients with iatrogenic CJD (p=0.030) but not... DisGeNET Detail
We provide a detailed analysis on clinical presentation and first diagnosis in a large group of pati... DisGeNET Detail
Association between the M129V variant allele of PRNP gene and mild temporal lobe epilepsy in women. DisGeNET Detail
A total of 616 chromosomes from control individuals of all major continental groups, and six individ... DisGeNET Detail
An important determinant for CJD risk and phenotype is the M129V polymorphism of the human prion pro... DisGeNET Detail
Moreover, the codon 129 polymorphism (M129V) of the PRNP gene (the PrP(C)-encoding gene) has been as... DisGeNET Detail
The association between the methionine/valine (M/V) polymorphism (rs1799990) in the PRNP gene and th... DisGeNET Detail
The polymorphism at codon 129 (M129V) of the human prion protein gene (PRNP) is a known risk factor ... DisGeNET Detail
The prion protein M129V polymorphism: longevity and cognitive impairment among Polish centenarians. DisGeNET Detail
Distribution of the M129V polymorphism of the prion protein gene in a Turkish population suggests a ... DisGeNET Detail
Prion protein gene polymorphism M129V represents a known risk factor for Creutzfeldt-Jakob disease. DisGeNET Detail
Prion protein expression and the M129V polymorphism of the PRNP gene in patients with colorectal can... DisGeNET Detail
M129V variation in the prion protein gene and psychotic disorders: relationship to neuropsychologica... DisGeNET Detail
Prion protein gene M129V polymorphism and variability in age at migraine onset. DisGeNET Detail
The polymorphism at codon 129 (M129V) of the prion protein gene (PRNP) is a recognized genetic marke... DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
Significant association of a M129V independent polymorphism in the 5' UTR of the PRNP gene with spor... DisGeNET Detail
In human prion diseases, the M129V prion protein polymorphism is known to confer susceptibility to t... DisGeNET Detail
The amount of PrP deposition including florid/amyloid plaques in the brain also gradually decreased ... DisGeNET Detail
So far, all clinical cases of new variant Creutzfeldt-Jakob disease (vCJD), thought to result from t... DisGeNET Detail
The genetic variant at codon 129 (M129V) of the prion protein gene (PRNP) is considered to be a majo... DisGeNET Detail
Our proband was MM homozygous for the M129V polymorphism within the prion protein gene (PRNP), a kno... 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
rs1799990 dbSNP
Genome
hg19
Position
chr20:4,680,251-4,680,251
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
201.29
Standard deviation of sample read depth (HGVD)
91.07
Number of reference allele (HGVD)
2323
Number of alternative allele (HGVD)
97
Allele Frequency (HGVD)
0.04008264462809917
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))
rs1799990
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0394
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
660
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8638
East Asian Allele Counts (ExAC)
208
East Asian Heterozygous Counts (ExAC)
200
East Asian Homozygous Counts (ExAC)
4
East Asian Allele Frequency (ExAC)
0.024079648066682103
Chromosome Counts in All Race (ExAC)
121156
Allele Counts in All Race (ExAC)
37289
Heterozygous Counts in All Race (ExAC)
24879
Homozygous Counts in All Race (ExAC)
6205
Allele Frequency in All Race (ExAC)
0.30777675063554427
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