Table 1 Significant gene-trait pairs for exome-wide gene-based burden test

From: Mapping rare protein-coding variants on multi-organ imaging traits

SYMBOL

CHR

MODEL

AF

BETA per s.d.

Phenotype

TYPE

LOG10P

PCK2

14

plof_int5.0.01

1.432%

0.27(0.21, 0.33)

Liver_iron_corrected_T1_40062

Abdominal MRI

17.9

SLC30A10

1

int5.0.001

0.111%

1(0.79, 1.22)

Liver_iron_corrected_T1_40062

Abdominal MRI

19.6

TANC1

2

plof.0.0001

0.007%

−1.32(−1.74, −0.9)

Posterior_thigh_fat_free_muscle_volume_right_22404

Abdominal MRI

9.1

SH2B3

12

plof_Alpha.0.01

0.41%

0.38(0.29, 0.48)

Spleen_volume_21083

Abdominal MRI

14.8

TNFRSF13B

17

plof_Alpha.0.01

1.443%

0.4(0.35, 0.45)

Spleen_volume_21083

Abdominal MRI

54.8

MYCBP2

13

plof.singleton

0.009%

−2.28(−2.99, −1.58)

IFO_FA

DTI

9.6

TTK

6

plof_int5.0.01

0.936%

0.23(0.15, 0.3)

IFO_AD

DTI

9.2

AMPD3

11

plof_Alpha.0.01

1.225%

−0.18(−0.24, −0.13)

SCC_AD

DTI

9.5

OMA1

1

int1.0.01

0.888%

−0.24(−0.31, −0.17)

CGC_MD

DTI

10.4

AMPD3

11

plof_Alpha.0.01

1.228%

−0.19(−0.25, −0.13)

SCC_MD

DTI

9.7

LPAR3

1

Alpha.singleton

0.014%

1.7(1.17, 2.23)

UNC_MD

DTI

9.4

MYCBP2

13

plof.singleton

0.009%

−2.85(−3.56, −2.15)

EC_MO

DTI

14.7

PIGX

3

Alpha.0.0001

0.012%

−1.95(−2.56, −1.33)

PLIC_MO

DTI

9.3

WIPF3

7

Alpha.singleton

0.006%

−2.84(−3.68, −2)

UNC_MO

DTI

10.4

HTRA1

10

Alpha.singleton

0.018%

1.67(1.19, 2.14)

ALIC_RD

DTI

11.1

GLUL

1

int5.singleton

0.008%

2.48(1.68, 3.27)

Visual2_Somatomotor_Mean_Resting

fMRI

9

PLCE1

10

plof_int5.0.01

0.812%

0.25(0.18, 0.32)

Cingulo-Opercular_Mean_Resting

fMRI

10.9

PLCE1

10

plof_int5.0.01

0.812%

0.25(0.18, 0.33)

Dorsal-Attention_Mean_Resting

fMRI

11.4

PLCE1

10

plof_int5.0.01

0.812%

0.24(0.17, 0.31)

Language_Mean_Resting

fMRI

10

PLCE1

10

plof_int5.0.01

0.812%

0.25(0.17, 0.32)

Frontoparietal_Mean_Resting

fMRI

10.7

PLCE1

10

plof_int5.0.01

0.812%

0.24(0.17, 0.31)

Default_Mean_Resting

fMRI

9.9

TTN

2

plof.0.0001

0.388%

0.4(0.32, 0.47)

LVESV

CMR

24.9

TTN

2

plof.0.0001

0.392%

−0.56(−0.66, −0.47)

LVEF

CMR

31.7

ANO1

11

lof_int1.0.01

1.243%

0.17(0.13, 0.22)

AAo_max_area

CMR

12.2

COL21A1

6

plof_Alpha.0.01

0.543%

−0.32(−0.39, −0.25)

AAo_max_area

CMR

18.4

GEM

8

plof.0.001

0.155%

−0.46(−0.59, −0.33)

AAo_max_area

CMR

11

ANO1

11

lof_int1.0.01

1.242%

0.18(0.13, 0.22)

AAo_min_area

CMR

12.8

COL21A1

6

plof_Alpha.0.01

0.543%

−0.3(−0.37, −0.23)

AAo_min_area

CMR

16

GEM

8

plof.0.001

0.155%

−0.47(−0.61, −0.34)

AAo_min_area

CMR

11.9

PLCE1

10

plof_int5.0.01

0.811%

0.17(0.12, 0.22)

DAo_max_area

CMR

9.7

PLCE1

10

plof_int5.0.01

0.811%

0.18(0.13, 0.23)

DAo_min_area

CMR

11.2

TAGLN

11

Alpha.0.001

0.046%

0.67(0.46, 0.88)

DAo_min_area

CMR

9.3

GOLM1

9

Alpha.singleton

0.006%

2.5(1.77, 3.24)

DAo_aortic_distensibility

CMR

10.5

TTN

2

plof.singleton

0.202%

0.45(0.32, 0.58)

Ecc_AHA_9

CMR

10.6

TTN

2

plof.0.0001

0.392%

0.34(0.25, 0.43)

Ecc_AHA_13

CMR

13.5

TTN

2

plof.singleton

0.202%

0.6(0.47, 0.73)

