Table 1 Mutations identified in LRP1, ALS2CL, ZNF480 and KPNA1 and occurrence in SCZ and CTR cohorts

Gene

Genomic Position^a

Nucleotide variant^b

AA Change

Type^d

dbSNP^e

ESV^f

1000 genomes^g

Inheritance^h

Pantherⁱ

Sift^j

PolyPhen^k

SCZ ^l cohort

CTR cohort

LRP1

chr12:57,579,450

Y2200X ^c

NS

de novo

LRP1

chr12:57,538,812

c.506G > A

G169D

MS

-

A = 2 / G = 10756

-

N/A

-

0.01

2.337

1/189

-

LRP1

chr12:57,539,265

c.833G > T

S278I

MS

-

-

-

T (mother)

−2.47064

0.08

1.73

1/189

-

LRP1

chr12:57,548,392

c.1135G > A

R379H

MS

-

-

-

N/A

−2.23136

0.07

1.571

1/189

-

LRP1

chr12:57,574,263

c.5386 + 1G > A

M1795I

MS

-

-

-

T (mother)

-

0.06

1.968

1/189

-

LRP1

chr12:57,577,915

c.5977C > T

R1993W

MS

rs141826184

T = 25 / C = 10733

T = 1 / C = 1093

N/A

-

0.05

0.037

2/189

-

LRP1

chr12:57,578,673

c.6238G > A

D2080N

MS

rs34577247

A = 159 / G = 10599

A = 26 / G = 2162

N/A

-

0.45

0.375

>5

-

LRP1

chr12:57,579,328

c.6478G > A

A2160T

MS

-

A = 1 / G = 10495

-

N/A

-

0.60

1.147

1/189

-

LRP1

chr12:57,587,040

c.7637G > A

G2546S

MS

rs113379328

A = 24 / G = 10734

-

N/A

-

0.13

0.836

>5

-

LRP1

chr12:57,587,717

c.7840G > A

R2613Q

MS

rs150340911

A = 12 / G = 10746

-

N/A

-

0.36

0.898

2/189

-

LRP1

chr12:57,588,275

c.8057G > A

R2686H

MS

rs148104493

A = 1 / G = 10755

-

N/A

-

0.12

0.999

1/189

-

LRP1

chr12:57,589,784

c.8699A > C

Q2900P

MS

rs7397167

A = 123 / C = 10635

A = 14 / C = 2174

N/A

-

0.53

-

>5

-

LRP1

chr12:57,590,916

c.9044G > A

G3015S

MS

rs145303173

A = 6 / G = 10752

-

N/A

-

0.76

0.357

2/189

-

LRP1

chr12:57,598,513

c.11175G > A

G3725E

MS

rs151301245

A = 12 / G = 10746

-

T (mother)

-

0.03

1.583

1/189

-

LRP1

chr12:57,600,508

c.11843G > A

G3948D

MS

-

-

-

N/A

-

0.50

1.357

1/189

-

ALS2CL

chr3:46,717,166

R733X ^c

NS

de novo

ALS2CL

chr3:46,717,175

c.2188C > T

G730S

MS

rs142971127

T = 80 / C = 10678

T = 12 / C = 2176

N/A

-

0.40

1.483

7/475

1/189

ALS2CL

chr3:46,718,458

c.1812G > T

P605T

MS

-

-

-

N/A

−1.70789

0.42

1.761

0/475

1/189

ALS2CL

chr3:46,718,477

c.1793C > T

R598H

MS

-

-

-

N/A

−2.73328

0.01

1.686

0/475

1/189

ALS2CL

chr3:46,719,769

c.1737G > A

P580S

MS

-

-

-

T (mother)

-

0.62

1.615

1/475

0/189

ALS2CL

chr3:46,719,861

c.1645T > C

N549S

MS

rs140347863

C = 9 / T = 10749

-

T (father). N/A. T (mother). N/A

-

0.35

1.851

3/475

1/189

ALS2CL

chr3:46,722,792

c.1380G > A

T460M

MS

-

A = 1 / G = 10757

-

T (father)

−2.00878

0.11

0.374

1/475

0/189

ALS2CL

chr3:46,725,290

c.894G > A

A298V

MS

rs141781567

A = 15 / G = 10757

-

N/A

−1.6125

0.14

1.366

2/475

0/189

ALS2CL

chr3:46,725,522

c.802T > A

T268S

MS

-

-

-

T (mother)

−1.48254

0.33

1.406

1/475

0/189

ALS2CL

chr3:46,728,477

c.530A > G

I176T

MS

rs145807890

G = 8 / A = 10746

-

N/A

−1.28647

0.39

1.351

0/475

1/189

ALS2CL

chr3:46,729,700

c.190C > A

E65X

NS

rs139496961

A = 20 / C = 10738

-

N/A. T (father). N/A. N/A

-

-

-

4/475

1/189

ALS2CL

chr3:46,729,756

c.134C > G

E45Q

MS

rs7642448

G = 4590 / C = 6166

-

N/A

-

0.28

1.042

>5

>5

ZNF480

chr19:52,826,001

R500X ^c

NS

de novo

ZNF480

chr19:52,825,329

c.826C > T

R276X

NS

-

-

-

N/A

-

-

-

1/475

0/189

ZNF480

chr19:52,825,495

c.992C > A

A331E

MS

-

-

-

N/A

-

0.95

0.838

0/475

1/189

ZNF480

chr19:52,826,001

c.1498C > T

R500X

NS

-

-

-

N/A

-

-

-

0/475

1/189

KPNA1

chr3:122,146,472

E448X ^c

NS

de novo

KPNA1

chr3:122,186,188

c.218C > T

S73N

MS

rs4678193

T = 79 / C = 10677

T = 11 / C = 2177

N/A

−2.16746

0.45

0.174

>5

-