NM_000527.5(LDLR):c.1783C>T (p.Arg595Trp) AND Hypercholesterolemia, familial, 1
- Germline classification:
- Pathogenic (15 submissions)
- Last evaluated:
- Jun 9, 2021
- Review status:
- 3 stars out of maximum of 4 starsreviewed by expert panel
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000237585.34
Allele description [Variation Report for NM_000527.5(LDLR):c.1783C>T (p.Arg595Trp)]
NM_000527.5(LDLR):c.1783C>T (p.Arg595Trp)
- Gene:
- LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 19p13.2
- Genomic location:
- Preferred name:
- NM_000527.5(LDLR):c.1783C>T (p.Arg595Trp)
- Other names:
- NM_000527.5(LDLR):c.1783C>T
- HGVS:
- NC_000019.10:g.11116936C>T
- NG_009060.1:g.32556C>T
- NM_000527.5:c.1783C>TMANE SELECT
- NM_001195798.2:c.1783C>T
- NM_001195799.2:c.1660C>T
- NM_001195800.2:c.1279C>T
- NM_001195803.2:c.1402C>T
- NP_000518.1:p.Arg595Trp
- NP_000518.1:p.Arg595Trp
- NP_001182727.1:p.Arg595Trp
- NP_001182728.1:p.Arg554Trp
- NP_001182729.1:p.Arg427Trp
- NP_001182732.1:p.Arg468Trp
- LRG_274t1:c.1783C>T
- LRG_274:g.32556C>T
- LRG_274p1:p.Arg595Trp
- NC_000019.9:g.11227612C>T
- NM_000527.3:c.1783C>T
- NM_000527.4:c.1783C>T
- P01130:p.Arg595Trp
- c.1783C>T
- p.ARG595TRP
This HGVS expression did not pass validation- Protein change:
- R427W
- Links:
- LDLR-LOVD, British Heart Foundation: LDLR_000239; UniProtKB: P01130#VAR_072856
- Molecular consequence:
- NM_000527.5:c.1783C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001195798.2:c.1783C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001195799.2:c.1660C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001195800.2:c.1279C>T - missense variant - [Sequence Ontology: SO:0001583]
- NM_001195803.2:c.1402C>T - missense variant - [Sequence Ontology: SO:0001583]
- Observations:
- 2
Condition(s)
- Name:
- Hypercholesterolemia, familial, 1
- Synonyms:
- LDL RECEPTOR DISORDER; Hyperlipoproteinemia Type IIa; HYPER-LOW-DENSITY-LIPOPROTEINEMIA; See all synonyms [MedGen]
- Identifiers:
- MONDO: MONDO:0007750; MedGen: C0745103; Orphanet: 391665; OMIM: 143890
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000295653 | LDLR-LOVD, British Heart Foundation | criteria provided, single submitter (ACGS Guidelines, 2013) | Likely pathogenic (Mar 25, 2016) | germline | literature only | |
SCV000494601 | U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 30, 2017) | germline | clinical testing | |
SCV000503414 | Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Dec 16, 2016) | germline | clinical testing | |
SCV000588606 | Laboratory of Genetics and Molecular Cardiology, University of São Paulo - HipercolBrasil | criteria provided, single submitter (ACMG Guidelines, 2015) | Uncertain significance (Mar 1, 2016) | germline | research | |
SCV000606512 | Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum | no assertion criteria provided | Pathogenic | germline | research | |
SCV000607640 | Fundacion Hipercolesterolemia Familiar - SAFEHEART | criteria provided, single submitter (ACMG Guidelines, 2015) | Uncertain significance (Mar 1, 2016) | germline | research | |
SCV000748099 | Iberoamerican FH Network | criteria provided, single submitter (ACMG Guidelines, 2015) | Uncertain significance (Mar 1, 2016) | germline | research | |
SCV001149823 | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | criteria provided, single submitter (Classification criteria August 2017) | Likely pathogenic (Dec 27, 2018) | de novo | clinical testing | |
SCV001440210 | Institute of Human Genetics, University of Leipzig Medical Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Uncertain significance (Sep 7, 2020) | unknown | clinical testing | |
SCV001960931 | ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel | reviewed by expert panel (ClinGen FH ACMG Specifications v1-1) | Pathogenic (Jun 9, 2021) | germline | curation | |
SCV002789296 | Fulgent Genetics, Fulgent Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 7, 2021) | unknown | clinical testing | |
SCV003827169 | Revvity Omics, Revvity | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 27, 2022) | germline | clinical testing | |
SCV004041644 | Zotz-Klimas Genetics Lab, MVZ Zotz Klimas | no assertion criteria provided | Pathogenic (Oct 9, 2023) | germline | clinical testing | |
SCV004804728 | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 17, 2024) | germline | research | |
SCV004822501 | All of Us Research Program, National Institutes of Health | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 9, 2024) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | de novo | yes | 1 | not provided | not provided | 1 | not provided | clinical testing |
not provided | germline | yes | 9 | 2 | not provided | 2605 | not provided | clinical testing, literature only |
not provided | germline | unknown | 3 | not provided | not provided | 108544 | not provided | clinical testing, research, curation |
not provided | unknown | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
Citations
PubMed
Mozas P, Castillo S, Tejedor D, Reyes G, Alonso R, Franco M, Saenz P, Fuentes F, Almagro F, Mata P, Pocoví M.
