chr1:55039974:G>T Detail (hg38) (PCSK9)

Information

Genome

Assembly Position
hg19 chr1:55,505,647-55,505,647 View the variant detail on this assembly version.
hg38 chr1:55,039,974-55,039,974

HGVS

Type Transcript Protein
RefSeq NM_174936.3:c.137G>T NP_777596.2:p.Arg46Leu
Ensemble ENST00000302118.5:c.137G>T ENST00000302118.5:p.Arg46Leu
ENST00000710286.1:c.494G>T ENST00000710286.1:p.Arg165Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

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

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 tgv298611060 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
association 2008-03-20 no assertion criteria provided Low density lipoprotein cholesterol level quantitative trait locus 1 germline Detail
Benign Likely benign 2024-01-31 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, autosomal dominant, 3 germline unknown Detail
Benign 2019-08-22 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, familial, 1 germline Detail
Pathogenic no assertion criteria provided germline Detail
Benign 2017-05-08 criteria provided, single submitter not specified germline Detail
Benign 2023-09-08 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Benign 2018-03-06 criteria provided, single submitter hypobetalipoproteinemia germline Detail
Benign 2020-12-10 criteria provided, single submitter familial hypercholesterolemia germline Detail
Benign 2017-03-16 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 atherosclerosis The Atherosclerosis Risk in Communities (ARIC) Study assessed risk factors and P... BeFree 18436227 Detail
0.013 Hypercholesterolemia, Familial We measured plasma PCSK9 concentrations in healthy men with a PCSK9 (proprotein ... BeFree 19797716 Detail
0.025 Coronary heart disease In the present study, we have determined the relative frequency of the R46L, I47... BeFree 17550346 Detail
0.012 Cardiovascular Diseases PCSK9 R46L, lower LDL, and cardiovascular disease risk in familial hypercholeste... BeFree 25278291 Detail
0.025 Coronary heart disease Caucasian carriers of the T allele at R46L in the proprotein convertase subtilis... BeFree 18262190 Detail
0.025 Coronary heart disease The R46L variant in the proprotein-convertase subtilisin-kexin type 9 (PCSK9) ge... BeFree 20699424 Detail
0.163 Hypercholesterolemia, Familial Loss-of-function mutation R46L in the PCSK9 gene has little impact on the levels... BeFree 19917273 Detail
0.163 Hypercholesterolemia, Familial Healthy individuals carrying the PCSK9 p.R46L variant and familial hypercholeste... BeFree 19797716 Detail
0.162 Hypercholesterolemia Using this cell-based assay of PCSK9 activity, we found that the relative potenc... BeFree 17493938 Detail
0.003 Myocardial Ischemia PCSK9 R46L, low-density lipoprotein cholesterol levels, and risk of ischemic hea... BeFree 20579540 Detail
0.004 arteriosclerosis The Atherosclerosis Risk in Communities (ARIC) Study assessed risk factors and P... BeFree 18436227 Detail
0.162 Hypercholesterolemia No association tests were performed for R46L variant because of its very low fre... BeFree 24793346 Detail
0.163 Hypercholesterolemia, Familial PCSK9 R46L, lower LDL, and cardiovascular disease risk in familial hypercholeste... BeFree 25278291 Detail
0.463 Hypercholesterolemia, Familial 1130 unrelated subjects with molecularly defined FH were screened for mutation R... BeFree 19917273 Detail
0.163 Hypercholesterolemia, Familial In the present study, we have determined the relative frequency of the R46L, I47... BeFree 17550346 Detail
<0.001 Xanthoma The aims of this cross-sectional cohort-study were to examine whether the PCSK9 ... BeFree 25278291 Detail
0.130 coronary artery disease The R46L variant in the proprotein-convertase subtilisin-kexin type 9 (PCSK9) ge... BeFree 20699424 Detail
<0.001 arteriosclerosis The Atherosclerosis Risk in Communities (ARIC) Study assessed risk factors and P... BeFree 18436227 Detail
0.012 atherosclerosis The Atherosclerosis Risk in Communities (ARIC) Study assessed risk factors and P... BeFree 18436227 Detail
