MYBPC3 variants in HCM cohorts

The table below lists the 636 rare (MAF<0.0001 in ExAC) protein-altering MYBPC3 variants identified in a cohort of 3267 HCM patients. When this rare variant frequency of 0.19467 is compared with a background population rate of 0.01970, there is a statistically significant case excess of 0.17497 (p<0.0001), which suggests that approximately 572 of these variants may be pathogenic.

Variant Type: All protein-altering variants - Truncating variants - Non-Truncating variants

Source: Combined (OMGL + LMM) - OMGL - LMM

No.	Variant (CDS)▼	Variant (Protein)	Variant Type▼	Cases (3267)▼	OMGL class	ExAC frequency
1.	c.1504C>T	p.R502W	missense	59	Pathogenic	0.000024
2.	c.772G>A	p.E258K	missense	47	Pathogenic	0.000039
3.	c.2373_2374insG	p.Trp792ValfsTer41	frameshift	40	Pathogenic	0.000037
4.	c.1624G>C	p.E542Q	missense	24	Pathogenic	0.000024
5.	c.655G>C	p.V219L	missense	18	Likely Pathogenic	0.000000
6.	c.2096delC		frameshift	15	Pathogenic	0.000000
7.	c.3226_3227insT		frameshift	12	Pathogenic	0.000000
8.	c.2827C>T	p.R943X	nonsense	11	Pathogenic	0.000017
9.	c.2429G>A	p.R810H	missense	11	VUS	0.000033
10.	c.1928-2A>G		essential splice site	10	Pathogenic	0.000000
11.	c.3613C>T	p.R1205W	missense	10	Likely Pathogenic	0.000016
12.	c.1483C>G	p.R495G	missense	10	Likely Pathogenic	0.000000
13.	c.3771C>A	p.N1257K	missense	9	Likely Pathogenic	0.000000
14.	c.927-2A>G		essential splice site	8	Pathogenic	0.000000
15.	c.2604_2605delinsA	p.S871fs	frameshift	8	Pathogenic	0.000000
16.	c.2864_2865delCT		frameshift	8	Pathogenic	0.000000
17.	c.2490_2491insT	p.His831SerfsTer2	frameshift	7	Pathogenic	0.000024
18.	c.3190+2T>G		essential splice site	7	Pathogenic	0.000016
19.	c.3627+1G>A		essential splice site	6	Pathogenic	0.000000
20.	c.3065G>C	p.R1022P	missense	5	Likely Pathogenic	0.000025
21.	c.2459G>A	p.R820Q	missense	5	VUS	0.000016
22.	c.2308G>A	p.D770N	missense	5	Likely Pathogenic	0.000008
23.	c.2610delC		frameshift	5	Pathogenic	0.000000
24.	c.2267delC		frameshift	5	Pathogenic	0.000000
25.	c.3163A>T	p.K1055X	nonsense	4	Pathogenic	0.000000
26.	c.484C>T	p.Q162X	nonsense	4	Pathogenic	0.000000
27.	c.821+2T>C		essential splice site	4	Pathogenic	0.000000
28.	c.442G>A	p.G148R	missense	4	Likely Pathogenic	0.000042
29.	c.2556_2557delinsTCT	p.Gly853fs	frameshift	4	Pathogenic	0.000000
30.	c.3798C>G	p.C1266W	missense	4	VUS	0.000000
31.	c.1484G>A	p.R495Q	missense	4	Likely Pathogenic	0.000008
32.	c.3697C>T	p.Q1233X	nonsense	4	Likely Pathogenic	0.000008
33.	c.3763G>A	p.A1255T	missense	3	VUS	0.000075
34.	c.2545del	p.Val849Serfs*30	frameshift	3	Pathogenic	0.000000
35.	c.3286G>T	p.E1096X	nonsense	3	Pathogenic	0.000000
36.	c.2210C>T	p.T737M	missense	3	VUS	0.000050
37.	c.710A>C	p.Y237S	missense	3	Likely Pathogenic	0.000000
38.	c.2905+1G>A		essential splice site	3	Pathogenic	0.000000
39.	c.1123G>A	p.V375M	missense	3	VUS	0.000009
40.	c.3408C>A	p.Y1136X	nonsense	3	Pathogenic	0.000000
