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Table 1 Causal gene characteristics.

From: A 2-step penalized regression method for family-based next-generation sequencing association studies

 

All variants

Variants with MAF <0.05

 

Variant counts

Causal

Total heritability

Variant counts

Causal

Total heritability

Gene

Total

Causal

avg. MAF

DBP

SBP

Total

Causal

avg. MAF

DBP

SBP

ABTB1

48

2

0.08870

0.00070

0.00132

41

0

-

-

-

ARF4

161

0

-

-

-

108

0

-

-

-

ARHGEF3

2134

10

0.08890

0.00026

0.00007

1266

8

0.00986

0.00023

0.00006

B4GALT4

217

1

0.05110

0.00004

0.00002

127

0

-

-

-

BTD

291

8

0.00889

0.00041

0.00011

220

8

0.00889

0.00041

0.00011

CXCR6

0

0

-

-

-

0

0

-

-

-

DNASE1L3

115

7

0.14061

0.00023

0.00030

71

3

0.01900

0.00016

0.00025

FBLN2

687

4

0.02193

0.00021

0.00008

456

3

0.01073

0.00016

0.00006

FLNB

956

6

0.08682

0.00087

0.00280

636

5

0.00524

0.00002

0.00007

GPR160

244

2

0.21515

0.00004

0

165

1

0.00660

0.00001

0

LOC152217

7

1

0.07880

0.00002

0.00001

4

0

-

-

-

MAP4

894

15

0.06428

0.06483

0.07792

745

12

0.01048

0.05277

0.06336

MLH1

310

9

0.03816

0.00024

0

254

8

0.00409

0.00017

0

MUC13

203

6

0.05675

0.00022

0

128

4

0.00790

0.00014

0

NMNAT3

559

9

0.07731

0.00036

0.00031

386

6

0.00903

0.00019

0.00017

PAK2

819

0

-

-

-

524

0

-

-

-

PDCD6IP

466

5

0.19472

0.00061

0.00028

319

2

0.02140

0.00004

0.00002

PPP2R3A

1081

12

0.01400

0.00046

0.00010

881

11

0.00461

0.00046

0.00010

PROK2

66

3

0.25297

0.00045

0

46

0

-

-

-

PTPLB

493

3

0.02483

0.00007

0.00006

334

2

0.00410

0.00005

0.00004

RAD18

694

2

0.19195

0.00004

0

448

1

0.00820

0.00004

0

RYBP

347

4

0.18135

0.00046

0

301

2

0.01660

0.00002

0

SCAP

207

2

0.00835

0

0.00004

176

2

0.00835

0

0.00004

SEMA3F

134

2

0.01145

0.00004

0.00001

83

2

0.01145

0.00004

0.00001

SENP5

409

5

0.00788

0

0.00007

279

5

0.00788

0

0.00007

SERP1

18

1

0.34670

0.00001

0

10

0

-

-

-

SUMF1

747

3

0.06460

0.00010

0.00008

527

2

0.00410

0

0

TFDP2

1221

5

0.00824

0

0.00005

855

5

0.00824

0

0.00005

TUSC2

11

0

-

-

-

10

0

-

-

-

VPS8

1042

6

0.00748

0.00025

0

847

6

0.00748

0.00025

0

ZBTB38

590

9

0.15292

0.00059

0.00090

415

4

0.00408

0.00003

0.00003

  1. Characteristics of the 31 causal genes (genes containing at least 1 causal variant as provided by the GAW18 simulation details). Total and causal variant counts are provided, as well as the average minor allele frequency for causal variants and the total gene-wide heritabilities for DBP and SBP. These metrics are provided using all variants in chromosome 3 (All variants) and after removing common variants (Variants with MAF ≥0.05). Discrepancies in mapping variants to genes between GRCh37/hg19 build annotations and the GAW18 simulations, result in some causal genes containing no mapped causal variants. Corresponding values for these genes are denoted by a dash but are retained for consistency.
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BMC Proceedings

ISSN: 1753-6561

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