Novel MYBPC3 Mutations in Indian Population with Cardiomyopathies

Figures & data

Table 1 Baseline Clinical Characteristics of HCM and DCM Patients along with Controls

Baseline Characteristics	HCM (N=115)	DCM (N=127)	Controls (N=197)
Age (Yrs)	49±10	48±12	51.0 ±0.2
Sex, males %	67	69	70
Consanguinity %	80.2	35.6	0
Dyspnea or shortness of breath %	65	69.2	0
Angina pectoris (chest pain) %	54	56	0
Syncope (fainting) %	33	30	0
Abnormal ECG %	62	68	0
LVEDD, mm	35± 7.8	67±10	51.5± 2.7
LVESD, mm	20.3 ± 4.7	54 ± 7.7	32.2± 1.2
Septum, mm	22.2 ± 5.3	6 ± 2.7	9.0 ± 0.4
Family History %	82	79	0
Sudden cardiac death %	28.8	14.2	0
LVEF %	49 ±7	31 ± 6.6	64.2 ± 5.1
NYHA Class III &IV	29	35.2	0

Abbreviations: NYHA, New York Heart Association; LVEDD, left ventricular end-diastolic dimension; LVESD, left ventricular end-systolic dimension; ECG, electrocardiogram; LVEF, left ventricular ejection fraction; SCD, sudden cardiac death.

Table 2 Comparing the Allele Frequencies of Detected Mutations in the MYBPC3 Gene of Indian Population vs Other Populations