41.	c.3600_3609delCTGCTGTGCT		frameshift	3	Pathogenic	0.000000
42.	c.3277G>T	p.G1093C	missense	3	VUS	0.000020
43.	c.3181C>T	p.Q1061X	nonsense	3	Pathogenic	0.000016
44.	c.1720C>T	p.R574W	missense	3	VUS	0.000054
45.	c.3129C>A	p.Y1043X	nonsense	3	Pathogenic	0.000000
46.	c.2309-1G>A		essential splice site	3	Pathogenic	0.000000
47.	c.2300A>G	p.K767R	missense	2	VUS	0.000016
48.	c.1483C>T	p.R495W	missense	2	Likely Pathogenic	0.000000
49.	c.2308+1G>A		essential splice site	2	Pathogenic	0.000000
50.	c.818G>A	p.R273H	missense	2	VUS	0.000042
51.	c.3582_3593delGGGCTACACTGC		inframe	2	Likely Pathogenic	0.000000
52.	c.2526C>G	p.Y842X	nonsense	2	Pathogenic	0.000000
53.	c.3627+1G>T		essential splice site	2	Pathogenic	0.000000
54.	c.3752A>G	p.Y1251C	missense	2	VUS	0.000000
55.	c.126G>A	p.W42X	nonsense	2	Pathogenic	0.000000
56.	c.2905+2dup		essential splice site	2	Likely Pathogenic	0.000000
57.	c.2524dup	p.Tyr842Leufs*42	frameshift	2	Pathogenic	0.000000
58.	c.2573G>A	p.S858N	missense	2	Likely Pathogenic	0.000000
59.	c.3271del	p.Asp1091Metfs*98	frameshift	2	Pathogenic	0.000000
60.	c.177_187del	p.Glu60AlafsX49	frameshift	2	Pathogenic	0.000000
61.	c.3455_3466del	p.Ala1152_Lys1155del	inframe	2	Likely Pathogenic	0.000000
62.	c.557C>T	p.P186L	missense	2	VUS	0.000047
63.	c.443dup	p.Ala149Serfs*4	frameshift	2	Pathogenic	0.000000
64.	c.2219G>C	p.G740A	missense	2	VUS	0.000000
65.	c.3470C>T	p.P1157L	missense	2	VUS	0.000093
66.	c.2905C>T	p.Q969X	nonsense	2	Pathogenic	0.000000
67.	c.747C>A	p.C249X	nonsense	2	Pathogenic	0.000000
68.	c.1828G>A	p.D610N	missense	2	VUS	0.000000
69.	c.2432A>G	p.K811R	missense	2	VUS	0.000000
70.	c.1505G>A	p.R502Q	missense	2	Pathogenic	0.000000
71.	c.25+1G>A		essential splice site	2	Pathogenic	0.000000
72.	c.3751T>C	p.Y1251H	missense	2	VUS	0.000000
73.	c.1886T>C	p.L629P	missense	2	VUS	0.000000
74.	c.3005G>A	p.R1002Q	missense	2	VUS	0.000046
75.	c.833delG	p.Gly278GlufsX22	frameshift	2	Pathogenic	0.000000
76.	c.1201C>T	p.Q401X	nonsense	1	Pathogenic	0.000000
77.	c.146_148delTCA	p.Ile49del	inframe	1	VUS	0.000039
78.	c.799C>G	p.L267V	missense	1	VUS	0.000080
79.	c.1841A>G	p.Y614C	missense	1	VUS	0.000000
80.	c.2449C>T	p.R817W	missense	1	VUS	0.000000
81.	c.459delC		frameshift	1	Pathogenic	0.000000
82.	c.2197C>T	p.R733C	missense	1	Likely Pathogenic	0.000085
83.	c.2558delG		frameshift	1	Pathogenic	0.000000
84.	c.655-2del		essential splice site	1	Pathogenic	0.000000
85.	c.3656T>C	p.L1219P	missense	1	VUS	0.000000
86.	c.3364A>T	p.T1122S	missense	1	Likely Pathogenic	0.000000
87.	c.1080G>C	p.K360N	missense	1	VUS	0.000000
88.	c.3792_3793del	p.Cys1264*	frameshift	1	Likely Pathogenic	0.000000
89.	c.1790G>A	p.R597Q	missense	1	VUS	0.000000
90.	c.351_352del	p.Gly118Argfs*8	frameshift	1	Pathogenic	0.000000
91.	c.3256T>C	p.W1086R	missense	1	VUS	0.000000
92.	c.187C>T	p.R63W	missense	1	VUS	0.000077
93.	c.1471G>A	p.V491M	missense	1	VUS	0.000058
94.	c.1351+1G>A		essential splice site	1	Pathogenic	0.000000
