MYBPC3 variants in HCM cohorts

The table below lists the 540 rare (MAF<0.0001 in ExAC) protein-altering MYBPC3 variants identified in a cohort of 2912 HCM patients. When this rare variant frequency of 0.18544 is compared with a background population rate of 0.01970, there is a statistically significant case excess of 0.16574 (p<0.0001), which suggests that approximately 481 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 (2912)▼	LMM class	ExAC frequency
1.	c.1504C>T	p.R502W	missense	45	Pathogenic	0.000024
2.	c.2373_2374insG	p.Trp792ValfsTer41	frameshift	26	Pathogenic	0.000037
3.	c.772G>A	p.E258K	missense	21	Pathogenic	0.000039
4.	c.1928-2A>G		essential splice site	20	Pathogenic	0.000000
5.	c.1624G>C	p.E542Q	missense	17	Likely Pathogenic	0.000024
6.	c.3330+2T>G		essential splice site	11	Pathogenic	0.000000
7.	c.1484G>A	p.R495Q	missense	10	VUS favour pathogenic	0.000008
8.	c.3697C>T	p.Q1233X	nonsense	9	Pathogenic	0.000008
9.	c.2309-2A>G		essential splice site	9	Pathogenic	0.000000
10.	c.655G>C	p.V219L	missense	8	Likely Pathogenic	0.000000
11.	c.2429G>A	p.R810H	missense	8	VUS favour pathogenic	0.000033
12.	c.442G>A	p.G148R	missense	7	VUS favour pathogenic	0.000042
13.	c.2827C>T	p.R943X	nonsense	7	Pathogenic	0.000017
14.	c.2670G>A	p.W890X	nonsense	7	Pathogenic	0.000000
15.	c.2864_2865delCT		frameshift	6	Pathogenic	0.000000
16.	c.3226_3227insT		frameshift	6	Pathogenic	0.000000
17.	c.2308G>A	p.D770N	missense	6	Likely Pathogenic	0.000008
18.	c.1505G>A	p.R502Q	missense	6	Pathogenic	0.000000
19.	c.913_914delTT		frameshift	5	Pathogenic	0.000000
20.	c.2374T>C	p.W792R	missense	5	Likely Pathogenic	0.000000
21.	c.3742_3759dup	p.Gly1248_Cys1253dup	inframe	4	Likely Pathogenic	0.000000
22.	c.2573G>A	p.S858N	missense	4	VUS favour pathogenic	0.000000
23.	c.2096delC		frameshift	4	Pathogenic	0.000000
24.	c.26-2A>G		essential splice site	4	Pathogenic	0.000051
25.	c.821+1G>A		essential splice site	4	Pathogenic	0.000043
26.	c.1483C>G	p.R495G	missense	4	Likely Pathogenic	0.000000
27.	c.2905+1G>A		essential splice site	4	Pathogenic	0.000000
28.	c.2454G>A	p.W818X	nonsense	4	Pathogenic	0.000000
29.	c.3064C>T	p.R1022C	missense	4	VUS favour pathogenic	0.000008
30.	c.2182G>T	p.E728X	nonsense	4	Pathogenic	0.000000
31.	c.3233G>A	p.W1078X	nonsense	3	Pathogenic	0.000022
32.	c.2311_2312insG	p.Val771GlyfsX62	frameshift	3	Pathogenic	0.000000
33.	c.1828G>A	p.D610N	missense	3	VUS	0.000000
34.	c.355G>A	p.E119K	missense	3	VUS	0.000000
35.	c.2873C>T	p.T958I	missense	3	VUS favour benign	0.000065
36.	c.1591G>A	p.G531R	missense	3	VUS favour pathogenic	0.000017
37.	c.3767_3769delCCA	p.Thr1256del	inframe	3	Likely Pathogenic	0.000000
38.	c.2905C>T	p.Q969X	nonsense	3	Pathogenic	0.000000
39.	c.2920C>T	p.Q974X	nonsense	3	Pathogenic	0.000000
40.	c.710A>C	p.Y237S	missense	3	Likely Pathogenic	0.000000
