TNNT2 protein-altering variants in HCM cohorts

The table below lists the 119 rare (MAF<0.0001 in ExAC) protein-altering TNNT2 variants identified in a cohort of 6103 HCM patients (3191 patients from OMGL, 2912 patients from LMM). When this rare variant frequency of 0.01950 is compared with a background population rate of 0.00242, there is a statistically significant case excess of 0.01708 (p<0.0001), which suggests that approximately 105 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 (6103)▼	OMGL class	LMM class	ExAC frequency
1.	c.487_489delGAG		inframe	14	Pathogenic (5)	Pathogenic (9)	0.000000
2.	c.236T>A	p.I79N	missense	10	Pathogenic (8)	Pathogenic (2)	0.000000
3.	c.274C>T	p.R92W	missense	8	Pathogenic (5)	Pathogenic (3)	0.000008
4.	c.856C>T	p.R286C	missense	6	Likely Pathogenic (4)	VUS favour pathogenic (2)	0.000011
5.	c.833G>C	p.R278P	missense	6	Likely Pathogenic (5)	VUS favour pathogenic (1)	0.000000
6.	c.785A>G	p.N262S	missense	5	VUS (4)	VUS (1)	0.000000
7.	c.388C>T	p.R130C	missense	4	Likely Pathogenic (2)	Likely Pathogenic (2)	0.000000
8.	c.281G>T	p.R94L	missense	4	Likely Pathogenic (3)	Pathogenic (1)	0.000000
9.	c.860G>A	p.W287X	nonsense	4		Pathogenic (4)	0.000011
10.	c.571-1G>A		essential splice site	4	VUS (4)		0.000017
11.	c.275G>A	p.R92Q	missense	4	Pathogenic (1)	Pathogenic (3)	0.000000
12.	c.281G>A	p.R94H	missense	4		Likely Pathogenic (4)	0.000000
13.	c.857G>A	p.R286H	missense	3		VUS favour pathogenic (3)	0.000078
14.	c.251G>C	p.R84T	missense	2		VUS favour pathogenic (2)	0.000000
15.	c.833G>A	p.R278H	missense	2	VUS (1)	VUS (1)	0.000021
16.	c.252A>T	p.R84S	missense	2		VUS (2)	0.000000
17.	c.311C>T	p.A104V	missense	2	VUS (1)	VUS favour pathogenic (1)	0.000008
18.	c.773A>T	p.K258I	missense	2		VUS favour pathogenic (2)	0.000000
19.	c.536C>T	p.S179F	missense	2		Likely Pathogenic (2)	0.000000
20.	c.257A>C	p.D86A	missense	2		Likely Pathogenic (2)	0.000008
21.	c.106G>C	p.A36P	missense	1		VUS (1)	0.000049
22.	c.805A>G	p.N269D	missense	1	VUS (1)		0.000017
23.	c.502G>C	p.A168P	missense	1	VUS (1)		0.000000
24.	c.400C>T	p.R134W	missense	1	VUS (1)		0.000000
25.	c.247G>A	p.E83K	missense	1		VUS (1)	0.000000
26.	c.460-1G>C		essential splice site	1	VUS (1)		0.000000
27.	c.767A>G	p.Q256R	missense	1	VUS (1)		0.000000
28.	c.534G>C	p.L178F	missense	1		VUS (1)	0.000000
29.	c.256G>T	p.D86Y	missense	1	VUS (1)		0.000000
30.	c.147_149delAGA	p.Glu51del	inframe	1	VUS (1)		0.000008
31.	c.807C>A	p.N269K	missense	1		Likely Pathogenic (1)	0.000000
32.	c.249G>C	p.E83D	missense	1		VUS (1)	0.000000
33.	c.244G>A	p.G82R	missense	1		Likely Pathogenic (1)	0.000000
34.	c.426T>G	p.N142K	missense	1	VUS (1)		0.000000
35.	c.392G>A	p.R131Q	missense	1	VUS (1)		0.000000
36.	c.330T>G	p.F110L	missense	1		Likely Pathogenic (1)	0.000000
37.	c.821+1G>T		essential splice site	1		Likely Pathogenic (1)	0.000000
38.	c.678_680del	p.Glu226del	inframe	1	VUS (1)		0.000000
39.	c.652G>T	p.V218L	missense	1		VUS favour benign (1)	0.000032
40.	c.451C>T	p.R151C	missense	1	VUS (1)		0.000000
41.	c.821+1G>C		essential splice site	1	Pathogenic (1)		0.000000
42.	c.421C>T	p.R141W	missense	1		Pathogenic (1)	0.000000
43.	c.238C>T	p.P80S	missense	1		VUS favour pathogenic (1)	0.000000
44.	c.649A>G	p.K217E	missense	1		VUS (1)	0.000000
45.	c.145G>C	p.E49Q	missense	1	VUS (1)		0.000008
46.	c.283A>G	p.M95V	missense	1		VUS (1)	0.000016
47.	c.487G>A	p.E163K	missense	1	Likely Pathogenic (1)		0.000000
48.	c.291G>T	p.K97N	missense	1	Likely Pathogenic (1)		0.000000
49.	c.269T>A	p.I90N	missense	1	VUS (1)		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.