95.	c.391dup	p.Ala131Glyfs*22	frameshift	1	Pathogenic	0.000000
96.	c.3297dup	p.Tyr1100Valfs*49	frameshift	1	Pathogenic	0.000000
97.	c.2149_2737del	p.Leu717Alafs*11	frameshift	1	Pathogenic	0.000000
98.	c.1153G>A	p.V385M	missense	1	VUS	0.000010
99.	c.177dup	p.Glu60Argfs*53	frameshift	1	Pathogenic	0.000000
100.	c.2953A>G	p.K985E	missense	1	Pathogenic	0.000000
101.	c.2188del	p.Thr730Profs*24	frameshift	1	Pathogenic	0.000000
102.	c.1404del	p.Gln469Serfs*19	frameshift	1	Pathogenic	0.000000
103.	c.1731G>C	p.W577C	missense	1	VUS	0.000000
104.	c.3452C>T	p.A1151V	missense	1	VUS	0.000078
105.	c.1231A>G	p.I411V	missense	1	VUS	0.000000
106.	c.3257G>A	p.W1086X	nonsense	1	Pathogenic	0.000021
107.	c.1455A>T	p.K485N	missense	1	VUS	0.000000
108.	c.1037G>A	p.R346H	missense	1	VUS	0.000000
109.	c.2953A>T	p.K985X	nonsense	1	Pathogenic	0.000000
110.	c.2503C>T	p.R835C	missense	1	VUS	0.000024
111.	c.532G>A	p.V178M	missense	1	VUS	0.000020
112.	c.3811C>T	p.R1271X	nonsense	1	VUS	0.000025
113.	c.2873C>T	p.T958I	missense	1	VUS	0.000065
114.	c.*26+2T>C		essential splice site	1	Likely Pathogenic	0.000000
115.	c.188G>A	p.R63Q	missense	1	VUS	0.000039
116.	c.731del	p.Lys244Argfs*56	frameshift	1	Pathogenic	0.000000
117.	c.3614G>C	p.R1205P	missense	1	Likely Pathogenic	0.000000
118.	c.1685C>T	p.A562V	missense	1	VUS	0.000008
119.	c.2265C>A	p.N755K	missense	1	Pathogenic	0.000000
120.	c.1097A>C	p.Q366P	missense	1	VUS	0.000000
121.	c.821+2T>G		essential splice site	1	Pathogenic	0.000000
122.	c.2748G>A	p.W916X	nonsense	1	Pathogenic	0.000000
123.	c.3739G>A	p.D1247N	missense	1	VUS	0.000000
124.	c.1273C>T	p.Q425X	nonsense	1	Pathogenic	0.000000
125.	c.241G>T	p.V81F	missense	1	VUS	0.000000
126.	c.3043dup	p.Ala1015Glyfs*36	frameshift	1	Pathogenic	0.000000
127.	c.1433C>T	p.S478L	missense	1	Likely Pathogenic	0.000017
128.	c.2603-1G>C		essential splice site	1	Pathogenic	0.000000
129.	c.3330+1G>C		essential splice site	1	Pathogenic	0.000000
130.	c.1A>T	p.Met1?	missense	1	Likely Pathogenic	0.000000
131.	c.1797del	p.His599Glnfs*3	frameshift	1	Pathogenic	0.000000
132.	c.2690_2696del	p.Gly897Glufs*25	frameshift	1	Pathogenic	0.000000
133.	c.1090+1G>T		essential splice site	1	Pathogenic	0.000000
134.	c.2247C>A	p.Y749X	nonsense	1	Pathogenic	0.000000
135.	c.2429_2503delins23	p.Arg810Profs*10	frameshift	1	Pathogenic	0.000000
136.	c.3617delG		frameshift	1	Pathogenic	0.000000
137.	c.1458G>A	p.W486X	nonsense	1	Pathogenic	0.000000
138.	c.3490+1G>A		essential splice site	1	Pathogenic	0.000000
139.	c.2065C>T	p.Q689X	nonsense	1	Pathogenic	0.000000
140.	c.1352_1353del	p.Glu451Alafs*23	frameshift	1	Pathogenic	0.000000
141.	c.2995-1G>A		essential splice site	1	Pathogenic	0.000000
142.	c.3373G>A	p.V1125M	missense	1	VUS	0.000022
143.	c.743_746delACTG		frameshift	1	Pathogenic	0.000000
144.	c.3019T>C	p.W1007R	missense	1	VUS	0.000000
145.	c.994G>A	p.E332K	missense	1	VUS	0.000009