Hum Mutat. 2004 Aug;24(2):187.
- PMID:
- 15241806
Damgaard D, Larsen ML, Nissen PH, Jensen JM, Jensen HK, Soerensen VR, Jensen LG, Faergeman O.
Atherosclerosis. 2005 May;180(1):155-60. Epub 2005 Jan 12.
- PMID:
- 15823288
Details of each submission
From LDLR-LOVD, British Heart Foundation, SCV000295653.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | literature only | PubMed (5) |
2 | not provided | 1 | not provided | not provided | literature only | PubMed (5) |
3 | not provided | 1 | not provided | not provided | literature only | PubMed (5) |
4 | not provided | 1 | not provided | not provided | literature only | PubMed (5) |
5 | not provided | 1 | not provided | not provided | literature only | PubMed (5) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
2 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
3 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
4 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided | |
5 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille, SCV000494601.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 3 | not provided | not provided | clinical testing | PubMed (1) |
Description
Dutch Lipid Clinic Scoring : Definite FH
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 3 | not provided | 2 | not provided |
From Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix, SCV000503414.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
Description
subject mutated among 2600 FH index cases screened = 1 / previously described in association with FH/software prediction damaging
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 2600 | not provided | not provided | 1 | not provided | not provided | not provided |
From Laboratory of Genetics and Molecular Cardiology, University of São Paulo - HipercolBrasil, SCV000588606.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | PubMed (1) |
Description
%MAF(ExAC):0.0008237
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum, SCV000606512.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Fundacion Hipercolesterolemia Familiar - SAFEHEART, SCV000607640.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | PubMed (1) |
Description
%MAF(ExAC):0.0008237
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Iberoamerican FH Network, SCV000748099.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | PubMed (1) |
Description
%MAF(ExAC):0.0008237
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV001149823.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | de novo | yes | 1 | blood | not provided | 1 | not provided | not provided | not provided |
From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440210.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel, SCV001960931.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | curation | not provided |
Description
NM_000527.5(LDLR):c.1783C>T (p.Arg595Trp) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PS4, PP1_Strong, PM2, PP3 and PP4) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: PS4 - Variant meets PM2. Variant identified in 12 index cases. PP1_strong - 10 informative meioses identified by Laboratory of Genetics and Molecular Cardiology. PM2 - PopMax MAF = 0.00001548 (0.0015%) in European non-Finnish (gnomAD v2.1.1). PP3 - REVEL: 0,89. PP4 - Variant meets PM2. Variant identified in 12 index cases fulfilling validated clinical criteria for FH (6 cases with Simon-Broome or DLCN criteria from Ambry Genetics; 2 cases with Simon-Broome from Color laboratory; 3 cases with Simon-Broome criteria from Laboratory of Genetics and Molecular Cardiology; 1 case with Simon-Broome criteria from GeneDx).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Fulgent Genetics, Fulgent Genetics, SCV002789296.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Revvity Omics, Revvity, SCV003827169.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Zotz-Klimas Genetics Lab, MVZ Zotz Klimas, SCV004041644.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004804728.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | research | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From All of Us Research Program, National Institutes of Health, SCV004822501.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 3 | not provided | not provided | clinical testing | PubMed (11) |
Description
This missense variant (also known as p.Arg574Trp in the mature protein) replaces arginine with tryptophan at codon 595 in the fifth LDLR type B repeat of the EGF precursor homology domain of the LDLR protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over 20 individuals affected with familial hypercholesterolemia (PMID: 11737238, 16250003, 20538126, 25461735, 28502510, 32044282, 32331935, 34037665, 34176852; Color internal data), including three homozygous individuals with severe phenotype (PMID: 27784735). This variant has been identified in 2/282862 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different missense variants occurring at the same codon (p.Arg595Leu and Arg595Gln) have been reported in individuals affected with familial hypercholesterolemia (ClinVar variation ID: 252029, 183126), suggesting that arginine at this position is a functionally and clinically important residue. Based on the available evidence, this variant is classified as Pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | 108544 | not provided | not provided | 3 | not provided | not provided | not provided |
Last Updated: Nov 3, 2024