41.	c.2450G>A	p.R817Q	missense	3	VUS favour pathogenic	0.000016
42.	c.3190+1G>A		essential splice site	3	Pathogenic	0.000000
43.	c.3491-2A>T		essential splice site	3	Pathogenic	0.000000
44.	c.2558delG		frameshift	2	Pathogenic	0.000000
45.	c.1828G>C	p.D610H	missense	2	VUS favour benign	0.000058
46.	c.2882C>T	p.P961L	missense	2	VUS	0.000048
47.	c.1037G>A	p.R346H	missense	2	VUS	0.000000
48.	c.1863delC	p.Phe621LeufsX42	frameshift	2	Pathogenic	0.000000
49.	c.1210C>T	p.Q404X	nonsense	2	Pathogenic	0.000000
50.	c.532G>A	p.V178M	missense	2	VUS favour pathogenic	0.000020
51.	c.1869C>A	p.C623X	nonsense	2	Pathogenic	0.000000
52.	c.436_437insA	p.Thr146AsnfsX7	frameshift	2	Pathogenic	0.000000
53.	c.3624delC		frameshift	2	Pathogenic	0.000000
54.	c.3190+2T>G		essential splice site	2	Pathogenic	0.000016
55.	c.1934C>T	p.P645L	missense	2	VUS	0.000000
56.	c.3192_3193insC	p.Lys1065GlnfsX12	frameshift	2	Pathogenic	0.000000
57.	c.3624_3625insC	p.Lys1209GlnfsX33	frameshift	2	Pathogenic	0.000000
58.	c.999C>G	p.Y333X	nonsense	2	Pathogenic	0.000000
59.	c.1766G>A	p.R589H	missense	2	VUS	0.000000
60.	c.1513_1515delAAG		inframe	2	VUS favour pathogenic	0.000000
61.	c.636C>G	p.S212R	missense	2	VUS favour pathogenic	0.000000
62.	c.1895delT	p.Met632ArgfsX31	frameshift	2	Pathogenic	0.000000
63.	c.3627+1G>A		essential splice site	2	Pathogenic	0.000000
64.	c.1357_1358delCC		frameshift	2	Pathogenic	0.000000
65.	c.772+1G>A		essential splice site	2	Pathogenic	0.000000
66.	c.2604_2605delinsA	p.S871fs	frameshift	2	Pathogenic	0.000000
67.	c.814C>T	p.R272C	missense	2	VUS	0.000083
68.	c.1790G>A	p.R597Q	missense	2	VUS favour pathogenic	0.000000
69.	c.1483C>T	p.R495W	missense	2	VUS favour pathogenic	0.000000
70.	c.2320G>A	p.A774T	missense	2	VUS	0.000000
71.	c.2943_2947delGACCA		frameshift	2	Pathogenic	0.000000
72.	c.1897+1G>A		essential splice site	2	Pathogenic	0.000000
73.	c.927-2A>G		essential splice site	2	Pathogenic	0.000000
74.	c.1693A>T	p.K565X	nonsense	1	Pathogenic	0.000000
75.	c.2234A>G	p.D745G	missense	1	VUS	0.000000
76.	c.3065G>C	p.R1022P	missense	1	VUS favour pathogenic	0.000025
77.	c.844C>T	p.R282W	missense	1	VUS favour pathogenic	0.000000
78.	c.1591G>C	p.G531R	missense	1	VUS favour pathogenic	0.000017
79.	c.1540A>G	p.I514V	missense	1	VUS	0.000008
80.	c.1575T>G	p.Y525X	nonsense	1	Pathogenic	0.000000
81.	c.1038_1042dupCGGCA		frameshift	1	Pathogenic	0.000008
82.	c.3735delC		frameshift	1	Likely Pathogenic	0.000000
83.	c.2533C>T	p.R845C	missense	1	VUS favour pathogenic	0.000000
84.	c.3676C>T	p.R1226C	missense	1	VUS	0.000058
85.	c.1358C>T	p.P453L	missense	1	VUS	0.000008
86.	c.2490_2491insT	p.His831SerfsTer2	frameshift	1	Pathogenic	0.000024
87.	c.3049G>A	p.E1017K	missense	1	VUS favour benign	0.000085
88.	c.1224-2A>G		essential splice site	1	Pathogenic	0.000000
89.	c.2163delC	p.Glu722ArgfsX32	frameshift	1	Pathogenic	0.000000