146.	c.3713T>C	p.L1238P	missense	1	Likely Pathogenic	0.000000
147.	c.2269G>A	p.V757M	missense	1	VUS	0.000066
148.	c.1174G>T	p.A392S	missense	1	VUS	0.000000
149.	c.148A>G	p.S50G	missense	1	VUS	0.000038
150.	c.772+1G>A		essential splice site	1	Pathogenic	0.000000
151.	c.1828G>C	p.D610H	missense	1	VUS	0.000058
152.	c.1898-1G>A		essential splice site	1	Pathogenic	0.000000
153.	c.611_618delinsT	p.Gly204Valfs*94	frameshift	1	Pathogenic	0.000000
154.	c.3357C>A	p.Y1119X	nonsense	1	Pathogenic	0.000000
155.	c.1591G>A	p.G531R	missense	1	Likely Pathogenic	0.000017
156.	c.100_110dup	p.Val38Serfs*5	frameshift	1	Pathogenic	0.000000
157.	c.1038_1042dupCGGCA		frameshift	1	Pathogenic	0.000008
158.	c.2807dup	p.Ala938Glyfs*113	frameshift	1	Pathogenic	0.000000
159.	c.1291G>A	p.D431N	missense	1	VUS	0.000028
160.	c.1789C>T	p.R597W	missense	1	VUS	0.000038
161.	c.256_258del	p.Ser86del	inframe	1	VUS	0.000000
162.	c.3206C>A	p.P1069H	missense	1	Likely Pathogenic	0.000000
163.	c.2371C>T	p.Q791X	nonsense	1	Pathogenic	0.000000
164.	c.2718_2719dup	p.Glu907Glyfs*18	frameshift	1	Pathogenic	0.000000
165.	c.2161_2168del	p.Thr721Profs*23	frameshift	1	Pathogenic	0.000000
166.	c.1376_1377del	p.Pro459Leufs*15	frameshift	1	Pathogenic	0.000000
167.	c.2381C>A	p.P794Q	missense	1	VUS	0.000000
168.	c.1569dup	p.His524Alafs*7	frameshift	1	Pathogenic	0.000000
169.	c.3253G>T	p.E1085X	nonsense	1	Pathogenic	0.000000
170.	c.1224-1G>T		essential splice site	1	Pathogenic	0.000000
171.	c.844C>T	p.R282W	missense	1	Likely Pathogenic	0.000000
172.	c.1021G>C	p.G341R	missense	1	VUS	0.000000
173.	c.811_817delTTCCGCC		frameshift	1	Pathogenic	0.000000
174.	c.506-1G>A		essential splice site	1	Pathogenic	0.000000
175.	c.932C>A	p.S311X	nonsense	1	Pathogenic	0.000000
176.	c.2198G>A	p.R733H	missense	1	VUS	0.000034
177.	c.2249C>T	p.T750M	missense	1	Likely Pathogenic	0.000024
178.	c.1090+2T>C		essential splice site	1	Pathogenic	0.000000
179.	c.365C>A	p.A122D	missense	1	VUS	0.000000
180.	c.1999_2000delinsG	p.Leu667AspfsX15	frameshift	1	Pathogenic	0.000000
181.	c.701C>A	p.T234N	missense	1	Likely Pathogenic	0.000000
182.	c.3676C>T	p.R1226C	missense	1	VUS	0.000058
183.	c.1624+1G>A		essential splice site	1	Pathogenic	0.000000
184.	c.3316del	p.Asp1106Thrfs*83	frameshift	1	Pathogenic	0.000000
185.	c.2738-2A>G		essential splice site	1	Pathogenic	0.000000
186.	c.1213A>G	p.M405V	missense	1	VUS	0.000000
187.	c.211_212delinsTA	p.Val71*	frameshift	1	Pathogenic	0.000000
188.	c.2968C>G	p.P990A	missense	1	Likely Pathogenic	0.000000
189.	c.1377delC		frameshift	1	Pathogenic	0.000000
190.	c.2584C>T	p.Q862X	nonsense	1	Pathogenic	0.000000
191.	c.1405C>T	p.Q469X	nonsense	1	Pathogenic	0.000000
192.	c.2502del	p.Arg835Alafs*2	frameshift	1	Pathogenic	0.000000
193.	c.1756C>G	p.P586A	missense	1	Likely Pathogenic	0.000000
194.	c.2603-2_2603-1delinsGA		essential splice site	1	Pathogenic	0.000000
195.	c.1090+1G>A		essential splice site	1	Pathogenic	0.000000
