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Table 5 Association with cardiometabolic endpoints for lead gene variants significant in WES+WGS meta-analysis or GWAS replication

From: Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations

      

Stroke + TIA

Stroke

CVD

Statin medication

GENE

Variant

Consequence

Pheno

PWES+WGS

PGWAS

OR

P

OR

P

OR

P

OR

P

DEFT1P

rs797006828

splice donor

VLDLPL XL

1.2×106

         

SBDS

rs113993993

splice donor

apoC-III

5.9×106

0.19

1.04

0.62

1.04

0.60

0.99

0.81

1.03

0.51

SBDS

rs113993991

stop gain

apoC-III

0.55

         

LIPC

rs121912502

p.Ser301Phe

apoA1

0.35

0.04*

2.01

0.0024

1.58

0.07

1.54

0.035

0.97

0.84

LIPC

rs3829462

p.Phe368Leu

apoA1

0.99

0.02

1.04

0.18

1.03

0.33

1.02

0.40

1

0.91

LIPC

rs113298164

p.Thr417Met

apoA1

7.8×108

0.89

0.93

0.15

0.98

0.67

0.97

0.43

1.02

0.52

GTF3C5

rs189383196

start lost, p.Met126Thr

Non-HDLC

0.38

0.17

0.99

0.81

0.96

0.48

1.02

0.75

1.12

0.0058

GTF3C5

rs202207045

p.Ala382Val

Non-HDLC

7.3×107

0.02

0.93

0.36

0.96

0.59

0.92

0.21

0.98

0.77

   

LDL Fried

1.3×106

0.02

        
   

CHOL CL

1.2×106

0.11

        

TRMT5

rs45604437

p.Ala456Val

VLDLPL XS

5.8×104

0.53

0.9

0.28

0.73

0.0035

0.88

0.11

1.08

0.25

TRMT5

rs115400838

p.Ser185Cys

VLDLPL XS

1.6×104

0.75

1.17

0.0010

1.21

6×104

1.12

0.012

1.06

0.12

RBM47

rs564837143

p.Ala496-Ala502del

apoC-III

2.5×106

0.08

1.03

0.67

0.97

0.66

1.02

0.70

1.05

0.33

MARCHF10

rs147046907

p.Thr560Ile

VLDLPL XS

1.07×106

0.76

1.08

0.30

1.09

0.32

0.99

0.89

0.99

0.87

MARCHF10

rs916315847

p.Gly143Arg

VLDLPL XS

0.03

         

RYR3

rs2229119

p.Asn898Ser

VLDLTG XS

7.42×103

0.22

0.99

0.86

1.04

0.55

1.03

0.50

1.08

0.0300

RYR3

rs200294137

p.Ile2417Val

VLDLTG XS

0.04

 

0.87

0.41

0.92

0.66

1.05

0.71

1.06

0.56

RYR3

rs61996335

p.Pro3085Arg

VLDLTG XS

0.03

0.22

0.92

0.27

0.86

0.05

1.02

0.81

1.04

0.38

RYR3

rs146201205

p.Met3641Val

VLDLTG XS

1.39×103

0.66

0.98

0.70

0.97

0.62

1.01

0.83

0.94

0.08

RYR3

rs202181075

p.Asn3849His

VLDLTG XS

0.01

0.68

0.97

0.55

0.96

0.36

1.04

0.25

1.08

0.0082

  1. The table includes PTVs and variants with p<0.05 either in the WES+WGS single-variant meta-analysis or in the FinnDiane GWAS replication for the genes significant in the WES+WGS gene-level meta-analysis. Clinical endpoints were queried in the FinnGen GWAS data: Stroke + TIA wide stroke definition including transient ischemic attack (TIA), Stroke “stroke, including SAH (no controls excluded)”, CVD “Hard cardiovascular diseases” including coronary revascularization event, myocardial infarctions, and strokes excluding subarachnoid hemorrhages