90.	c.2938C>T	p.R980C	missense	1	VUS	0.000062
91.	c.2170C>T	p.R724W	missense	1	VUS	0.000019
92.	c.3408C>A	p.Y1136X	nonsense	1	Pathogenic	0.000000
93.	c.459delC		frameshift	1	Pathogenic	0.000000
94.	c.2525A>G	p.Y842C	missense	1	VUS	0.000000
95.	c.2013_2016delinsGG	p.Pro672AspfsX20	frameshift	1	Pathogenic	0.000000
96.	c.3G>C	p.Met1?	missense	1	Likely Pathogenic	0.000000
97.	c.2557G>A	p.G853S	missense	1	VUS	0.000008
98.	c.3763G>A	p.A1255T	missense	1	VUS favour pathogenic	0.000075
99.	c.431_432delGT	p.Gly144AlafsX8	frameshift	1	Pathogenic	0.000000
100.	c.1294G>A	p.A432T	missense	1	VUS	0.000037
101.	c.566T>A	p.V189D	missense	1	VUS	0.000000
102.	c.3040delC	p.Leu1014TrpfsX6	frameshift	1	Pathogenic	0.000000
103.	c.2197C>T	p.R733C	missense	1	VUS	0.000085
104.	c.2436G>T	p.K812N	missense	1	VUS	0.000000
105.	c.2737+2T>A		essential splice site	1	Pathogenic	0.000000
106.	c.3605G>A	p.C1202Y	missense	1	Likely Pathogenic	0.000000
107.	c.1960C>T	p.R654C	missense	1	VUS favour benign	0.000008
108.	c.613C>T	p.Q205X	nonsense	1	Pathogenic	0.000000
109.	c.2308+1G>T		essential splice site	1	Pathogenic	0.000000
110.	c.3332_3335dupAGTG	p.W1112X	nonsense	1	Pathogenic	0.000000
111.	c.2953A>T	p.K985X	nonsense	1	Pathogenic	0.000000
112.	c.1168delC		frameshift	1	Pathogenic	0.000000
113.	c.1535T>A	p.L512Q	missense	1	VUS favour pathogenic	0.000000
114.	c.1624+2T>C		essential splice site	1	Pathogenic	0.000000
115.	c.2833_2834delCG		frameshift	1	Pathogenic	0.000000
116.	c.3742G>A	p.G1248R	missense	1	VUS	0.000033
117.	c.2654C>T	p.T885M	missense	1	VUS	0.000022
118.	c.932C>A	p.S311X	nonsense	1	Pathogenic	0.000000
119.	c.1343T>C	p.F448S	missense	1	Likely Pathogenic	0.000000
120.	c.1586C>G	p.T529S	missense	1	VUS favour pathogenic	0.000000
121.	c.103C>T	p.R35W	missense	1	VUS	0.000056
122.	c.1924C>T	p.Q642X	nonsense	1	Pathogenic	0.000000
123.	c.966G>A	p.W322X	nonsense	1	Pathogenic	0.000000
124.	c.2737+1G>C		essential splice site	1	Pathogenic	0.000000
125.	c.3277G>T	p.G1093C	missense	1	VUS	0.000020
126.	c.3548T>G	p.F1183C	missense	1	Likely Pathogenic	0.000000
127.	c.3791G>A	p.C1264Y	missense	1	VUS	0.000008
128.	c.2556_2557delinsTCT	p.Gly853fs	frameshift	1	Pathogenic	0.000000
129.	c.3181C>T	p.Q1061X	nonsense	1	Pathogenic	0.000016
130.	c.2517_2538del	p.Val840ThrfsX32	frameshift	1	Pathogenic	0.000000
131.	c.2149-1G>A		essential splice site	1	Pathogenic	0.000000
132.	c.821+1G>C		essential splice site	1	Pathogenic	0.000000
133.	c.223G>A	p.D75N	missense	1	VUS favour pathogenic	0.000091
134.	c.1678delG	p.Asp560ThrfsX19	frameshift	1	Pathogenic	0.000000
135.	c.333_334insT	p.E112X	nonsense	1	Pathogenic	0.000000
136.	c.2459G>A	p.R820Q	missense	1	Likely Pathogenic	0.000016
137.	c.2906-2A>G		essential splice site	1	Pathogenic	0.000000
138.	c.533delT	p.Val178GlyfsX7	frameshift	1	Pathogenic	0.000000
