Table 2 Recurrent SNV, CNV, de novo and likely gene-disruptive variations, found at least twice per gene

From: An examination of multiple classes of rare variants in extended families with bipolar disorder

Gene

ExAC (z-score)

PED (N)

N variants (type)

N aff (unaff) relatives

PGC1-BD VEGAS P

PGC2-SCZ VEGAS P

ANGPTL5 NB

−1.85

2

1 SNV (mis)

6 (2)

0.045

0.863

DGCR5

ND

2

2 CNVs (dup, del)

8 (2)

0.611

0.125

DNAH14 NB

−0.68

1

2 SNVs (fs)

4 (1)

0.201

0.338

FAT2

−1.01

2

2 SNVs (mis)

6 (2)

0.791

0.22

HECTD4

6.77

2

2 SNVs (mis)

7 (1)

0.367

0.146

HYDIN

ND

3

2 SNVs (mis)

9 (2)

0.651

0.009

KIAA1731

−0.18

2

2 SNVs (mis)

8 (1)

0.654

0.955

MAP4

−0.94

3

1 SNV (mis); 1 DN (mis)

5 (1)

0.61

0.032

MIA3

−1.43

2

2 SNVs (mis)

6 (0)

0.111

0.027

MUC5B NB

6.3

5

6 SNVs (mis)

10 (8)

0.254

0.08

NEB NB

−3.74

3

4 SNVs (mis)

9 (3)

0.098

0.033

NRG1

0.62

2

2 SNVs (mis)

6 (1)

0.232

0.47

OBSCN

−1.17

2

2 SNVs (mis)

6 (2)

0.947

0.289

PCDHA8

2.24

3

3 CNVs (del)

9 (1)

0.022

6.10E-05

PCDHA9

2.28

3

3 CNVs (del)

9 (1)

0.02

7.20E-05

PCDHA10

1.2

2

2 CNVs (del)

7 (1)

0.023

8.30E-05

PCDH15

−2.88

3

3 SNVs (mis)

9 (2)

0.101

0.042

PRODH

0.77

2

1 SNV; 2 CNVs (dup, del)

9 (3)

0.934

0.451

PRUNE2

−1.48

2

2 SNVs (mis)

7 (0)

0.427

0.728

SCN10A NB

−1.8

2

4 SNVs (mis)

7 (4)

0.291

0.089

SETX

−1.62

2

2 SNVs (mis)

8 (1)

0.085

0.479

SLC5A10

0.23

1

2 SNVs (mis)

3 (1)

0.061

0.002

SOGA1

2.17

2

2 SNVs (mis)

7 (1)

0.358

0.089

TNC

−0.12

3

3 SNVs (mis)

8 (3)

0.367

0.055

TTN NB

−4.93

7

13 SNVs (mis)

19 (7)

0.014

0.16

VMAC

0.81

2

2 SNVs (mis)

7 (1)

0.002

0.32

XDH NB

−2.01

2

2 SNVs (mis)

6 (0)

0.466

0.434

ZNF506

0.09

2

2 SNVs (mis, fs)

6 (1)

0.43

0.221

ZNF812 NB

−4.76

2

2 SNVs (mis, fs)

7 (1)

0.851

0.639

  1. For each gene, a measure of functional constraint in the form of ExAC missense z-score36 is provided. The number of pedigrees (PED N) with converging evidence for each gene is given, along with the number and type of variant identified (SNV single-nucleotide variant, CNV copy number variant, DN de novo variant, mis missense, fs frameshift, dup duplication, del deletion). The total number of affected relatives (N aff) and total number of unaffected relatives (N unaff) who carry a variant in the gene are indicated. Evidence of gene-level association with BD and schizophrenia was derived from summary statistics from Psychiatric Genomics Consortium GWAS6,37 with VEGAS2, where p-values < 0.05 are indicated in bold text. Postsynaptic density (PSD) gene names33 are indicated in bold. NB, genes with negligible expression in the brain (RPKM < 1 in developmental transcriptomics RNA-seq data; http://www.brainspan.org/rnaseq/search/index.html). Further information on variants described above is reported in Supplementary Table S1, S2 and S3
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