	Chromosome Position	Position	Major>Minor Allele	Location	SNP Reference	AA Change	PolyPhen-2	SIFT	Predictions	CON/197	HCM/115	DCM/127	IN_AF	ASN_AF	AFR_AF	AMR_AF	EUR_AF	Mean India	Mean ASN-EUR
1	1,147,374,209	g.1045	C>T	5’UTR	Novel-ss6322063401	-	-	-	-	0	0	0.28	0	0	0	0	0	0.001	0
2	1,147,374,129	g.1125	G>T	Intron 1	Reported	-	-	-	-	0	0	0.28	0	0	0	0	0	0.001	0
3	1,147,372,908	g.2346	C>T	Exon 2	Reported	A58A	-	-	-	0	0	0.28	0	0	0	0	0	0.001	0
4	1,147,372,749	g.2505	G>C	Intron 2	rs3729985	-	-	-	Polymorphic	0.73	3.3	10.5	0.03	0.06	0.01	0.03	0.03	0.048	0.045
5	1,147,372,149	g.3105	C>A	Exon 3	Reported	L104M	Benign	Damaging	-	0	0.5	0.28	0	0	0	0	0	0.002	0
6	1,147,371,633	g.3621	C>A	Exon 4	Novel-ss6322063400	T146N	Benign	Tolerated	Benign	0	0	0.28	0	0	0	0	0	0.001	0
7	1,147,371,632	g.3622	C>A	Exon 4	Novel-ss6322063399	T146T	-	-	-	0	0	0.28	0	0	0	0	0	0.001	0
8	1,147,371,620	g.3634	C>A	Exon 4	Novelss6322063398	P150P	-	-	-	0	0	0.28	0	0	0	0	0	0.001	0
9	1,147,371,608	g.3656	G>A	Exon 4	rs3729986	V158M	Possibly Damaging	Damaging	Pathogenic	0	0.75	0.56	0	0	0	0	0	0.003	0
10	1,147,371,442	g.3812	C>T	Exon 5	rs11570051	A179S	Benign	Tolerated	Polymorphic	0	0.25	0	0.02	0.004	0.002	0.07	0.03	0.001	0.01675
11	1,147,371,421	g.3833	G>T	Exon 5	Novel_ss6322063397	P186P	-	-	-	0	0.50	0	0	0	0	0	0	0.001	0
12	1,147,370,041	g.5213	A>G	Exon 6	rs3729989	S236G	Benign	Tolerated	Polymorphic	0	0.25	0.56	0.09	0.02	0.07	0.1	0.14	0.004	0.08
13	1,147,370,029	g.5225	G>A	Exon 6	Reported	E240K	Probably Damaging	Tolerated	-	0	0.25	0	0	0	0	0	0	0.001	0
14	1,147,370,015	g.5239	G>A	Exon 6	Novel_ss6322063396	K244K	-	-	-	0	0.25	0	0	0	0	0	0	0.001	0
15	1,147,369,975	g.5279	G>A	Exon 6	CM981322	E258K	Possibly Damaging	Damaging	Pathogenic	0	0.25	0	0	0	0	0	0	0.001	0
16	1,147,369,973	g.5281	T>G[IVS6+2T]	Intron 6	Novel_ss6322063395	SD	-	-	Pathogenic	0	0.25	0	0	0	0	0	0	0.001	0
17	1,147,369,445	g.5809	A>T	Exon 7	Novel-ss6322063394	T262S	Benign	Tolerated	Benign	0	0.25	0	0	0	0	0	0	0.001	0
18	1,147,369,443	g.5811	C>T	Exon 7	rs11570058	T262T	-	-	Polymorphic	0	1.02	1.4	0.07	0.02	0.03	0.1	0.13	0.008	0.075
19	1,147,369,415	g.5839	A>T	Exon 7	rs397516075	R272C	Probably Damaging	Damaging	Pathogenic	0	0.25	0.28	0	0	0	0	0	0.002	0
20	1,147,369,009	g.6232	A>T	Exon 9	Novel-ss6322063392	H287L	Benign	Damaging	-	0	0.25	0	0	0	0	0	0	0.001	0
21	1,147,369,014	g.6240	A>G	Exon 9	Reported	T290A	Benign	Tolerated	Benign	0	0.25	0.28	0	0	0	0	0	0.002	0
22	1,147,369,022	g.6245	G>A	Exon 9	Novel-ss6322063393	G291G	-	-	-	0	0	0.28	0	0	0	0	0	0.001	0
23	1,147,368,195	g.7059	C>T	Exon 10	rs200713257	D303D	-	-	-	0	0	0.28	0	0	0	0	0	0.001	0
24	1,147,367,887	g.7367	G>C	Exon 11	Novel-ss6322063391	V321L	Benign	Damaging	-	0	0	0.28	0	0	0	0	0	0.003	0
25	1,147,365,092	g.10162	G>A	Exon 12	Novel-ss6322063390	A392T	Probably Damaging	Damaging	Pathogenic	0	0	0.56	0	0	0	0	0	0.003	0
26	1,147,365,089	g.10165	G>A	Exon 12	Novel-ss6322063389	E393K	Benign	Damaging	-	0	0	0.56	0	0	0	0	0	0.003	0
27	1,147,365,060	g.10194	G>A	Exon 12	Novel-ss6322063388	E402E	-	-	-	0	0.51	1.13	0	0	0	0	0	0.005	0
28	1,147,365,043	g.10211	G>T	Exon 12	Novel-ss6322063387	R408IM	Possibly Damaging	Damaging	Pathogenic	0	0.25	0	0	0	0	0	0	0.001	0
29	1,147,365,014	g.10240	G>A	Intron 12	rs11570078	-	-	-	Polymorphic	0	0	0.28	0.09	0.06	0.03	0.1	0.14	0.001	0.1
30	1,147,364,392	g.10862	G>A	Exon 14	Novel-ss6322063386	A482A	-	-	-	0	0.51	0	0	0	0	0	0	0.002	0
31	1,147,364,387	g.10867	T>C	Exon 14	Novel-ss6322063385	V483A	Probably Damaging	Damaging	Pathogenic	0	0.25	0	0	0	0	0	0	0.001	0
32	1,147,364,185	g.11069	G>A	Exon 15	Novel-ss6322063384	G522E	Probably Damaging	Damaging	Pathogenic	0	0.76	0.85	0	0	0	0	0	0.005	0
33	1,147,363,535	g.11719	G>A	Intron 16	Novel-ss2137544465	-	-	-	-	0	0	0.85	0	0	0	0	0	0.003	0
34	1,147,362,650	g.12548	C>T	Exon 20	Reported	A626V	Probably Damaging	Damaging	Pathogenic	0	1.27	0.85	0	0	0	0	0	0.007	0

Note: Reverse strand sequences https://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?handle=THANGARAJ_DEEPA_CCMB.

