ClinVar Genomic variation as it relates to human health
NM_000237.3(LPL):c.106G>A (p.Asp36Asn)
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
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NM_000237.3(LPL):c.106G>A (p.Asp36Asn)
Variation ID: 1552 Accession: VCV000001552.35
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 8p21.3 8: 19948197 (GRCh38) [ NCBI UCSC ] 8: 19805708 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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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 Feb 6, 2015 Oct 8, 2024 Jan 31, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000237.3:c.106G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000228.1:p.Asp36Asn missense NC_000008.11:g.19948197G>A NC_000008.10:g.19805708G>A NG_008855.2:g.51481G>A LRG_1298:g.51481G>A LRG_1298t1:c.106G>A LRG_1298p1:p.Asp36Asn P06858:p.Asp36Asn - Protein change
- D36N
- Other names
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D9N
- Canonical SPDI
- NC_000008.11:19948196:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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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.
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0.01757 (A)
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Allele frequency
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The frequency of the allele represented by this VCV record.
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1000 Genomes Project 0.01757
1000 Genomes Project 30x 0.01796
The Genome Aggregation Database (gnomAD) 0.01951
Trans-Omics for Precision Medicine (TOPMed) 0.02455
- 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 | ||
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HI score
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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. |
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LPL | - | - |
GRCh38 GRCh37 |
780 | 869 |
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. |
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risk factor (1) |
no assertion criteria provided
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Aug 1, 1999 | RCV000001617.4 | |
risk factor (1) |
no assertion criteria provided
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Sep 15, 2014 | RCV000157298.1 | |
Likely benign (2) |
criteria provided, multiple submitters, no conflicts
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Dec 10, 2021 | RCV000454647.5 | |
Benign (4) |
criteria provided, multiple submitters, no conflicts
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Jun 10, 2021 | RCV000352575.9 | |
Benign/Likely benign; other (5) |
criteria provided, multiple submitters, no conflicts
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Jan 31, 2024 | RCV000733476.18 | |
Benign (1) |
criteria provided, single submitter
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Mar 21, 2019 | RCV002408446.2 | |
LPL-related disorder
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Benign (1) |
no assertion criteria provided
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Sep 25, 2019 | RCV003924794.2 |
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. |
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Likely benign
(Mar 28, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000539547.1
First in ClinVar: Apr 09, 2017 Last updated: Apr 09, 2017 |
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency, association with hyperlipidemia. (less)
Method: Genome/Exome Filtration
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Benign
(May 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Hyperlipoproteinemia, type I
Affected status: unknown
Allele origin:
unknown
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Mendelics
Accession: SCV001137594.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
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Benign
(Jun 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hyperlipoproteinemia, type I
Affected status: no
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV001737362.1
First in ClinVar: Jun 19, 2021 Last updated: Jun 19, 2021 |
Sex: mixed
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Likely benign
(Dec 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002050870.1
First in ClinVar: Jan 08, 2022 Last updated: Jan 08, 2022 |
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Benign
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001731106.3
First in ClinVar: Jun 15, 2021 Last updated: Feb 20, 2024 |
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other
(Jun 13, 2018)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000861552.1
First in ClinVar: Dec 16, 2018 Last updated: Dec 16, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Benign
(Mar 06, 2018)
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criteria provided, single submitter
Method: clinical testing
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Hyperlipoproteinemia, type I
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000472748.3
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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. (less)
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Benign
(Oct 22, 2019)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001843677.1
First in ClinVar: Sep 10, 2021 Last updated: Sep 10, 2021 |
Comment:
This variant is associated with the following publications: (PMID: 11260209, 8839720, 15049943, 9678774, 28267856, 8872057, 10517255, 8541837, 8199176, 7749858, 26934567, 27055971, 24503134, 24123366, 21146168, 18823627, … (more)
This variant is associated with the following publications: (PMID: 11260209, 8839720, 15049943, 9678774, 28267856, 8872057, 10517255, 8541837, 8199176, 7749858, 26934567, 27055971, 24503134, 24123366, 21146168, 18823627, 12535736, 18922999, 28008009, 10364086) (less)
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Benign
(Mar 21, 2019)
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criteria provided, single submitter
Method: clinical testing
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Cardiovascular phenotype
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002720847.2
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)
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Likely benign
(-)
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criteria provided, single submitter
Method: not provided
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not provided
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005220605.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
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risk factor
