Table 1.
Name of the genes analyzed, Ensembl accession number, and chromosomal position.
Fig 1.
Flowchart of noncoding data analysis.
Variants that were independently selected by at least two tools and presented a read depth of 20 or more in the 26 targeted genes were annotated with ANNOVAR. In silico predictions were carried out for noncoding variants that were not classified as either benign/likely benign or pathogenic/likely pathogenic in NCBI ClinVar. All variants with scores above the indicated threshold were single nucleotide substitutions (SNVs). GWAVA: Genome-Wide Annotation of Variants. CADD: Combined Annotation Dependent Depletion. SPIDEX: Splicing Index. R.S.: Region score. PHRED: phred quality score. dPSI: percent of spliced in.
Table 2.
Putative HCM-causing variants located in exons and exon-intron boundaries.
VUS, variant of uncertain significance. ACMG, American College of Medical Genetics and Genomics.
Fig 2.
Assessment of intronic variants.
A) Schematic diagram depicting the position of intronic variants prioritized by each prediction tool. B) Venn diagram illustrating intronic variants that are simultaneously prioritized by multiple prediction tools.
Table 3.
Prioritized intronic variants.
For each variant, minor allele frequency (MAF) was determined using European populations in the 1000 genomes project database (52) and gnomAD database (53). CADD Phred score (45); GWAVA Region score (44); Genomiser Variant score (46); SPIDEX dPSI score (22). HGVS, Human Genome Variation Society.
Fig 3.
The MYBPC3 splice site (c.1227-13G>A Het) and missense (p.Arg495Gln) mutations, and the VCL variant (c.499+367T>C) identified in probands (arrows) were studied in family members, and their clinical status was ascertained. Circles denote females, squares males, solid symbols clinically affected individuals, open symbols clinically unaffected individuals, and NA unknown clinical status.
Table 4.
Clinical, electrocardiographic and echocardiographic data for the proband and relatives of families 6 and 15 (pedigrees are illustrated in Fig 3).
Fig 4.
Variants located at binding sites for transcription and splicing factors.
A) The VCL variant c.499+367T>C (rs113195070) is located at a binding site for transcription factors FOS, JUN and EP300. B) The PRKAG2 variant c.115-30242C>T (rs114394151) is located at a binding site for transcription factors FOS and JUN. C) The TTN variant c.32077+31C>G (rs72650063) is predicted to disrupt the binding site of splicing factor SRSF1.