139.	c.2524_2525insT	p.Tyr842LeufsX42	frameshift	1	Pathogenic	0.000000
140.	c.1800delA		frameshift	1	Pathogenic	0.000000
141.	c.1273C>T	p.Q425X	nonsense	1	Pathogenic	0.000000
142.	c.1456T>G	p.W486G	missense	1	Likely Pathogenic	0.000000
143.	c.2518G>A	p.V840M	missense	1	VUS	0.000016
144.	c.1090+1G>T		essential splice site	1	Pathogenic	0.000000
145.	c.1672G>A	p.A558T	missense	1	VUS	0.000008
146.	c.3415G>A	p.V1139I	missense	1	VUS	0.000087
147.	c.2210C>T	p.T737M	missense	1	VUS	0.000050
148.	c.3476_3477delTT		frameshift	1	Pathogenic	0.000000
149.	c.3797G>A	p.C1266Y	missense	1	Likely Pathogenic	0.000000
150.	c.290C>T	p.A97V	missense	1	VUS favour pathogenic	0.000000
151.	c.373G>T	p.A125S	missense	1	VUS	0.000000
152.	c.2780_2781delCA		frameshift	1	Pathogenic	0.000000
153.	c.3083C>G	p.T1028S	missense	1	VUS	0.000000
154.	c.1351+1G>A		essential splice site	1	Pathogenic	0.000000
155.	c.2528_2536delAGATGCGCG	p.Glu843_Arg845del	inframe	1	Pathogenic	0.000000
156.	c.436A>C	p.T146P	missense	1	VUS	0.000000
157.	c.506-1G>T		essential splice site	1	Pathogenic	0.000000
158.	c.1999_2000delinsG	p.Leu667AspfsX15	frameshift	1	Pathogenic	0.000000
159.	c.1021G>A	p.G341S	missense	1	VUS favour pathogenic	0.000025
160.	c.326C>T	p.A109V	missense	1	VUS	0.000000
161.	c.2040_2041insT	p.Val681CysfsX12	frameshift	1	Pathogenic	0.000000
162.	c.1000G>T	p.E334X	nonsense	1	Pathogenic	0.000000
163.	c.2723A>G	p.Y908C	missense	1	VUS	0.000062
164.	c.3580G>A	p.A1194T	missense	1	VUS	0.000008
165.	c.3335G>A	p.W1112X	nonsense	1	Pathogenic	0.000000
166.	c.1188G>T	p.W396C	missense	1	VUS	0.000000
167.	c.1699_1700delGA	p.Glu567GlyfsX4	frameshift	1	Pathogenic	0.000000
168.	c.481C>A	p.P161T	missense	1	VUS favour pathogenic	0.000041
169.	c.2394_2395insT	p.Gly799TrpfsX34	frameshift	1	Pathogenic	0.000000
170.	c.931T>A	p.S311T	missense	1	VUS	0.000000
171.	c.3166_3167insG	p.Ala1056GlyfsX9	frameshift	1	Pathogenic	0.000000
172.	c.2747G>A	p.W916X	nonsense	1	Pathogenic	0.000000
173.	c.2965G>T	p.E989X	nonsense	1	Pathogenic	0.000000
174.	c.821+2T>C		essential splice site	1	Pathogenic	0.000000
175.	c.3476_3479dupTTAT	p.Pro1161TyrfsX9	frameshift	1	Pathogenic	0.000000
176.	c.2308+1G>A		essential splice site	1	Pathogenic	0.000000
177.	c.932C>T	p.S311L	missense	1	VUS	0.000000
178.	c.1397T>A	p.M466K	missense	1	VUS	0.000008
179.	c.655-1G>A		essential splice site	1	Pathogenic	0.000000
180.	c.2993A>G	p.Q998R	missense	1	VUS favour pathogenic	0.000000
181.	c.2269G>A	p.V757M	missense	1	VUS	0.000066
182.	c.3811C>T	p.R1271X	nonsense	1	Pathogenic	0.000025
183.	c.3776delA		frameshift	1	Pathogenic	0.000000
184.	c.2828G>A	p.R943Q	missense	1	VUS	0.000025
185.	c.1213A>G	p.M405V	missense	1	Pathogenic	0.000000
186.	c.2671C>T	p.R891W	missense	1	Likely Pathogenic	0.000031
187.	c.1841A>G	p.Y614C	missense	1	VUS favour pathogenic	0.000000