(Aug 01, 1999)
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no assertion criteria provided
Method: literature only
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COMBINED HYPERLIPIDEMIA, FAMILIAL, SUSCEPTIBILITY TO
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000021773.3
First in ClinVar: Apr 04, 2013 Last updated: Jun 03, 2019 |
Comment on evidence:
Nevin et al. (1994) reported that mutations in the LPL gene, including D9N, are present in a subgroup of FCHL patients (144250). Reymer et al. … (more)
Nevin et al. (1994) reported that mutations in the LPL gene, including D9N, are present in a subgroup of FCHL patients (144250). Reymer et al. (1995) claimed that 20% of Dutch hyperlipidemic individuals have the N291S mutation (609708.0033). De Bruin et al. (1996) screened a group of 28 probands with familial combined hyperlipidemia and group of 91 population controls for the 2 LPL gene mutations, D9N and N291S. In this way, 2 pedigrees from probands with the D9N mutation and 2 pedigrees from probands with the N291S mutation were studied, representing a total of 24 subjects. Both LPL gene mutations were associated with a significant effect on plasma lipids and apolipoproteins. Presence of the D9N mutation (n = 7) was associated with hypertriglyceridemia and reduced plasma high-density lipoprotein cholesterol concentrations. LPL-D9N carriers had higher diastolic blood pressure than noncarriers. Linkage analysis revealed no significant relationship between the D9N or N291S LPL gene mutations and the FCH phenotype (hypertriglyceridemia, hypercholesterolemia, or increased apo-B concentrations). De Bruin et al. (1996) concluded that the LPL gene did not represent the major single gene causing familial combined hyperlipidemia in the 4 pedigrees studied, but that the D9N and N291S mutations had significant additional effects on lipid and apolipoprotein phenotype. Wittrup et al. (1999) undertook to test the hypothesis that the D9N substitution and the -93T-G mutation (609708.0038) in the promoter of the LPL gene affect plasma lipid levels and thereby the risk of IHD. They genotyped 9,033 men and women from a general population sample and 940 patients with IHD. The frequency of both the G allele and the asn9 allele in the general population sample was approximately 0.015 for both men and women. These 2 mutations appeared together in 95% of carriers. The average triglyceride-raising effect associated with double heterozygosity for the 2 mutations was 0.28 mmol/L (p = 0.004) and 0.16 mmol/L (p = 0.10) in men and women, respectively. Of the overall risk of IHD in men in the general population, the fraction attributable to double heterozygosity was 3%, similar to the 5% attributable to diabetes mellitus. The results demonstrated that the D9N substitution is in linkage disequilibrium with the -93T-G mutation and that the double-heterozygous carrier status is associated with elevated plasma triglycerides and an increased risk of IHD in men. Boer et al. (1999) studied the interaction between the common D9N mutation in the LPL gene and physical activity, as well as other lifestyle factors, on lipid traits in a population-based sample of 379 Dutch men and women. Nonfasting blood samples were used for determination of lipid traits and the D9N genotype. Fifteen subjects (4%) were found to have the mutation; all 15 had higher levels of total cholesterol, apoB, and triglycerides as compared to noncarriers. While no interactions with overweight, alcohol consumption, and smoking were found, a strong interaction between the D9N mutation and physical activity was apparent. The 5 physically inactive D9N carriers had significantly higher total cholesterol and apoB levels as compared to noncarriers, whereas their HDL cholesterol concentrations were lower. The same was not the case for the 10 physically active carriers. (less)
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Benign
(Jan 02, 2020)
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no assertion criteria provided
Method: clinical testing
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Lipoprotein lipase deficiency
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001454747.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001970444.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021 |
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Benign
(Sep 25, 2019)
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no assertion criteria provided
Method: clinical testing
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LPL-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004743366.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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risk factor
(Sep 15, 2014)
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no assertion criteria provided
Method: clinical testing
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Coronary heart disease
Affected status: yes
Allele origin:
germline
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Blueprint Genetics
Accession: SCV000207030.1
First in ClinVar: Feb 06, 2015 Last updated: Feb 06, 2015 |
Number of individuals with the variant: 1
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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 |
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LPL polymorphism (D9N) predicts cardiovascular disease risk directly and through interaction with CETP polymorphism (TaqIB) in women with high HDL cholesterol and CRP. | Corsetti JP | Atherosclerosis | 2011 | PMID: 21146168 |
Physical activity modulates the effect of a lipoprotein lipase mutation (D9N) on plasma lipids and lipoproteins. | Boer JM | Clinical genetics | 1999 | PMID: 10517255 |
Mutations in the lipoprotein lipase gene associated with ischemic heart disease in men. The Copenhagen city heart study. | Wittrup HH | Arteriosclerosis, thrombosis, and vascular biology | 1999 | PMID: 10364086 |
Lipoprotein lipase gene mutations D9N and N291S in four pedigrees with familial combined hyperlipidaemia. | de Bruin TW | European journal of clinical investigation | 1996 | PMID: 8872057 |
A frequently occurring mutation in the lipoprotein lipase gene (Asn291Ser) contributes to the expression of familial combined hyperlipidemia. | Reymer PW | Human molecular genetics | 1995 | PMID: 8541837 |
The LPL gene in individuals with familial combined hyperlipidemia and decreased LPL activity. | Nevin DN | Arteriosclerosis and thrombosis : a journal of vascular biology | 1994 | PMID: 8199176 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=LPL | - | - | - | - |
Text-mined citations for rs1801177 ...
HelpRecord last updated Oct 13, 2024
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.