0.012 Cardiovascular Diseases Our data support the concept that the rare allele of the R46L SNP at the PCSK9 l... BeFree 18262190 Detail
0.010 Coronary Arteriosclerosis The R46L variant in the proprotein-convertase subtilisin-kexin type 9 (PCSK9) ge... BeFree 20699424 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu) AND Low density lipoprotein cholesterol level quantitative ... ClinVar Detail
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu) AND Hypercholesterolemia, autosomal dominant, 3 ClinVar Detail
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu) AND Hypercholesterolemia, familial, 1 ClinVar Detail
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu) AND Hypocholesterolemia ClinVar Detail
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu) AND not specified ClinVar Detail
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu) AND not provided ClinVar Detail
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu) AND Hypobetalipoproteinemia ClinVar Detail
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu) AND Familial hypercholesterolemia ClinVar Detail
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu) AND Cardiovascular phenotype ClinVar Detail
The Atherosclerosis Risk in Communities (ARIC) Study assessed risk factors and PCSK9 variants Y142X ... DisGeNET Detail
We measured plasma PCSK9 concentrations in healthy men with a PCSK9 (proprotein convertase subtilisi... DisGeNET Detail
In the present study, we have determined the relative frequency of the R46L, I474V and E670G variant... DisGeNET Detail
PCSK9 R46L, lower LDL, and cardiovascular disease risk in familial hypercholesterolemia: a cross-sec... DisGeNET Detail
Caucasian carriers of the T allele at R46L in the proprotein convertase subtilisin/kexin type 9 (PCS... DisGeNET Detail
The R46L variant in the proprotein-convertase subtilisin-kexin type 9 (PCSK9) gene was associated wi... DisGeNET Detail
Loss-of-function mutation R46L in the PCSK9 gene has little impact on the levels of total serum chol... DisGeNET Detail
Healthy individuals carrying the PCSK9 p.R46L variant and familial hypercholesterolemia patients car... DisGeNET Detail
Using this cell-based assay of PCSK9 activity, we found that the relative potencies of several PCSK9... DisGeNET Detail
PCSK9 R46L, low-density lipoprotein cholesterol levels, and risk of ischemic heart disease: 3 indepe... DisGeNET Detail
The Atherosclerosis Risk in Communities (ARIC) Study assessed risk factors and PCSK9 variants Y142X ... DisGeNET Detail
No association tests were performed for R46L variant because of its very low frequency, whereas the ... DisGeNET Detail
PCSK9 R46L, lower LDL, and cardiovascular disease risk in familial hypercholesterolemia: a cross-sec... DisGeNET Detail
1130 unrelated subjects with molecularly defined FH were screened for mutation R46L in the PCSK9 gen... DisGeNET Detail
In the present study, we have determined the relative frequency of the R46L, I474V and E670G variant... DisGeNET Detail
The aims of this cross-sectional cohort-study were to examine whether the PCSK9 R46L loss of functio... DisGeNET Detail
The R46L variant in the proprotein-convertase subtilisin-kexin type 9 (PCSK9) gene was associated wi... DisGeNET Detail
The Atherosclerosis Risk in Communities (ARIC) Study assessed risk factors and PCSK9 variants Y142X ... DisGeNET Detail
The Atherosclerosis Risk in Communities (ARIC) Study assessed risk factors and PCSK9 variants Y142X ... DisGeNET Detail
Our data support the concept that the rare allele of the R46L SNP at the PCSK9 locus significantly l... DisGeNET Detail
The R46L variant in the proprotein-convertase subtilisin-kexin type 9 (PCSK9) gene was associated wi... 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
hg38
Position
chr1:55,039,974-55,039,974
Variant Type
snv
Reference Allele
G
Alternative Allele
T
East Asian Chromosome Counts (ExAC)
1548
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
31082
Allele Counts in All Race (ExAC)
689
Heterozygous Counts in All Race (ExAC)
679
Homozygous Counts in All Race (ExAC)
5
Allele Frequency in All Race (ExAC)
0.022167170709735538
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