Identification of novel variants in the LDLR gene in Russian patients with familial hypercholesterolemia using targeted sequencing

Abstract

Familial hypercholesterolemia (FH) is caused by mutations in various genes, including the LDLR , APOB and PSCK9 genes; however, the spectrum of these mutations in Russian individuals has not been fully investigated. In the present study, mutation screening was performed on the LDLR gene and other FH-associated genes in patients with definite or possible FH, using next-generation sequencing. In total, 59 unrelated patients were recruited and sorted into two separate groups depending on their age: Adult (n=31; median age, 49; age range, 23-70) and children/adolescent (n=28; median age, 11; age range, 2-21). FH-associated variants were identified in 18 adults and 25 children, demonstrating mutation detection rates of 58 and 89% for the adult and children/adolescent groups, respectively. In the adult group, 13 patients had FH-associated mutations in the LDLR gene, including two novel variants [NM_000527.4: c.433_434dupG p.(Val145Glyfs*35) and c.1186G>C p.(Gly396Arg)], 3 patients had APOB mutations and two had ABCG5/G8 mutations. In the children/adolescent group, 21 patients had FH-causing mutations in the LDLR gene, including five novel variants [NM_000527.4: c.325T>G p.(Cys109Gly), c.401G>C p.(Cys134Ser), c.616A>C p.(Ser206Arg), c.1684_1691delTGGCCCAA p.(Pro563Hisfs*14) and c.940+1_c.940+4delGTGA], and 2 patients had APOB mutations, as well as ABCG8 and LIPA mutations, being found in different patients. The present study reported seven novel LDLR variants considered to be pathogenic or likely pathogenic. Among them, four missense variants were located in the coding regions, which corresponded to functional protein domains, and two frameshifts were identified that produced truncated proteins. These variants were observed only once in different patients, whereas a splicing variant in intron 6 (c.940+1_c.940+4delGTGA) was detected in four unrelated individuals. Previously reported variants in the LDLR, APOB, ABCG5/8 and LIPA genes were observed in 33 patients. The LDLR p.(Gly592Glu) variant was detected in 6 patients, representing 10% of the FH cases reported in the present study, thus it may be a major variant present in the Russian population. In conclusion, the present study identified seven novel variants of the LDLR gene and broadens the spectrum of mutations in FH-related genes in the Russian Federation.

Targeted Sequencing of 242 Clinically Important Genes in the Russian Population From the Ivanovo Region

“…Moreover, this whole-exome study demonstrated the overrepresentation of several disease-causing variants for Mendelian disorders, such as phenylketonuria (PAH, rs5030858), Wilson's disease (ATP7B, rs76151636), factor VII deficiency (F7, rs36209567), and the kyphoscoliosis type of Ehlers-Danlos syndrome (FKBP14, rs542489955). For the Russian population, however, pathogenic variant frequencies were reported mostly for relatively small cohorts including patients and their families and targeted at specific genes and disorders, for example, familial hypercholesterolemia (Meshkov et al, 2021;Miroshnikova et al, 2021); cystic fibrosis, phenylketonuria, alpha-1 antitrypsin deficiency, and sensorineural hearing loss (Kiseleva et al, 2020;Petrova et al, 2020); cardiomyopathy (Marakhonov et al, 2019;Zaklyazminskaya et al, 2019;Kulikova et al, 2021;Shestak et al, 2021); and breast and ovarian cancer (Brovkina et al, 2018;Solodskikh et al, 2019).…”

Analysis of Rare Variants in Genes Related to Lipid Metabolism in Patients with Familial Hypercholesterolemia in Western Siberia (Russia)

“…All missense variants were heterozygous. Some of the identified variants (Cys352Tyr, Cys340Phe, and Leu401His) have been described in patients with familial hypercholesterolemia in Russia [26][27][28][29][30]. The variant most common in our participations-rs121908038-was found in three unrelated families (six subjects total).…”

“…Molecular genetic research on familial hypercholesterolemia in Russia has been conducted for more than 30 years in different regions of the country [29]. It is worth mentioning some variants of the LDLR gene that not only occur in most regions of Russia but are also the most common variants of this gene: rs121908038 and rs761954844 [28][29][30][31][32]57]. Additionally, these variants have been found in populations of Northern and Central Europe (rs121908038) and in populations of Central and Eastern Europe, Southeast Asia, and North America (rs761954844) [40].…”

“…The small sample sizes do not allow us to assess clinicalcourse features of the disease that are associated with various pathogenic variants in lipid metabolism genes and to evaluate the spectrum of pathogenic variants in lipid metabolism genes in the population of Russia. Targeted sequencing can be useful not only for rapid and cost-effective diagnosis of familial hypercholesterolemia, but also for investigation of rare variants of lipid metabolism genes and their influence on the patients' phenotype [30,57,58]. This method may help to combine the efforts of physicians and investigators from different regions for the research on familial hypercholesterolemia.…”

Analysis of the low density lipoprotein receptor gene (<i>LDLR</i>) mutation spectrum in Russian familial hypercholesterolemia

“…Most of the mutations leading to FH, as expected, were found in the LDLR gene, 187 pathogenic or likely pathogenic variants of which were identified in Russia (Meshkov et al, 2021a); 67 out of 187 were not described in other populations of the world. An important article on the genetics of FH in St. Petersburg was later published based on targeted sequencing of genes involved in the origin of the disease (Miroshnikova et al, 2021). As a result, 23 variants of the LDLR gene sequence were found in the St. Petersburg population, most of which had not been described in that area (Mandelshtam et al, 1993;Tatishcheva et al, 2001;Zakharova et al, 2005Zakharova et al, , 2007Vasilyev et al, 2020).…”