ClinVar Genomic variation as it relates to human health
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_174936.4(PCSK9):c.137G>T (p.Arg46Leu)
Variation ID: 2878 Accession: VCV000002878.31
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 1p32.3 1: 55039974 (GRCh38) [ NCBI UCSC ] 1: 55505647 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Sep 29, 2024 Jan 31, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_174936.4:c.137G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_777596.2:p.Arg46Leu missense NC_000001.11:g.55039974G>T NC_000001.10:g.55505647G>T NG_009061.1:g.5428G>T LRG_275:g.5428G>T LRG_275t1:c.137G>T LRG_275p1:p.Arg46Leu Q8NBP7:p.Arg46Leu - Protein change
- R46L
- Other names
-
PCSK9, ARG46LEU (rs11591147)
- Canonical SPDI
- NC_000001.11:55039973:G:T
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
PCSK9 | Dosage sensitivity unlikely | No evidence available |
GRCh38 GRCh37 |
1338 | 1353 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
association (1) |
no assertion criteria provided
|
Mar 20, 2008 | RCV000003012.3 | |
Benign/Likely benign (4) |
criteria provided, multiple submitters, no conflicts
|
Jan 31, 2024 | RCV000203182.17 | |
Benign (4) |
criteria provided, multiple submitters, no conflicts
|
Aug 22, 2019 | RCV000256313.8 | |
Benign (1) |
criteria provided, single submitter
|
May 8, 2017 | RCV000605465.3 | |
Pathogenic (1) |
no assertion criteria provided
|
- | RCV000508774.1 | |
Benign/Likely benign (3) |
criteria provided, multiple submitters, no conflicts
|
Sep 8, 2023 | RCV000985896.12 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
|
Jul 1, 2022 | RCV001523785.3 | |
Benign (1) |
criteria provided, single submitter
|
Mar 6, 2018 | RCV001099060.4 | |
Benign (1) |
criteria provided, single submitter
|
Mar 16, 2017 | RCV002381236.2 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Benign
(Jun 11, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
Hypercholesterolemia, autosomal dominant, 3
Affected status: unknown
Allele origin:
unknown
|
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000258263.2
First in ClinVar: Dec 27, 2015 Last updated: Dec 27, 2015 |
|
|
Benign
(Mar 01, 2016)
|
criteria provided, single submitter
Method: research
|
Familial hypercholesterolemia
Affected status: unknown
Allele origin:
germline
|
Laboratory of Genetics and Molecular Cardiology, University of São Paulo
Study: HipercolBrasil
Accession: SCV000588678.1 First in ClinVar: Aug 13, 2017 Last updated: Aug 13, 2017 |
Observation 1:
Comment on evidence:
%MAF(ExAC):2.217
Observation 2:
Comment on evidence:
Assay description:Heterologous cells (HepG2), FACS and WB assays
Result:
Increase 10-20% LDLR activity (+ 5-10% LDLR at cell surface, +15-20% LDL internalization); normal PCSK9 autocatalytic activity
|
|
Benign
(Mar 01, 2016)
|
criteria provided, single submitter
Method: research
|
Familial hypercholesterolemia
Affected status: unknown
Allele origin:
germline
|
Fundacion Hipercolesterolemia Familiar
Study: SAFEHEART
Accession: SCV000607712.1 First in ClinVar: Aug 13, 2017 Last updated: Aug 13, 2017 |
Observation 1:
Comment on evidence:
%MAF(ExAC):2.217
Observation 2:
Comment on evidence:
Heterologous cells (HepG2), FACS and WB assays
Result:
Increase 10-20% LDLR activity (+ 5-10% LDLR at cell surface, +15-20% LDL interlization); normal PCSK9 autocatalytic activity
|
|
Benign
(May 08, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000730049.1
First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
|
|
Benign
(Aug 22, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Hypercholesterolemia, familial, 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
|
Robarts Research Institute, Western University
Accession: SCV000484817.2
First in ClinVar: Dec 06, 2016 Last updated: Sep 11, 2019 |
Number of individuals with the variant: 1
|
|
Benign
(Mar 06, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Hypobetalipoproteinemia
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV001255475.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
|
|
Likely benign
(Mar 06, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Hypercholesterolemia, autosomal dominant, 3
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000358213.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. (less)
|
|
Benign
(Dec 10, 2020)
|
criteria provided, single submitter
Method: clinical testing
|
Familial hypercholesterolemia
Affected status: unknown
