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