A de novo mutation of the LDL receptor gene as the cause of familial hypercholesterolemia identified using whole exome sequencing

doi:10.1016/j.cca.2015.12.028

Clinica Chimica Acta

Volume 453, 30 January 2016, Pages 194-196

https://doi.org/10.1016/j.cca.2015.12.028 Get rights and content

Highlights

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We report a rare case of heterozygous FH caused by a de novo mutation in LDLR gene.
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Only one de novo mutation was observed in the entire exome region.
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Comprehensive genetic analysis is useful to determine molecular diagnosis of FH.

Abstract

We report a rare case of heterozygous familial hypercholesterolemia (FH) caused by a de novo mutation in LDL receptor (LDLR) gene identified using whole exome sequencing.

An 11-year-old female without any family histories of hypercholesterolemia was referred to our hospital to make clinical as well as molecular diagnoses. She was first diagnosed as hypercholesterolemia at the age of 3 (initial total cholesterol = 381 mg/dl) without any secondary causes. Because of her lipid profile, heterozygous FH was initially suspected, however; the lipid levels of her parents were normal. Accordingly, she was suspected as a recessive form of hypercholesterolemia, such as sitosterolemia or autosomal recessive hypercholesterolemia. Whole exome sequencing was performed on 4 individuals, including the proband, her parents, and her unaffected younger sister. The initial analysis assuming a recessive inheritance was unsuccessful, leaving a few candidate genes without any evidence supporting cholesterol metabolism. However, we found only one de novo mutation in LDLR gene across her whole exome region, assuming de novo mutation occurrence (c.1136G > A or p.Cys379Tyr). This mutation has already been reported to cause FH, including Japanese, and finally, she was diagnosed as heterozygous FH caused by a de novo mutation in LDLR gene.

Comprehensive genetic analysis is quite useful to make a correct diagnosis in such cases.

Introduction

Heterozygous familial hypercholesterolemia (FH) has a mutant allele of either of the three FH-associated genes (FH genes), namely LDL receptor (LDLR), apolipoprotein B-100 (APOB) or PCSK9 genes, and the frequency of which is estimated to be at least 1 in 200 to 500 general populations worldwide [1], [2]. Those patients exhibit premature coronary atherosclerosis due to extremely high LDL cholesterol levels. According to the diagnostic criteria for heterozygous FH in children, family history of FH or premature cardiovascular diseases are emphasized since many children do not develop physical signs associated with hyper LDL cholesterolemia [3]. We encountered a Japanese child whose LDL cholesterol levels was as high as typical heterozygous FH without any family histories of FH nor premature cardiovascular diseases. We used a whole exome sequencing (WES) technique to make her molecular diagnosis based on a number of recent findings that WES is quite useful, especially, in a recessive form of genetic disorders [4], [5].

Section snippets

Case report

An 11- year-old female without any family histories of hypercholesterolemia was referred to our hospital to make clinical as well as molecular diagnoses. She was first suspected as heterozygous FH at the age of 3 (initial total cholesterol = 381 mg/dl) without any secondary causes. During 9 years of her clinical course, her LDL cholesterol level had been elevated consistently (Supplemental Fig. 1). However, she did not have any physical signs of cutaneous and tendious xanthomas, nor any family

Discussion

We experienced a rare case of FH caused by a de novo mutation in LDLR gene. In our analysis using WES, there were several advantages to make a correct diagnosis as 1) we could verify the family relationship between the proband and her parents, 2) we could identify that there is only one de novo mutation in LDLR gene across the entire exome region, and 3) we could rule out other recessive form of diseases except for a few genes none of which have any evidence relating cholesterol metabolism.

Conflict of interest

None declared.

