Novel 327bp Alu element insertion in LDLR exon 17 causes alternative splicing and familial hypercholesterolemia

BACKGROUND

Homozygous familial hypercholesterolemia (HoFH) is a severe form of familial hypercholesterolemia (FH) characterized by high low-density lipoprotein cholesterol (LDL-C) levels and increased coronary artery disease risk. This study reports a novel Alu insertion in the LDLR gene in a consanguineous Indian family, causing FH.

OBJECTIVE

To identify and characterize the mutation causing HoFH in a proband and their family members.

METHODS

Clinical exome sequencing was conducted on the proband with subsequent bioinformatic analysis of single nucleotide variants, loss-of-function variants, structural variants, and mobile element insertions (MEI). Polymerase chain reaction (PCR) amplification and Sanger sequencing of exon 17 of the LDLR gene were performed to elucidate the sequence and length of the Alu insertion. Additionally, RNA analysis of the proband identified splice site events.

RESULTS

Bioinformatic analysis revealed a small sequence duplication followed by an Alu element insertion. PCR amplification and Sanger sequencing uncovered a 17 base pair (bp) duplication at the breakpoint, a “T” base insertion, followed by a 309 bp Alu Yb8 insertion. This led to a 70 bp deletion at the beginning of exon 17 due to alternative splicing, resulting in a frameshift and extended protein truncation. The proband and siblings were homozygous for the mutation, while the parents and 2 other family members were heterozygous.

CONCLUSION

Our study uncovers a novel AluYb8 element insertion in the LDLR gene, highlighting the need for MEI detection in genetic screening for FH. Reanalyzing FH cohorts for MEIs could significantly improve diagnostic accuracy and enhance our understanding of FH genetics.