Table 1 Clinically relevant SNVs and indels in NDD-genes identified in eleven of 259 adults with schizophrenia.

From: Genome sequencing broadens the range of contributing variants with clinical implications in schizophrenia

Case

Sex

AAO (y)

FHx

ID/ syndromic

Rare CNV group

Clinically relevant CNV

Gene (transcript)

OMIM ID

Variant type

Variant

Chromosomal position (GRCh37/hg19)

Allele frequency (ExAC/gnomAD)

Validation

Gene function

591

F

20

No

No/No

No

No

KCNQ5 (NM_001160130.1)

607357

Stopgain

c.C1984T: p.(Q662*)

chr6:73904349C>T

0/0

NA

Synaptic transmission

367

F

52

No

No/No

No

No

SCN8A (NM_001177984.2)

600702

Deletion (frameshift)

c.1940_1957delins: p.(G647Vfs*18)

chr12:52115634 GCGTGGTGTCCCTCATCG>GT

0/0

NA

 

592

M

17

No

Mild/Yes

No

No

CACNA1A (NM_001127221.1)

601011

Deletion (frameshift)

c.2042_2043del: p.(Q681Rfs*100)

chr19:13414644 CCT>C

0/4.06 × 10−6

NA

 

567

F

NA

Yes

Mild/No

No

No

SHANK3 (NM_033517.1)

606230

Deletion (frameshift)

c.2183_2184del: p.(Q728Qfs*12)

chr22:51153434 CAG>C

0/0

NA

 

28

M

20

Yes

No/No

YesVUS

No

RYR2 (NM_001035.2)

180902

Missense

c.C13489T: p.(R4497C)

chr1:237954741C>T

0/0

NA

 

56

F

16

No

Mild/Yes

Yes

16p11.2 microduplication

SCN1B (NM_001037.4)

600235

Missense

c.C363G: p.(C121W)

chr19:35524558C>G

8.24 × 10−6 /4.06 × 10−6

Sangermat

 

55

F

31

Yes

Mild/Yes

Yes

16p11.2 microduplication

SYN1 (NM_133499.2)

313440

Missense

c.G1648A: p.(A550T)

chrX:47433735C>T

0/0

Sanger

 

573

M

44

No

Mild/No

YesVUS

No

MEIS2 (NM_001220482.1)

601740

Stopgain

c.C1099T: p.(Q367*)

chr15:37187379G>A

0/0

NA

Regulation of gene expression

625

F

24

No

Borderline/Yes

No

No

BRPF1 (NM_001003694.1)

602410

Stopgain

c.C3346T: p.(R1116*)

chr3:9788005C>T

0/0

Sanger

 

609

M

24

No

Borderline/Yes

No

No

BRPF1 (NM_001003694.1)

602410

Insertion (frameshift)

c.2228dupA: p.(E743fs*5)

chr3:9784853G>GA

0/0

WES, DNV

 

92

F

29

Yes

No/No

YesVUS

No

MECP2 (NM_004992.3)

300005

Deletion (frameshift)

c.1157_1163del: p.(L386Hfs*21)

chrX:153296115 TGGGGGCA>T

0/0

Sanger

 
  1. Rare SNVs and indels considered clinically relevant, together with their key genetic parameters are shown. Two of these individuals also have clinically relevant CNVs (16p11.2 microduplications)
  2. F female, M male, AAO age at onset, y years, NA not available, FHx family history of schizophrenia/psychosis, ID borderline to mild intellectual disability, CNV copy number variant, VUS CNV of uncertain clinical significance, OMIM online mendelian inheritance in man, mat maternally inherited, WES whole-exome sequencing, DNV de novo variant. See Supplementary Table S3 for VUS CNVs.
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