Exome Sequencing Identifies a Novel LMNA Splice-Site Mutation and Multigenic Heterozygosity of Potential Modifiers in a Family with Sick Sinus Syndrome, Dilated Cardiomyopathy, and Sudden Cardiac Death

Abstract

The goals are to understand the primary genetic mechanisms that cause Sick Sinus Syndrome and to identify potential modifiers that may result in intrafamilial variability within a multigenerational family. The proband is a 63-year-old male with a family history of individuals (>10) with sinus node dysfunction, ventricular arrhythmia, cardiomyopathy, heart failure, and sudden death. We used exome sequencing of a single individual to identify a novel LMNA mutation and demonstrated the importance of Sanger validation and family studies when evaluating candidates. After initial single-gene studies were negative, we conducted exome sequencing for the proband which produced 9 gigabases of sequencing data. Bioinformatics analysis showed 94% of the reads mapped to the reference and identified 128,563 unique variants with 108,795 (85%) located in 16,319 genes of 19,056 target genes. We discovered multiple variants in known arrhythmia, cardiomyopathy, or ion channel associated genes that may serve as potential modifiers in disease expression. To identify candidate mutations, we focused on ~2,000 variants located in 237 genes of 283 known arrhythmia, cardiomyopathy, or ion channel associated genes. We filtered the candidates to 41 variants in 33 genes using zygosity, protein impact, database searches, and clinical association. Only 21 of 41 (51%) variants were validated by Sanger sequencing. We selected nine confirmed variants with minor allele frequencies <1% for family studies. The results identified LMNA c.357-2A>G, a novel heterozygous splice-site mutation as the primary mutation with rare or novel variants in HCN4, MYBPC3, PKP4, TMPO, TTN, DMPK and KCNJ10 as potential modifiers and a mechanism consistent with haploinsufficiency.

A de novo 1q22q23.1 Interstitial Microdeletion in a Girl with Intellectual Disability and Multiple Congenital Anomalies Including Congenital Heart Defect

“…Dilated cardiomyopathy type 1A (OMIM 115200); Emery-Dreifuss muscular dystrophy (OMIM 181350); heart-hand syndrome, Slovenian type (OMIM 610140); Hutchinson-Gilford progeria (OMIM 176670); lipodystrophy, familial partial, type 2 (OMIM 151660); Malouf syndrome (OMIM 212112); muscular dystrophy, congenital (OMIM 613205), and muscular dystrophy, limb-girdle, type 1B (OMIM 159001) allelic disorders follow a pattern of autosomal dominant inheritance. Loss-of-function variants and deletions that result in haploinsufficiency are associated with dilated cardiomyopathy [Benedetti et al, 2007;Zaragoza et al, 2016]. We cannot exclude the possibility of this disorder in our patient when she grows older.…”

Age of heart disease presentation and dysmorphic nuclei in patients with LMNA mutations

“…One particularly severe example is Hutchinson-Gilford Progeria Syndrome (HGPS) in which a mutation in the Lamin A/C ( LMNA ) gene causes premature aging up to seven times faster than normal, usually culminating in death due to cardiovascular complications [ 1 ]. Other types of LMNA gene mutations are associated with a range of heart disease symptoms including cardiomyopathy, heart failure, and arrhythmia [ 2 , 4 , 5 ]. While the exact mechanism by which LMNA mutations cause heart disease is under investigation, it is known that the LMNA gene expresses both the Lamin A and C proteins via alternative splicing.…”

“…This is especially interesting as some nuclear envelope protein mutations lead to organ specific pathologies in patients. For example, there are a variety of LMNA mutations including heterozygous splice site, nonsense, and missense mutation, which cause diverse heart diseases with no other major pathologies [ 4 , 9 , 10 ]. Furthermore, even patients with the same mutation can exhibit a variety of heart disease symptoms with different presentation ages from 36–54 years [ 4 ].…”

Heart‐hand syndrome IV: a second family with LMNA‐related cardiomyopathy and brachydactyly

“…The proband, who recently died at age 57, had DCM and ‘small hands.’ His family had German and Irish ancestry and multiple individuals born with ‘small hands’ and later developed heart disease. Eleven individuals were classified as affected or unaffected for heart disease 4 and hand anomalies (Fig. S1 and Table S1, Supporting Information).…”

“…To identify the causative variant(s) for the cardiac and/or limb phenotypes, exome sequencing for the proband was conducted 4. The results included 14 gigabases of data from 164 million reads, 91% of mapped reads to hg19, and 134X average read coverage of each exon.…”