Allele origin:
germline
|
Color Diagnostics, LLC DBA Color Health
Accession: SCV000690958.2
First in ClinVar: Feb 19, 2018 Last updated: Jun 19, 2021 |
|
|
Benign
(Apr 28, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Hypercholesterolemia, autosomal dominant, 3
Affected status: unknown
Allele origin:
unknown
|
Fulgent Genetics, Fulgent Genetics
Accession: SCV002798957.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
|
|
Benign
(Jan 31, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Hypercholesterolemia, autosomal dominant, 3
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000291595.8
First in ClinVar: Jul 01, 2016 Last updated: Feb 14, 2024 |
|
|
Benign
(Sep 08, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV002505975.3
First in ClinVar: May 07, 2022 Last updated: Feb 20, 2024 |
|
|
Benign
(Mar 16, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Cardiovascular phenotype
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV002696724.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation … (more)
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
|
|
Benign
(Jul 01, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Familial hypercholesterolemia
Affected status: unknown
Allele origin:
germline
|
GENinCode PLC
Accession: SCV005077864.1
First in ClinVar: Jul 15, 2024 Last updated: Jul 15, 2024 |
|
|
Benign
(Mar 01, 2016)
|
criteria provided, single submitter
Method: research
|
Familial hypercholesterolemia
Affected status: yes
Allele origin:
germline
|
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge
Accession: SCV000323030.1
First in ClinVar: Oct 15, 2016 Last updated: Oct 15, 2016 |
Comment:
3/100 normolipidemic controls; 0/100 normolipidemic individuals
Observation 1:
Comment on evidence:
%MAF (ExAC):2.217
Observation 2:
Comment on evidence:
Heterologous cells (HepG2), FACS and WB assays
Result:
Increase 10-20% LDLR activity (+ 5-10% LDLR at cell surface, +15-20% LDL internalization); normal PCSK9 autocatalytic activity
|
|
Benign
(Jan 06, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001134562.5
First in ClinVar: Jan 05, 2020 Last updated: Jan 06, 2024 |
|
|
Likely benign
(-)
|
criteria provided, single submitter
Method: not provided
|
not provided
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
|
Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005257970.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
|
|
Pathogenic
(-)
|
no assertion criteria provided
Method: research
|
Hypocholesterolemia
Affected status: unknown
Allele origin:
germline
|
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum
Accession: SCV000606676.1
First in ClinVar: Oct 01, 2017 Last updated: Oct 01, 2017 |
|
|
association
(Mar 20, 2008)
|
no assertion criteria provided
Method: literature only
|
LOW DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 1
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000023170.2
First in ClinVar: Apr 04, 2013 Last updated: Jun 23, 2019 |
Comment on evidence:
Cohen et al. (2006) found that the arg46-to-leu (R46L) substitution (rs11591147) in white subjects in a longitudinal study was associated with significant reduction in plasma … (more)
Cohen et al. (2006) found that the arg46-to-leu (R46L) substitution (rs11591147) in white subjects in a longitudinal study was associated with significant reduction in plasma levels of total cholesterol (9%) and LDL cholesterol (15%) (see 603776). Cohen et al. (2006) found that persons who were heterozygous or homozygous for PCSK9(46L) had a 47% reduction in the rate of coronary events (6.3% vs 11.8%). Kathiresan (2008) reported a significant association between the R46L variant and decreased risk of early-onset myocardial infarction in a study of 1,454 patients from 5 different study sites (metaanalysis odds ratio of 0.40; p = 2.0 x 10(-5)). The R46L allele frequency in 1,617 controls was 2.4%. (less)
|
|
click to load more click to collapse |
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
PCSK9 rs11591147 R46L loss-of-function variant protects against liver damage in individuals with NAFLD. | Grimaudo S | Liver international : official journal of the International Association for the Study of the Liver | 2021 | PMID: 33091218 |
Large-Scale Phenome-Wide Association Study of PCSK9 Variants Demonstrates Protection Against Ischemic Stroke. | Rao AS | Circulation. Genomic and precision medicine | 2018 | PMID: 29997226 |