Ecc_AHA_14

CMR

18.5

TTN

2

plof.0.0001

0.392%

0.32(0.23, 0.42)

Ecc_AHA_15

CMR

10.6

TTN

2

plof.0.0001

0.392%

0.36(0.26, 0.46)

Ecc_AHA_16

CMR

12.8

TTN

2

plof.0.0001

0.391%

0.42(0.33, 0.5)

Ecc_global

CMR

20.9

PLCE1

10

plof_int5.0.01

0.815%

0.23(0.16, 0.31)

Net25_Node3

fMRI

9.2

PLCE1

10

plof_int5.0.01

0.814%

0.23(0.16, 0.31)

Net25_Node5

fMRI

9.1

PLCE1

10

lof_int1.0.01

2.118%

0.17(0.12, 0.21)

Net25_Node9

fMRI

11.6

PLCE1

10

plof_int5.0.01

0.815%

0.25(0.17, 0.32)

Net100_Node4

fMRI

10.6

PLCE1

10

plof_int5.0.01

0.816%

0.24(0.17, 0.31)

Net100_Node9

fMRI

9.9

PLCE1

10

plof_int5.0.01

0.815%

0.26(0.18, 0.33)

Net100_Node12

fMRI

11.1

PLCE1

10

plof_int5.0.01

0.815%

0.22(0.15, 0.29)

Net100_Node15

fMRI

9.2

KCNA5

12

plof_Alpha.0.001

0.132%

0.59(0.41, 0.76)

Net100_Node17

fMRI

10.5

PLCE1

10

plof_int5.0.01

0.815%

0.25(0.17, 0.32)

Net100_Node18

fMRI

10.7

PLCE1

10

lof_int1.0.01

2.114%

0.15(0.11, 0.2)

Net100_Node27

fMRI

10.3

PLCE1

10

plof_int5.0.01

0.815%

0.25(0.18, 0.33)

Net100_Node34

fMRI

11

PLCE1

10

plof_int5.0.01

0.815%

0.23(0.15, 0.3)

Net100_Node40

fMRI

9.1

OMA1

1

lof_int1.0.01

0.966%

−0.15(−0.19, −0.1)

left.lateral.orbitofrontal

Regional brain volume

9.8

OMA1

1

lof_int1.0.01

0.966%

−0.17(−0.22, −0.12)

left.precentral

Regional brain volume

10.7

OMA1

1

lof_int1.0.01

0.966%

−0.16(−0.2, −0.11)

left.superior.frontal

Regional brain volume

11.5

TTK

6

int5.0.01

0.933%

−0.16(−0.2, −0.11)

left.superior.frontal

Regional brain volume

10.6

RBL1

20

plof.0.001

0.128%

0.42(0.29, 0.55)

left.insula

Regional brain volume

9.7

OMA1

1

lof_int1.0.01

0.966%

−0.14(−0.19, −0.1)

right.lateral.orbitofrontal

Regional brain volume

9.2

OMA1

1

lof_int1.0.01

0.966%

−0.18(−0.23, −0.13)

right.precentral

Regional brain volume

12.4

TTK

6

int5.0.01

0.933%

−0.15(−0.2, −0.1)

right.rostral.middle.frontal

Regional brain volume

9.3

OMA1

1

lof_int1.0.01

0.966%

−0.16(−0.21, −0.12)

right.superior.frontal

Regional brain volume

13.8

PRKRA

2

plof_Alpha.0.01

0.558%

−0.19(−0.24, −0.13)

right.superior.frontal

Regional brain volume

10.8

TTK

6

int5.0.01

0.933%

−0.14(−0.18, −0.1)

right.superior.frontal

Regional brain volume

10

OMA1

1

lof_int1.0.01

0.966%

−0.17(−0.22, −0.12)

right.superior.parietal

Regional brain volume

9.9

RBL1

20

plof.0.001

0.128%

0.41(0.29, 0.54)

right.insula

Regional brain volume

9.6

COL21A1

6

plof_int5.0.01

0.507%

−0.28(−0.36, −0.19)

CSF

Regional brain volume

9.4

SCUBE2

11

lof_int1.0.01

1.1%

−0.14(−0.18, −0.1)

left.cerebellum.exterior

Regional brain volume

9.7

PTEN

10

plof_int5.0.0001

0.009%

2.77(2.22, 3.32)

total.brain.volume

Regional brain volume

22.2

  1. Here we present non-redundant results for gene-trait pairs that passed our stringent multiple testing threshold at P < 1 × 10−9 based on empirical null distribution (Method). P-values are derived from two-sided tests based on z-scores (or equivalently a χ2 test with one degree of freedom). As a gene-trait pair may appear in multiple burden models and MAF cutoffs, only the association with the smallest P-value is included. Values in column ‘AF’ stand for the MAF of the gene burden models and is rounded to three decimal places after taking percentage. Column “Phenotype” corresponds to the column “Phenotype_ID” in Supplementary Data S1. Parentheses in the column “BETA per s.d.” indicate the 95% confidence interval for the effect sizes in s.d. In the column “TYPE”, we define the label for each phenotype (consistent with the keys in Supplementary Data S1). Values in the LOG10P column are rounded to one decimal place. More details about the phenotype information can be found in Supplementary Data S1 and a more comprehensive version of this table including effect sizes in original units can be found in Supplementary Data S7.
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