196.	c.1266_1267insTGAT	p.Ile423*	frameshift	1	Pathogenic	0.000000
197.	c.3614G>A	p.R1205Q	missense	1	VUS	0.000016
198.	c.1457G>A	p.W486X	nonsense	1	Pathogenic	0.000000
199.	c.3316G>A	p.D1106N	missense	1	VUS	0.000061
200.	c.3572C>T	p.S1191L	missense	1	VUS	0.000016
201.	c.1072G>A	p.D358N	missense	1	VUS	0.000008
202.	c.982delG		frameshift	1	Pathogenic	0.000000
203.	c.711C>A	p.Y237X	nonsense	1	Pathogenic	0.000000
204.	c.2304_2308+2delCATCGGT		essential splice site	1	Pathogenic	0.000000
205.	c.821+1G>A		essential splice site	1	Pathogenic	0.000043
206.	c.2504G>T	p.R835L	missense	1	Likely Pathogenic	0.000074
207.	c.373G>T	p.A125S	missense	1	VUS	0.000000
208.	c.2030C>T	p.P677L	missense	1	VUS	0.000000
209.	c.3728C>G	p.P1243R	missense	1	VUS	0.000000
210.	c.631G>A	p.D211N	missense	1	VUS	0.000009
211.	c.1120C>T	p.Q374X	nonsense	1	Pathogenic	0.000000
212.	c.49C>T	p.R17W	missense	1	VUS	0.000023
213.	c.255del	p.Ser86Profs*10	frameshift	1	Pathogenic	0.000000
214.	c.1456T>G	p.W486G	missense	1	VUS	0.000000
215.	c.553_562del	p.Lys185Trpfs*12	frameshift	1	Pathogenic	0.000000
216.	c.3334_3351del	p.Trp1112_Glu1117del	inframe	1	Likely Pathogenic	0.000000
217.	c.1021_1028del	p.Gly341*	frameshift	1	Pathogenic	0.000000
218.	c.2789del	p.Leu930Argfs*2	frameshift	1	Pathogenic	0.000000
219.	c.2708G>A	p.G903D	missense	1	Likely Pathogenic	0.000000
220.	c.1112C>T	p.P371L	missense	1	VUS	0.000028
221.	c.121dup	p.Arg41Profs*8	frameshift	1	Pathogenic	0.000000
222.	c.2834G>A	p.R945Q	missense	1	VUS	0.000000
223.	c.1303C>T	p.Q435X	nonsense	1	Pathogenic	0.000000
224.	c.2512dup	p.Glu838Glyfs*46	frameshift	1	Pathogenic	0.000000
225.	c.1523_1525delinsT	p.Gln508Leufs*22	frameshift	1	Pathogenic	0.000000
226.	c.2054_2067+11del	p.Lys685Argfs*3	frameshift	1	Pathogenic	0.000000
227.	c.1359del	p.Val454Cysfs*12	frameshift	1	Pathogenic	0.000000
228.	c.3624delC		frameshift	1	Pathogenic	0.000000
229.	c.1223+2T>C		essential splice site	1	Pathogenic	0.000000
230.	c.3605delG		frameshift	1	Pathogenic	0.000000
231.	c.2909G>A	p.R970Q	missense	1	Likely Pathogenic	0.000032
232.	c.2534_2538delGCGTC		frameshift	1	Pathogenic	0.000000
233.	c.3064C>T	p.R1022C	missense	1	VUS	0.000008
234.	c.1021G>A	p.G341S	missense	1	VUS	0.000025

References

1. Roddy Walsh, Kate L. Thomson, James S. Ware, Birgit H. Funke, Jessica Woodley, Karen J. McGuire, Francesco Mazzarotto, Edward Blair, Anneke Seller, Jenny C. Taylor, Eric V. Minikel, Exome Aggregation Consortium, Daniel G. MacArthur, Martin Farrall, Stuart A. Cook and Hugh Watkins. Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med. 2016 doi:10.1038/gim.2016.90.

2. Alfares AA, Kelly MA, McDermott G, Funke BH, Lebo MS, Baxter SB, Shen J, McLaughlin HM, Clark EH, Babb LJ, Cox SW, DePalma SR, Ho CY, Seidman JG, Seidman CE, Rehm HL. Results of clinical genetic testing of 2,912 probands with hypertrophic cardiomyopathy: expanded panels offer limited additional sensitivity. Genet Med. 2015 Nov;17(11):880-8.