Table 1 Significant associations with VTE in the gene-level collapsing analysis

From: Genetic associations of protein-coding variants in venous thromboembolism

Gene

Chr

Variant type; Frequency cutoff

Case count (n = 14,723)

Control count (n = 334,315)

OR

95% CI

P-value

FinnGen VTE OR

FinnGen VTE P-valuea

P-value (mBAT-combo)b

SERPINC1

1

LOF; MAF<1e−4

6

5

1.19

1.11–1.28

8.89 × 10−7

1.46

0.00139

0.0279

PROC

2

LOF & Dmis; MAF < 0.001

25

143

1.07

1.05–1.10

1.22 × 10−10

1.07

9.2 × 10−7

9.09 × 10−6

PROS1

3

LOF & Dmis; MAF < 1e−5

24

114

1.08

1.06–1.11

1.31 × 10−9

1.28

9.65 × 10−8

7.28 × 10−5

PHPT1

9

LOF; MAF < 0.001

17

91

1.08

1.05–1.11

6.82 × 10−7

0.97

0.06

1

STAB2

12

LOF & Dmis; MAF < 0.01

412

6973

1.01

1.01–1.02

5.98 × 10−8

1.53

3.39 × 10−24

5.44 × 10−14

SRSF6

20

LOF & Dmis; MAF < 0.001

45

443

1.04

1.02–1.06

6.57 × 10−7

1.26

3.35 × 10−4

0.442

  1. Case and control columns denote the count of QVs aggregated in the gene in the respective population. Genes highlighted in bold are not previously reported. P values shown are two-sided and unadjusted unless otherwise noted.
  2. LOF loss-of-function, Dmis likely deleterious missense, MAF minor allele frequency.
  3. aFinnGen VTE P-value after Bonferroni correction.
  4. bP-value in gene-based association analysis using “mBAT-combo” method in GCTA software after Bonferroni correction.
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