Analysis of publicly available LDLR, APOB, and PCSK9 variants associated with familial hypercholesterolemia: application of ACMG guidelines and implications for familial hypercholesterolemia diagnosis. | Chora JR | Genetics in medicine : official journal of the American College of Medical Genetics | 2018 | PMID: 29261184 |
Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease. | Lu X | Nature genetics | 2017 | PMID: 29083407 |
Spectrum of mutations in Italian patients with familial hypercholesterolemia: New results from the LIPIGEN study. | Pirillo A | Atherosclerosis. Supplements | 2017 | PMID: 28965616 |
PCSK9 Loss-of-Function Variants, Low-Density Lipoprotein Cholesterol, and Risk of Coronary Heart Disease and Stroke: Data From 9 Studies of Blacks and Whites. | Kent ST | Circulation. Cardiovascular genetics | 2017 | PMID: 28768753 |
Polygenic Versus Monogenic Causes of Hypercholesterolemia Ascertained Clinically. | Wang J | Arteriosclerosis, thrombosis, and vascular biology | 2016 | PMID: 27765764 |
Trafficking Dynamics of PCSK9-Induced LDLR Degradation: Focus on Human PCSK9 Mutations and C-Terminal Domain. | Poirier S | PloS one | 2016 | PMID: 27280970 |
PCSK9 R46L Loss-of-Function Mutation Reduces Lipoprotein(a), LDL Cholesterol, and Risk of Aortic Valve Stenosis. | Langsted A | The Journal of clinical endocrinology and metabolism | 2016 | PMID: 27218270 |
Variants with large effects on blood lipids and the role of cholesterol and triglycerides in coronary disease. | Helgadottir A | Nature genetics | 2016 | PMID: 27135400 |
The loss-of-function PCSK9 p.R46L genetic variant does not alter glucose homeostasis. | Bonnefond A | Diabetologia | 2015 | PMID: 26049403 |
Both rare and common variants in PCSK9 influence plasma low-density lipoprotein cholesterol level in American Indians. | Tsai CW | The Journal of clinical endocrinology and metabolism | 2015 | PMID: 25412415 |
PCSK9 R46L, lower LDL, and cardiovascular disease risk in familial hypercholesterolemia: a cross-sectional cohort study. | Saavedra YG | Arteriosclerosis, thrombosis, and vascular biology | 2014 | PMID: 25278291 |
Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks. | Peloso GM | American journal of human genetics | 2014 | PMID: 24507774 |
Regional distribution and metabolic effect of PCSK9 insLEU and R46L gene mutations and apoE genotype. | Awan Z | The Canadian journal of cardiology | 2013 | PMID: 23743349 |
PCSK9 R46L, low-density lipoprotein cholesterol levels, and risk of ischemic heart disease: 3 independent studies and meta-analyses. | Benn M | Journal of the American College of Cardiology | 2010 | PMID: 20579540 |
Loss-of-function mutation R46L in the PCSK9 gene has little impact on the levels of total serum cholesterol in familial hypercholesterolemia heterozygotes. | Strøm TB | Clinica chimica acta; international journal of clinical chemistry | 2010 | PMID: 19917273 |
Longitudinal association of PCSK9 sequence variations with low-density lipoprotein cholesterol levels: the Coronary Artery Risk Development in Young Adults Study. | Huang CC | Circulation. Cardiovascular genetics | 2009 | PMID: 20031607 |
Healthy individuals carrying the PCSK9 p.R46L variant and familial hypercholesterolemia patients carrying PCSK9 p.D374Y exhibit lower plasma concentrations of PCSK9. | Humphries SE | Clinical chemistry | 2009 | PMID: 19797716 |
Genetic and metabolic determinants of plasma PCSK9 levels. | Lakoski SG | The Journal of clinical endocrinology and metabolism | 2009 | PMID: 19351729 |
Polymorphisms associated with cholesterol and risk of cardiovascular events. | Kathiresan S | The New England journal of medicine | 2008 | PMID: 18354102 |
Effect of mutations in the PCSK9 gene on the cell surface LDL receptors. | Cameron J | Human molecular genetics | 2006 | PMID: 16571601 |
Sequence variations in PCSK9, low LDL, and protection against coronary heart disease. | Cohen JC | The New England journal of medicine | 2006 | PMID: 16554528 |
Missense mutations in the PCSK9 gene are associated with hypocholesterolemia and possibly increased response to statin therapy. | Berge KE | Arteriosclerosis, thrombosis, and vascular biology | 2006 | PMID: 16424354 |
Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. | Cohen J | Nature genetics | 2005 | PMID: 15654334 |
click to load more click to collapse |
Text-mined citations for this variant ...
HelpRecord last updated Jan 13, 2025
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.