Acknowledgments

This work is supported in part by the Practical Research Project for Rare/Intractable Diseases from Japan Agency for Medical Research and Development, AMED (grant number 15gk0110012h1601 to A.T.). We express our special thanks to Professor Masakazu Yamagishi (grammatical assistance in drafting the manuscript), Dr. Takayuki Kannon (valuable discussion and comments), Dr. Shoichiro Tange (valuable discussion and comments), Ms. Yoko Iwauchi (technical assistance), and Education Center for

References (14)

H. Mabuchi et al.
Molecular genetic epidemiology of homozygous familial hypercholesterolemia in the Hokuriku district of Japan
Atherosclerosis
(2011)
H. Tada et al.
Whole exome sequencing combined with integrated variant annotation prediction identifies asymptomatic Tangier disease with compound heterozygous mutations in ABCA1 gene
Atherosclerosis
(2015)
S. Purcell et al.
PLINK: a tool set for whole-genome association and population-based linkage analyses
Am. J. Hum. Genet.
(2007)
L. Pisciotta et al.
A "de novo" mutation of the LDL-receptor gene as the cause of familial hypercholesterolemia
Biochim. Biophys. Acta
(2002)
M.A. Kawashiri et al.
Current perspectives in genetic cardiovascular disorders: from basic to clinical aspects
Heart Vessel.
(2014)
T. Teramoto et al.
Familial hypercholesterolemia
J. Atheroscler. Thromb.
(2014)
H. Tada et al.
Whole exome sequencing in monogenic dyslipidemias
J. Atheroscler. Thromb.
(2015)

There are more references available in the full text version of this article.

