chr1:55529187:G>A Detail (hg19) (PCSK9)

Information

Genome

Assembly Position
hg19 chr1:55,529,187-55,529,187
hg38 chr1:55,063,514-55,063,514 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_174936.3:c.2009G>A NP_777596.2:p.Gly670Glu
Ensemble ENST00000673903.1:c.1634G>A ENST00000673903.1:p.Gly545Glu
ENST00000710286.1:c.2366G>A ENST00000710286.1:p.Gly789Glu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.954
ToMMo:0.953
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.946

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 607786 OMIM
HGNC 20001 HGNC
Ensembl ENSG00000169174 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv1592049 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2017-06-22 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, familial, 1 germline Detail
Benign 2016-10-07 criteria provided, multiple submitters, no conflicts not specified germline Detail
Likely benign 2017-04-27 criteria provided, single submitter hypobetalipoproteinemia germline Detail
Benign Likely benign 2024-02-05 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, autosomal dominant, 3 germline Detail
Benign 2023-11-29 criteria provided, single submitter not provided germline Detail
Benign 2015-12-08 criteria provided, single submitter germline Detail
Benign 2023-02-09 no assertion criteria provided familial hypercholesterolemia germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.025 Coronary heart disease In the present study, we have determined the relative frequency of the R46L, I47... BeFree 17550346 Detail
0.163 Hypercholesterolemia, Familial In the present study, we have determined the relative frequency of the R46L, I47... BeFree 17550346 Detail
<0.001 Polygenic hypercholesterolemia The E670G SNP in the PCSK9 gene is associated with polygenic hypercholesterolemi... BeFree 16875509 Detail
0.010 Coronary Arteriosclerosis The PCSK9 gene E670G polymorphism affects low-density lipoprotein cholesterol le... BeFree 19191720 Detail
0.130 coronary artery disease The PCSK9 gene E670G polymorphism affects low-density lipoprotein cholesterol le... BeFree 19191720 Detail
0.010 Coronary Arteriosclerosis Effect of E670G Polymorphism in PCSK9 Gene on the Risk and Severity of Coronary ... BeFree 24599757 Detail
0.025 Coronary heart disease The PCSK9 gene E670G polymorphism affects low-density lipoprotein cholesterol le... BeFree 19191720 Detail
0.130 coronary artery disease The E670G polymorphism of the PCSK9 gene is mainly associated with a increased r... BeFree 24599757 Detail
0.025 Coronary heart disease Effect of E670G Polymorphism in PCSK9 Gene on the Risk and Severity of Coronary ... BeFree 24599757 Detail
<0.001 Ischemic stroke Effect of E670G Polymorphism in PCSK9 Gene on the Risk and Severity of Coronary ... BeFree 24599757 Detail
<0.001 Ischemic Cerebrovascular Accident Effect of E670G Polymorphism in PCSK9 Gene on the Risk and Severity of Coronary ... BeFree 24599757 Detail
0.010 Coronary Arteriosclerosis A common PCSK9 haplotype, encompassing the E670G coding single nucleotide polymo... BeFree 15893176 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_174936.4(PCSK9):c.2009G>A (p.Gly670Glu) AND Hypercholesterolemia, familial, 1 ClinVar Detail
NM_174936.4(PCSK9):c.2009G>A (p.Gly670Glu) AND not specified ClinVar Detail
NM_174936.4(PCSK9):c.2009G>A (p.Gly670Glu) AND Hypobetalipoproteinemia ClinVar Detail
NM_174936.4(PCSK9):c.2009G>A (p.Gly670Glu) AND Hypercholesterolemia, autosomal dominant, 3 ClinVar Detail
NM_174936.4(PCSK9):c.2009G>A (p.Gly670Glu) AND not provided ClinVar Detail
NM_174936.4(PCSK9):c.2009G>A (p.Gly670Glu) AND Cardiovascular phenotype ClinVar Detail
NM_174936.4(PCSK9):c.2009G>A (p.Gly670Glu) AND Familial hypercholesterolemia ClinVar Detail
In the present study, we have determined the relative frequency of the R46L, I474V and E670G variant... DisGeNET Detail
In the present study, we have determined the relative frequency of the R46L, I474V and E670G variant... DisGeNET Detail
The E670G SNP in the PCSK9 gene is associated with polygenic hypercholesterolemia in men but not in ... DisGeNET Detail
The PCSK9 gene E670G polymorphism affects low-density lipoprotein cholesterol levels but is not a ri... DisGeNET Detail
The PCSK9 gene E670G polymorphism affects low-density lipoprotein cholesterol levels but is not a ri... DisGeNET Detail
Effect of E670G Polymorphism in PCSK9 Gene on the Risk and Severity of Coronary Heart Disease and Is... DisGeNET Detail
The PCSK9 gene E670G polymorphism affects low-density lipoprotein cholesterol levels but is not a ri... DisGeNET Detail
The E670G polymorphism of the PCSK9 gene is mainly associated with a increased risk and severity of ... DisGeNET Detail
Effect of E670G Polymorphism in PCSK9 Gene on the Risk and Severity of Coronary Heart Disease and Is... DisGeNET Detail
Effect of E670G Polymorphism in PCSK9 Gene on the Risk and Severity of Coronary Heart Disease and Is... DisGeNET Detail
Effect of E670G Polymorphism in PCSK9 Gene on the Risk and Severity of Coronary Heart Disease and Is... DisGeNET Detail
A common PCSK9 haplotype, encompassing the E670G coding single nucleotide polymorphism, is a novel g... 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
-
Genome
hg19
Position
chr1:55,529,187-55,529,187
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1205
Mean of sample read depth (HGVD)
43.16
Standard deviation of sample read depth (HGVD)
18.86
Number of reference allele (HGVD)
111
Number of alternative allele (HGVD)
2298
Allele Frequency (HGVD)
0.9539227895392279
Gene Symbol (HGVD)
PCSK9
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))
rs505151
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9528
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
15969
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8616
East Asian Allele Counts (ExAC)
8151
East Asian Heterozygous Counts (ExAC)
445
East Asian Homozygous Counts (ExAC)
3853
East Asian Allele Frequency (ExAC)
0.9460306406685237
Chromosome Counts in All Race (ExAC)
120760
Allele Counts in All Race (ExAC)
113911
Heterozygous Counts in All Race (ExAC)
6017
Homozygous Counts in All Race (ExAC)
53947
Allele Frequency in All Race (ExAC)
0.9432842000662471
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