ClinVar Genomic variation as it relates to human health

The c.2389+1G>T intronic pathogenic mutation results from a G to T substitution one nucleotide after coding exon 16 of the LDLR gene. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNAdecay; however, direct evidence is unavailable. The exact functional effect of the missing amino acids is unknown; however, the impacted region is critical for protein function (Ambry internal data; Holla ØL et al. Mol. Genet. Metab., 2009 Apr;96:245-52). This variant has been detected in multiple individuals who met diagnostic or clinical criteria for familial hypercholesterolemia (Lombardi MP et al. Clin. Genet., 2000 Feb;57:116-24; Bertolini S et al. Atherosclerosis, 2013 Apr;227:342-8; van der Graaf A et al. Circulation, 2011 Mar;123:1167-73). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

This sequence change affects a donor splice site in intron 16 of the LDLR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in LDLR are known to be pathogenic (PMID: 20809525, 28645073). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with LDLR-related conditions (PMID: 10735632, 32041611, 32977124; internal data). ClinVar contains an entry for this variant (Variation ID: 252300). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

The LDLR c.2389+1G>T variant (rs879255186, ClinVar Variation ID 252300) is reported in the literature in multiple individuals affected with familial hypercholesteremia (FH), either as a heterozygote, or as part of a compound heterozygous pair (Lombardi 2000, Fouchier 2001, van der Graaf 2011, Bertolini 2013, Bertolini 2020, Dron 2020). This variant is absent from the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. This variant disrupts the canonical splice donor site of intron 16, which is likely to negatively impact gene function, and functional analyses of patients harboring this variant indicate that this is likely a receptor negative variant (Bertolini 2020). Additionally, other variants at this position (c.2389+1G>A) have been reported in individuals with FH and are considered pathogenic (selected reference: Bertolini 2020). Based on available information, the c.2389+1G>T variant is considered pathogenic. References: Bertolini S et al. Spectrum of mutations and phenotypic expression in patients with autosomal dominant hypercholesterolemia identified in Italy. Atherosclerosis. 2013 Apr;227(2):342-8. PMID: 23375686. Bertolini S et al. Homozygous familial hypercholesterolemia in Italy: Clinical and molecular features. Atherosclerosis. 2020 Nov;312:72-78. PMID: 32977124. Dron JS et al. Six years' experience with LipidSeq: clinical and research learnings from a hybrid, targeted sequencing panel for dyslipidemias. BMC Med Genomics. 2020 Feb 10;13(1):23. PMID: 32041611 Fouchier SW et al. The molecular basis of familial hypercholesterolemia in The Netherlands. Hum Genet. 2001 Dec;109(6):602-15. doi: 10.1007/s00439-001-0628-8. Epub 2001 Nov 9. PMID: 11810272. Lombardi MP et al. Molecular genetic testing for familial hypercholesterolemia: spectrum of LDL receptor gene mutations in The Netherlands. Clin Genet. 2000 Feb;57(2):116-24. PMID: 10735632. van der Graaf A et al. Molecular basis of autosomal dominant hypercholesterolemia: assessment in a large cohort of hypercholesterolemic children. Circulation. 2011 Mar 22;123(11):1167-73. PMID: 21382890.