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Citation Excerpt :
For example, in cases in which genetic test results identify probands who are double heterozygotes (e.g., pathogenic variants in both LDLR and APOB), this finding affects the recurrence risk to relatives and the recommended approaches to cascade testing. Specifically, for probands whose genetic testing diagnoses them as compound or double heterozygotes or homozygotes, parents of the proband should undergo known familial variant testing to determine which variant was maternally inherited and which was paternally inherited and/or whether one of the variants is de novo, which although rare, is possible (64); thus, all maternal and paternal relatives with FH can next be identified by testing for the appropriate variant on each side of the family. Known familial variant testing for both variants identified in the proband is recommended for siblings of the proband and for children of the proband.
Although awareness of familial hypercholesterolemia (FH) is increasing, this common, potentially fatal, treatable condition remains underdiagnosed. Despite FH being a genetic disorder, genetic testing is rarely used. The Familial Hypercholesterolemia Foundation convened an international expert panel to assess the utility of FH genetic testing. The rationale includes the following: 1) facilitation of definitive diagnosis; 2) pathogenic variants indicate higher cardiovascular risk, which indicates the potential need for more aggressive lipid lowering; 3) increase in initiation of and adherence to therapy; and 4) cascade testing of at-risk relatives. The Expert Consensus Panel recommends that FH genetic testing become the standard of care for patients with definite or probable FH, as well as for their at-risk relatives. Testing should include the genes encoding the low-density lipoprotein receptor (LDLR), apolipoprotein B (APOB), and proprotein convertase subtilisin/kexin 9 (PCSK9); other genes may also need to be considered for analysis based on patient phenotype. Expected outcomes include greater diagnoses, more effective cascade testing, initiation of therapies at earlier ages, and more accurate risk stratification.
Compound heterozygous familial hypercholesterolemia in a Chinese boy with a de novo and transmitted low-density lipoprotein receptor mutation
2018, Journal of Clinical Lipidology
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Unfortunately, data on lipid levels and clinical features of the patient and his family members were not available. Interestingly, very few disease-causing de novo variants have been reported in LDLR previously.19–21 De novo mutations are rare, and in comprehensive genetic analyses, around 50 de novo mutations were observed in a person across the genome with only 1 mutation in the exome.22
Homozygous familial hypercholesterolemia is characterized by extremely elevated serum low-density lipoprotein cholesterol (LDL-C) levels and increased risk of cardiovascular complications due to biallelic mutations in LDL receptor (LDLR).
We present a 10-year-old Chinese homozygous familial hypercholesterolemia boy with biallelic LDLR mutations including an extremely rare de novo mutation.
Detailed family history and clinical and biochemical data were gathered from the pedigree. Genomic DNA was isolated and the reported LDL-related genes (LDLR, APOB, PCSK9, ABCG5, ABCG8, ANGPTL3, APOC3, and LDLRAP1) were sequenced.
The proband displayed extensive cutaneous and tendon xanthomas together with elevated serum LDL-C level of 14.87 mmol/L (575 mg/dL). A combination of simvastatin 40 mg daily and ezetimibe 10 mg daily resulted in 57% lowering of LDL-C. The proband had compound heterozygous LDLR disease-causing mutations, including p.(His583Tyr) variant transmitted from the mother and a de novo p.(Gln242*) variant on the paternal allele.
Our report supports the role of genetic testing in the proband and the parents for accurate genetic counseling. Our patient had marked lowering of LDL-C with a combination of statin and ezetimibe but may require additional therapy.
The study of familial hypercholesterolemia in Italy: A narrative review
2017, Atherosclerosis Supplements
Citation Excerpt :
The haplotype analysis of the LDLR locus revealed that in one of these patients the “de novo” mutation had occurred in the paternal germ line [16]. To the best of our knowledge, only five FH patients carrying de novo LDLR mutations have been reported so far [17–19]. One of our patients with the clinical diagnosis of homozygous FH was found to be homozygous for a mutation in exon 12 [c.1775G>A, p.(Gly592Glu)] known to be pathogenic and heterozygous for a rare variant in intron 14 (c.2140 +5G>A).
In this review we outline our experience in the clinical and molecular diagnosis of familial hypercholesterolemia (FH), built up over more than three decades. We started our work by selecting FH patients on the basis of stringent clinical criteria, including extensive family studies. In most patients we confirmed the clinical diagnosis by showing a reduced LDLR activity in skin fibroblasts. After the isolation of LDLR cDNA and the characterization of the corresponding gene by the Dallas group, we started a systematic molecular investigation of our patients first using Southern blotting, and, subsequently Sanger sequencing. Up to now we have been able to identify 260 mutations of LDLR gene in more than 1000 genotyped FH patients, including 68 homozygotes. During this survey we identified 13 mutation clusters located in different geographical districts, which gave us the chance to compare the phenotype of patients carrying the most common mutations. We also found that mutations in APOB and PCSK9 genes were a rare cause of FH in our cohort. Despite our efforts, we failed to identify mutations in candidate genes in ∼20% of cases of definite FH. An exome-wide study, conducted within the context of an international collaboration, excluded the presence of other major genes in our unexplained FH cases. Recently, we have adopted sequencing technology of the next generation (NGS) with the parallel sequencing of a panel of FH targeted genes as a way of obtaining a more comprehensive picture of the gene variants potentially involved in the disease.
Whole Exome Sequencing Insufficient for a Definitive Diagnosis of a Patient with Compound Heterozygous Familial Hypercholesterolemia
2022, Internal Medicine
The Digenic Causality in Familial Hypercholesterolemia: Revising the Genotype–Phenotype Correlations of the Disease
2021, Frontiers in Genetics

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Case ReportA de novo mutation of the LDL receptor gene as the cause of familial hypercholesterolemia identified using whole exome sequencing

Highlights

Abstract

Introduction

Section snippets

Case report

Discussion

Conflict of interest

Acknowledgments

Atherosclerosis

Atherosclerosis

Am. J. Hum. Genet.

Biochim. Biophys. Acta

Current perspectives in genetic cardiovascular disorders: from basic to clinical aspects

Heart Vessel.

Familial hypercholesterolemia

J. Atheroscler. Thromb.

Whole exome sequencing in monogenic dyslipidemias

J. Atheroscler. Thromb.

Case Report
A de novo mutation of the LDL receptor gene as the cause of familial hypercholesterolemia identified using whole exome sequencing