188.	c.3825A>G	p.X1275TrpextX77	nonsense	1	Likely Pathogenic	0.000000
189.	c.451G>A	p.D151N	missense	1	VUS	0.000041
190.	c.2641G>A	p.V881I	missense	1	VUS	0.000018
191.	c.2939G>A	p.R980H	missense	1	VUS	0.000000
192.	c.1892delT		frameshift	1	Pathogenic	0.000000
193.	c.3815-1G>A		essential splice site	1	Pathogenic	0.000000
194.	c.104G>A	p.R35Q	missense	1	VUS	0.000079
195.	c.3753T>G	p.Y1251X	nonsense	1	Pathogenic	0.000000
196.	c.2449C>T	p.R817W	missense	1	VUS	0.000000
197.	c.518C>A	p.T173N	missense	1	VUS	0.000000
198.	c.177_187del	p.Glu60AlafsX49	frameshift	1	Pathogenic	0.000000
199.	c.1950C>G	p.D650E	missense	1	VUS	0.000000
200.	c.1458-1G>A		essential splice site	1	Pathogenic	0.000000
201.	c.3331-1G>A		essential splice site	1	Pathogenic	0.000000
202.	c.3373G>A	p.V1125M	missense	1	VUS favour pathogenic	0.000022
203.	c.551_552insT	p.Lys185GlufsX56	frameshift	1	Pathogenic	0.000000
204.	c.2541C>A	p.Y847X	nonsense	1	Pathogenic	0.000000
205.	c.1505G>T	p.R502L	missense	1	VUS favour pathogenic	0.000000
206.	c.2048G>A	p.W683X	nonsense	1	Pathogenic	0.000000
207.	c.2534_2538delGCGTC		frameshift	1	Pathogenic	0.000000
208.	c.3286G>T	p.E1096X	nonsense	1	Pathogenic	0.000000
209.	c.3288delG		frameshift	1	Pathogenic	0.000000
210.	c.713G>A	p.R238H	missense	1	VUS	0.000074
211.	c.2560A>G	p.M854V	missense	1	VUS	0.000000
212.	c.1156G>T	p.E386X	nonsense	1	Pathogenic	0.000000
213.	c.3098G>A	p.R1033Q	missense	1	VUS	0.000000
214.	c.1628delA		frameshift	1	Pathogenic	0.000000
215.	c.2610_2611insC	p.Ser871GlnfsX13	frameshift	1	Pathogenic	0.000000
216.	c.1090+1G>A		essential splice site	1	Pathogenic	0.000000
217.	c.3065G>A	p.R1022H	missense	1	VUS favour pathogenic	0.000000
218.	c.3746G>T	p.G1249V	missense	1	VUS	0.000000
219.	c.833delG	p.Gly278GlufsX22	frameshift	1	Pathogenic	0.000000
220.	c.2905+1G>C		essential splice site	1	Pathogenic	0.000000
221.	c.3068_3069insA	p.Asn1023LysfsX28	frameshift	1	Pathogenic	0.000000
222.	c.853G>A	p.D285N	missense	1	VUS	0.000000
223.	c.3694A>T	p.K1232X	nonsense	1	Pathogenic	0.000000
224.	c.2113_2114insA	p.Thr705AsnfsX3	frameshift	1	Pathogenic	0.000000
225.	c.1778C>T	p.S593F	missense	1	VUS favour pathogenic	0.000034
226.	c.3281A>T	p.N1094I	missense	1	VUS	0.000000
227.	c.1351+2T>C		essential splice site	1	Pathogenic	0.000000
228.	c.1418T>C	p.F473S	missense	1	VUS	0.000000
229.	c.2875_2876delAC	p.Thr959GlyfsX91	frameshift	1	Pathogenic	0.000000
230.	c.3690_3691delCA	p.Phe1230LeufsX11	frameshift	1	Pathogenic	0.000000
231.	c.2437A>T	p.K813X	nonsense	1	Pathogenic	0.000000
232.	c.3413G>C	p.R1138P	missense	1	VUS	0.000000
233.	c.3253G>T	p.E1085X	nonsense	1	Pathogenic	0.000000
234.	c.2312T>C	p.V771A	missense	1	VUS	0.000000
235.	c.993_994insT	p.E332X	nonsense	1	Pathogenic	0.000000
236.	c.3600_3609delCTGCTGTGCT		frameshift	0	Pathogenic	0.000000

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.