De novo and inherited variants in coding and regulatory regions in genetic cardiomyopathies

Table 4 Rare noncoding variants identified in regulatory elements of definitive cardiomyopathy genes in the case-control analysis

Proband ID	Disease	Genomic position (GRCh38)	Gene	MAF Controls	p value	FATHMM-MKL score	Motifs
P01	HCM	chr1:156,106,052 G > T	LMNA	0	0.0415	0.08434
P02	HCM	chr1:156,106,161 T > C	LMNA	0	0.0415	0.05647
P03	DCM	chr1:156,106,287 T > G	LMNA	0	0.0415	0.39668	Bcl6, EHF, ELF1, ELF3, ELF4, ELF5, STAT1, STAT3, Stat4, Stat5a::Stat5b
P04	DCM	chr1:156,106,347 T > G	LMNA	0	0.0415	0.31391
P05	DCM	chr1:156,106,457 C > T	LMNA	0	0.0415	0.54018
P06	HCM	chr1:201,377,783 C > A	TNNT2	0	0.0415	0.22864	PLAG1
P07; P08	HCM; HCM	chr1:201,377,789 G > A	TNNT2	2.57E-05	0.005	0.19213	PLAG1, RREB1, ZNF263
P09	HCM	chr1:201,377,790 A > G	TNNT2	0	0.0415	0.15782	RREB1
P10, P11	HCM; HCM	chr10:110,637,018 C > A	RBM20	7.71E-05	0.0158	0.56143
P12	HCM	chr10:119,651,128 G > C	BAG3	0	0.0415	0.65553
P13	LVNC	chr10:119,651,207 G > C	BAG3	0	0.0415	0.66491	HINFP
P14	HCM	chr10:119,651,329 T > C	BAG3	0	0.0415	0.54331	EGR3, EGR4, SP2
P15	HCM	chr10:119,651,409 T > C	BAG3	0	0.0415	0.98892
P16	HCM	chr2:219,419,925 C > T	DES	0	0.0415	0.89101
P17	ARVC	chr2:219,419,965 C > G	DES	0	0.0415	0.26643
P18	HCM	chr3:52,452,725 T > G	TNNC1	0	0.0415	0.89566	CTCF, Hic1, HIC2, Myod1, SNAI2
P19	HCM	chr6:7,541,668 G > C	DSP	0	0.0415	0.36401
P20	HCM	chr6:7,542,061 C > T	DSP	0	0.0415	0.20036
P21	HCM	chr6:7,542,062 C > G	DSP	0	0.0415	0.38808
P22	HCM	chr6:7,542,072 T > C	DSP	0	0.0415	0.90083
P23	ARVC	chr6:7,542,155 G > C	DSP	0	0.0415	0.1913
P24	HCM	chr6:7,542,266 G > C	DSP	0	0.0415	0.19228
P25	HCM	chr6:118,537,675 A > C	PLN	0	0.0415	0.89431	Nr1h3::Rxra
P26	HCM	chr6:118,537,684 T > C	PLN	0	0.0415	0.90162	Nr1h3::Rxra
P27	HCM	chr6:118,537,778 A > G	PLN	0	0.0415	0.22901

P values are calculated using the Fisher’s exact test. Motifs column indicate functional motifs present according to the funMotifs framework. The FATHMM-MKL score indicates the pathogenic impact of individual SNVs. Predictions are given as p values in the range 0 to 1; values > 0.5 are predicted to be deleterious

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