Abbreviations: SNP, single nucleotide polymorphism; AA, amino acids; rs#.No, reference SNP number; PolyPhen-2, Phenotyping v2; SIFT, sorting intolerant from tolerant; CON, controls; HCM, hypertrophic cardiomyopathy; DCM, dilated cardiomyopathy; IN_AF, Allele frequency of Indian Ancestry; ASN_AF, Allele frequency of Asian Ancestry; AFR_AF, Allele frequency of African Ancestry; AMR_AF, Allele frequency of American Ancestry; EUR_AF, Allele frequency of European Ancestry.

Table 3 Missense Mutations in Myosin Binding Protein C (MYBPC3) Gene

S:NO	Chromosome Position	Position	Major>Minor Allele	Location	SNP Reference	AA change	PolyPhen-2	SIFT	CON 197	HCM 115	DCM 127
1	1,147,371,608	g.3656	G>A	Exon 4	rs3729986	V158M	Possibly Damaging	Damaging	-	2	1
2	1,147,369,975	g.5279	G>A	Exon 6	CM981322	E258K	Possibly Damaging	Damaging	-	2	-
3	1,147,369,415	g.5839	A>T	Exon 7	rs397516075	R272C	Probably Damaging	Damaging	-	1	1
4	1,147,365,092	g.10162	G>A	Exon 12	Novel-ss6322063390	A392T	Probably Damaging	Damaging	-	-	2
5	1,147,364,387	g.10867	T>C	Exon 14	Novel-ss6322063385	V483A	Probably Damaging	Damaging	-	1	-
6	1,147,364,185	g.11069	G>A	Exon 15	Novel-ss6322063384	G522E	Probably Damaging	Damaging	-	2	2
7	1,147,362,650	g.12548	C>T	Exon 20	rs1352376969	A626V	Probably Damaging	Damaging	-	2	2
Total									-	10/115= 8.7%	8/127= 6.3%

Abbreviations: SNP, single nucleotide polymorphism; AA, amino acids; rs#.No, reference SNP number; PolyPhen-2, Phenotyping v2; SIFT, sorting intolerant from tolerant; CON, controls; HCM, hypertrophic cardiomyopathy; DCM, dilated cardiomyopathy.

Table 4 Compound Mutations in Myosin Binding Protein C (MYBPC3) Gene

S:No	SNP_AA Change	CON	HCM	DCM
1	K244K, E258K, T>G[IVS6+2T]	–	1(HU22)	–
2	L104M, G522E, A626V	–	1(HU1)	–
3	P186P, G522E, A626V	–	1(HU28)	–
4	5’UTR, A392T, E393K	–	–	1(DU79)
5	V158M, G522E	–	–	1(DU106)
6	V158M+T262T+A626V	–	–	1(DU99)

Abbreviations: SNP, single nucleotide polymorphism; AA, amino acids; CON, controls; HCM, hypertrophic cardiomyopathy; DCM, dilated cardiomyopathy.

Figure 1 (A) Schematic representation of the MYBPC3 structure. (B) Highlighted are the observed exonic, and splice sites variations. (The 10 amino acid substitutions, and 1 splice-site mutation were indicated in red color). (C) Electropherograms (arrows) showing 10 missense mutations [V158M, E258K, R272C, H287L, V321L, E392T, R408M, V483A, and a G522E, A626V), and a splice-donor mutation (T>G[IVS6+2T]) in the MYBPC3 gene. (D) Multiple alignments of amino acid sequences in the MYBPC3gene of several species, showing that those were highly conserved across many species.