Total submissions: 17
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
LDLR- |
RCV000237729 | SCV000295371 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2016-03-25 | criteria provided, single submitter | literature only | |
Centre de Génétique Moléculaire et Chromosomique, |
RCV000237729 | SCV000503334 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2016-12-16 | criteria provided, single submitter | clinical testing | subjects mutated among 2600 FH index cases screened = 10 , family members = 5 with co-segregation / previously described in association with FH / Software predictions: Damaging |
Invitae | RCV000791422 | SCV000544664 | pathogenic | Familial hypercholesterolemia | 2023-12-01 | criteria provided, single submitter | clinical testing | This sequence change replaces tryptophan, which is neutral and slightly polar, with cysteine, which is neutral and slightly polar, at codon 443 of the LDLR protein (p.Trp443Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hypercholesterolemia (PMID: 1301956, 9664576, 9727746, 11196104, 22390909). This variant is also known as p.Trp422Cys. ClinVar contains an entry for this variant (Variation ID: 251792). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt LDLR protein function with a positive predictive value of 95%. This variant disrupts the p.Trp443 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 28458923), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. |
Gene |
RCV000494596 | SCV000583130 | likely pathogenic | not provided | 2022-05-20 | criteria provided, single submitter | clinical testing | Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published in vivo analysis suggest a statistically significant elevation of LDL-C levels in patients with W443C compared to wild type patients (Huijgen et al., 2021); Also known as W422C and FH North Platt; This variant is associated with the following publications: (PMID: 31447099, 32220565, 9664576, 1301956, 9727746, 11810272, 21382890, 11845603, 11196104, 12436241, 33111339, 34037665, 34363016, 32770674, 33740630, 22390909) |
U4M - |
RCV000237729 | SCV000583822 | pathogenic | Hypercholesterolemia, familial, 1 | 2017-03-30 | criteria provided, single submitter | clinical testing | |
Laboratory for Molecular Medicine, |
RCV000844741 | SCV000731444 | pathogenic | Homozygous familial hypercholesterolemia | 2017-01-31 | criteria provided, single submitter | clinical testing | The p.Trp443Cys variant in LDLR has been reported in >90 individuals with famili al hypercholesterolemia (FH) and was absent from large population studies. In vi tro functional studies demonstrate that this variant results in reduced protein activity (Hobbs 1992). Computational prediction tools and conservation analysis suggest that the p.Trp443Cys variant may impact the protein. In summary, this variant meets criteria to be classified as pathogenic for FH in an autosomal dom inant manner based upon prevalence among probands, absence from controls, and fu nctional evidence. |
Quest Diagnostics Nichols Institute San Juan Capistrano | RCV000494596 | SCV001134249 | pathogenic | not provided | 2019-06-05 | criteria provided, single submitter | clinical testing | Not found in the total gnomAD dataset, and the data is high quality (0/282626 chr). Statistically enriched in patients compared to ethnically matched controls. Found in at least one symptomatic patient. Predicted to have a damaging effect on the protein. Multiple pathogenic or likely pathogenic variants affect the same amino acid. Assessment of experimental evidence suggests this variant results in abnormal protein function. |
Ce |
RCV000494596 | SCV001246007 | pathogenic | not provided | 2023-06-01 | criteria provided, single submitter | clinical testing | LDLR: PM1:Strong, PS1, PM2, PS4:Supporting |
Color Diagnostics, |
RCV000791422 | SCV001346787 | pathogenic | Familial hypercholesterolemia | 2023-03-29 | criteria provided, single submitter | clinical testing | This missense variant (also known as p.Trp422Cys in the mature protein) replaces tryptophan with cysteine at codon 443 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). A functional study has shown that human cells compound heterozygous for this variant and p.Pro685Leu show 5-15% LDLR activity (PMID: 1301956). This variant has been reported in over 90 individuals affected with familial hypercholesterolemia (PMID: 1301956, 11196104, 9664576, 9727746, 22390909, 33740630). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. |
