Table 1 Variants associated with LQTS present in the ESP population

From: High prevalence of genetic variants previously associated with LQT syndrome in new exome data

        

Level of LQTS evidence

Gene

Variant

Amino acid

Type

Minor allele a

Total alleles a

Variant associated with

PolyPhen-2 results

Family co-segregation

Functional data

KCNQ1

c.532G>A

A178T

Missense

2

10 756

LQT1b

Probably damaging

Equivocal

No data available

 

c.613G>A

V205M

Missense

1

10 756

LQT1c

Probably damaging

Yes, but incomplete penetrance

Loss of function

 

c.959C>A

P320H

Missense

1

10 754

LQT1c

Probably damaging

Yes

Loss of function

 

c.1189C>T

R397W

Missense

2

10 758

LQT1b

Probably damaging

No data available

No data available

 

c.1352G>A

R451Q

Missense

1

10 754

LQT1c

Possibly damaging

No data available

No data available

 

c.1354C>T

R452W

Missense

2

10 754

LQT1c

Probably damaging

No data available

No data available

 

c.1576A>G

K526E

Missense

2

10 758

LQT1b

Probably damaging

No data available

No data available

 

c.1831G>A

D611N

Missense

3

10 716

LQT1d

Possibly damaging

No data available

No data available

 

c.1927G>A

G643S

Missense

79

10 528

aLQTSd

Benign

Yes, but incomplete penetrance

Loss of function

KCNH2

c.1039G>A

P347S

Missense

7

10 758

LQT2c

Benign

Equivocal

Loss of function

 

c.1912A>G

K638E

Missense

1

10 732

LQT2b

Probably damaging

No data available

No data available

 

c.2653G>A

R885C

Missense

1

10 758

LQT2c

Probably damaging

No data available

No effect

 

c.2660G>A

R887H

Missense

1

10 758

LQT2b

Probably damaging

No data available

No data available

 

c.2948G>A

T983I

Missense

3

10 740

LQT2b

Probably damaging

No data available

No data available

SCN5A

c.647G>A

S216L

Missense

11

10 248

LQT3d

Probably damaging

No data available

Gain of function

 

c.1384G>A

E462K

Missense

1

9966

LQT3b

Probably damaging

No data available

No data available

 

c.1715G>T

A572D

Missense

18

10 194

sLQTSc

Benign

No

Gain of function

 

c.1844C>T

G615E

Missense

3

10 264

diLQTSc

Benign

No data available

Gain of function/no effect

 

c.1852G>A

L618F

Missense

21

10 274

diLQTSb

Probably damaging

No data available

No effect

 

c.1855G>A

L619F

Missense

1

10 262

LQT3c

Benign

Equivocal

Gain of function

 

c.2066G>A

R689H

Missense

1

10 488

LQT3b

Benign

No data available

No data available

 

c.2074G>T

Q692K

Missense

2

10 494

LQT3c

Benign

No data available

No data available

 

c.3578G>A

R1193Q

Missense

7

10 747

aLQTSb

Benign

No data available

Gain of function

 

c.3911G>A

T1304M

Missense

5

10 384

LQT3b

Probably damaging

Yes

Gain of function

 

c.5336C>T

T1779M

Missense

1

10 758

LQT3b

Probably damaging

No data available

No data available

 

c.5360C>T

S1787N

Missense

6

10 758

LQT3b

Possibly damaging

No data available

Gain of function

 

c.5711C>T

S1904L

Missense

10 

10 416

LQT3d

Probably damaging

Equivocal

Gain of function

 

c.5848C>A

V1951L

Missense

17

10 278

LQT3d

Benign

No data available

Gain of function

 

c.5873C>T

R1958Q

Missense

2

10 258

LQT3b

Benign

No data available

No data available

 

c.6016G>C

P2006A

Missense

12

10 108

sLQTSb

Benign

Yes, but incomplete penetrance

Gain of function

ANK2

—

—

—

—

—

—

—

—

—

KCNE1

c.253C>T

D85N

Missense

94

10 758

aLQTSb

Benign

No data available

Loss of function

 

c.325G>A

V109I

Missense

2

10 758

LQT5c

Benign

Equivocal

Loss of function

KCNE2

c.22A>G

T8A

Missense

48

10 758

diLQTSb

Probably damaging

No data available

Loss of function

 

c.161T>C

M54T

Missense

3

10 758

LQT6d

Probably damaging

No data available

Loss of function

 

c.170T>C

I57T

Missense

4

10 758

LQT6d

Probably damaging

Equivocal

No effect/loss of function

 

c.229C>T

R77W

Missense

2

10 758

LQT6c

Probably damaging

No data available

No effect

KCNJ2

—

—

—

—

—

—

—

—

—

CACNA1C

—

—

—

—

—

—

—

—

—

CAV3

c.233C>T

T78M

Missense

46

10 758

LQT9c

Probably damaging

No data available

Gain of function

SCN4B

—

—

—

—

—

—

—

—

—

AKAP9

c.4709C>T

S1570L

Missense

1

10 758

LQT11d

Benign

Yes

Loss of function

SNTA1

c.1169C>T

A390V

Missense

1

10 758

LQT12b

Possibly damaging

No data available

Gain of function

KCNJ5 e

—

—

—

—

—

—

—

—

—

  1. Abbreviations: aLQTS, acquired LQTS; diLQTS, drug-induced LQTS; sLQTS, suspected LQTS.
  2. aData from NHLBI Exome Sequencing Project (ESP).4
  3. bHedley et al1 and HGMD.5
  4. cHGMD.5
  5. dHedley et al.1
  6. eYang et al.2
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