Table 2 Significant genes with non-hematological trait associations in other RVAS

From: Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes

category

gene name

biomarker

analysis

p value

effect

test

Nvariant

Ncarrier

OMIM

traits (examples)15,16

bone and joint

HSPG2

ALP

AA

2.27e-19

m

K

1424

10,275

r

repair of conjunctiva

bone and joint

B4GALNT3

ALP

AA

3.91e-14

m

gbvc

246

2499

 

height

bone and joint

FLG

Vitamin D

AA

1.54e-10

p

gbvc

350

2448

d,r

asthma, eczema

cardiovascular

APOB

LDL direct (+5)

AA

9.69e-159

m

K

855

3948

d,r

high cholesterol (diag.)

cardiovascular

PCSK9

LDL direct (+2)

AA

4.58e-88

m

gbvc

186

968

d

high cholesterol (diag.)

cardiovascular

APOC3

Triglycerides (+2)

AA

2.18e-74

m

K

28

297

m

lipid-lowering med

cardiovascular

LDLR

LDL direct (+3)

AA

2.29e-50

m

gbvc

214

1303

d,r

high cholesterol (diag.)

cardiovascular

PDE3B

Triglycerides (+1)

AA

7.66e-24

m

K

225

1510

 

height, mass

cardiovascular

JAK2

HDL (+6)

AA

5.22e-19

m

K

254

1022

m,s

neoplasms

cardiovascular

G6PC

CRP (+4)

AA

1.62e-13

m

gbvc

85

828

r

arm fat free mass

cardiovascular

TM6SF2

Triglycerides (+2)

AA

3.10e-13

m

gbvc

85

1392

 

liver fat percentage

cardiovascular

SRSF2

HDL

EUR*

6.19e-09

m

K

10

51

 

myeloid leukemia

diabetes

PIEZO1

HbA1c

AA

5.59e-108

m

K

1,011

8021

d,r

varicose veins, height, mass

diabetes

GCK

HbA1c (+1)

EUR

1.36e-40

m

gbvc

53

144

d,r

T2D

diabetes

GIGYF1

HbA1c (+4)

AA

1.14e-10

p

gbvc

41

68

 

T2D, education score Engl.

diabetes

HBB

HbA1c

AA

1.10e-09

m

K

33

92

d,r

thalassemia

hormonal

SHBG

SHBG (+1)

AA

4.64e-227

m

K

105

669

 

heel bone mineral density

hormonal

IGFALS

IGF-1

AA

1.14e-78

m

K

242

1900

r

height, mass

hormonal

GH1

IGF-1

AA

1.85e-10

s

gbvc

49

470

d,r

height, mass

hormonal

GHRH

IGF-1

AA

2.07e-09

m

gbvc

22

117

m

height, mass

hormonal

PAPPA2

IGF-1

AA

5.38e-09

m

gbvc

288

1208

r

height, mass

liver

UGT1A1

Total bilirubin (+1)

AA

2.90e-67

m

K

148

864

m,r

Gilbert’s syndrome

liver

ABCB4

ALT

AA

2.30e-10

m

gbvc

226

1192

d,r

cholelithiasis

liver

SYNJ2

GGT

AA

1.55e-08

m

gbvc

434

3020

 

hearing loss

renal

SLC22A12

Urate (+1)

AA

0

m

gbvc

151

1044

r

gout

renal

ALDH16A1

Urate

EUR*

4.40e-23

m

K

266

2060

 

gout

renal

ABCG2

Urate

AA

2.19e-14

m

gbvc

170

1575

m

gout

renal

TNFRSF13B

Total protein

AA

1.62e-12

m

gbvc

76

898

d,r

interpol. age when op.

renal

ANKRD12

Total protein

AA

3.18e-11

p

gbvc

53

121

 

walking pace: slow

renal

PKD1

Creatinine

EUR*

2.77e-10

m

K

1,255

10,695

d

cystic kidney disease

  1. Table showing the most significant gene-biomarker associations (FWER ≤ 0.05) for all genes that were also significantly associated with non-hematological traits (e.g., disease diagnoses or anthropometric traits) in ref. 15 or ref. 16 in either the all-ancestry analysis (AA) or the EUR-ancestry analysis (EUR). Only example traits are shown in column "traits". The full data are available in Supplementary Data 4. The numbers in brackets indicate how many other biomarkers are associated with the same gene in our analysis. effect: the lead variant effect type (m: missense pLOF, p: pLOF, s: splice + pLOF). test: the test-type which gave the lowest p value. OMIM: If disorders are linked to the gene in OMIM, their inheritance patterns (d: dominant, m: missing, r: recessive, s: somatic). Associations marked with (*) were not significant in the AA-analysis, see Supplementary Data 1 and 3 for details.
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