Institute of Human Genetics, |
RCV000237729 | SCV001440625 | pathogenic | Hypercholesterolemia, familial, 1 | 2019-01-01 | criteria provided, single submitter | clinical testing | |
Mayo Clinic Laboratories, |
RCV000494596 | SCV001715488 | likely pathogenic | not provided | 2020-12-30 | criteria provided, single submitter | clinical testing | PS3_moderate, PS4_moderate, PM2_supporting, PP3 |
Human Genome Sequencing Center Clinical Lab, |
RCV000237729 | SCV001754788 | pathogenic | Hypercholesterolemia, familial, 1 | 2020-03-19 | criteria provided, single submitter | clinical testing | The c.1329G>C (p.Trp443Cys) variant in the LDLR gene results in an amino acid change at residue 443 from a tryptophan to a cysteine. This variant has been reported in multiple unrelated individuals and families with familial hypercholesterolemia (PMID: 1301956, 11196104, 9664576, 9727746, 22390909). It has not been observed in the population database (gnomAD). It is located within the functionally important LDL-receptor class B repeat 2 region of the encoded protein. Multiple lines of in silico algorithms predicts this p.Trp443Cys change to be deleterious. A different nucleotide change at the same position (c.1329G>T) resulting in the same amino acid change (p.Trp443Cys) is considered pathogenic. Another variant that changes the residue 443 from tryptophan to arginine has been reported as pathogenic (PMID: 28290784 and 28458923). Therefore, this variant c.1329G>C (p.Trp443Cys) in LDLR is interpreted as pathogenic. |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000791422 | SCV002511543 | pathogenic | Familial hypercholesterolemia | 2022-04-05 | criteria provided, single submitter | clinical testing | Variant summary: LDLR c.1329G>C (p.Trp443Cys) results in a non-conservative amino acid change located in the LDLR class B repeat (IPR000033) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251246 control chromosomes (gnomAD). c.1329G>C has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (e.g. Weiss_2000, Kusters_2013, Leren_2021). These data indicate that the variant is very likely to be associated with disease. Twelve ClinVar submitters (evaluation after 2014) cite the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. |
Ambry Genetics | RCV002379064 | SCV002691627 | pathogenic | Cardiovascular phenotype | 2021-04-10 | criteria provided, single submitter | clinical testing | The p.W443C pathogenic mutation (also known as c.1329G>C), located in coding exon 9 of the LDLR gene, results from a G to C substitution at nucleotide position 1329. The tryptophan at codon 443 is replaced by cysteine, an amino acid with highly dissimilar properties, and is located in the EGF-like precursor domain. This alteration has been reported (also described as p.W422C and North Platt) in numerous individuals with familial hypercholesterolemia (FH) from a variety of ethnic backgrounds (Hobbs HH et al. Hum. Mutat., 1992;1:445-66; Fouchier SW et al. Hum. Genet., 2001 Dec;109:602-15; Vergotine J et al. S. Afr. Med. J., 2001 Dec;91:1053-9; van der Graaf A et al. Circulation, 2011 Mar;123:1167-73). An alternate change at this nucleotide, c.1329G>T, with the same amino acid substitution has also been detected in individuals with FH (Huijgen R et al. Eur. Heart J., 2012 Sep;33:2325-30). Furthermore, additional amino acid substitutions at this position, p.W443S and p.W443R, have been reported in FH cohorts (Sozen M et al. Atheroscler Suppl, 2004 Dec;5:7-11; Korneva VA et al. Cholesterol, 2017 Mar;2017:9375818). Internal structural analysis has also determined that this alteration disrupts the structure in a structural hotspot cluster (Lo Surdo P et al. EMBO Rep., 2011 Dec;12:1300-5). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. |
Fulgent Genetics, |
RCV000237729 | SCV002786656 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2022-01-10 | criteria provided, single submitter | clinical testing | |
Revvity Omics, |
RCV000237729 | SCV003827828 | pathogenic | Hypercholesterolemia, familial, 1 | 2022-11-08 | criteria provided, single submitter | clinical testing | |
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, |
RCV000237729 | SCV000606396 | pathogenic | Hypercholesterolemia, familial, 1 | no assertion criteria provided | research |