Table 2 Rare variants unique to CDD probands

M

Hemizygous

NRK

K336R

chrX:105150568

A

G

Yes

5.88

n/a

0.999 (Mis3)

n/a

ID: 1 DN, 7 n/a missense [42–44]

M

Hemizygous

TBC1D8B

L653I

chrX:106093374

C

A

Yes

4.84

-1.15

0.999 (Mis3)

n/a

ASD: 1 DN missense [23]; ID: 1 DN, 2 n/a missense [42, 43]

M

Hemizygous

NKRF

K50R

chrX:118725239

T

C

Yes

1.39

-0.54

0.005 (Mis1)

n/a

ID: 3 n/a missense [44]

M

Hemizygous

SAGE1

A362V

chrX:134989926

C

T

Yes

-0.03

0.01

0.000 (Mis1)

n/a

ASD: 1 DN missense [23]; ID: 4 n/a missense [42, 44]

M

Homozygous

TCTEX1D2

R110C

chr3:196022930

G

A

Yes

2.69

0.28

1.000 (Mis3)

n/a

SCZ: 1 DN, 20 n/a deletion [45, 46]

M

Hemizygous

USP26

P683L

chrX:132160201

G

A

No

-1.09

0.46

0.000 (Mis1)

n/a

ID: 4 n/a missense [42, 44]

M

De novo

BBS9

L376P

chr7:33376163

T

C

Yes

5.72

1.05

0.222 (Mis1)

Bardet-Biedl syndrome 9 (615986, AR)

Syndromic ID

M

De novo

TRRAP

P1781S

chr7:98548580

C

T

Yes

7.70

-6.14

1.000 (Mis3)

n/a

ASD: 3 DN missense [23]; EE: 1 DN missense [47]; SCZ: 1 DN missense, 1 DN SS [48]; DD: 3 DN missense [49]

M

Homozygous

DNMT3B

A364T

chr20:31383238

G

A

Yes

0.31

-1.70

0.000 (Mis1)

Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (242860, AR)

Syndromic ID

M

Hemizygous

CDR1

G161R

chrX:139866051

C

T

Yes

0.37

0.15

0.995 (Mis3)

n/a

ID: 2 n/a missense [42]

M

Hemizygous

FAM50A

E136K

chrX:153674872

G

A

Yes

6.75

-0.01

0.010 (Mis1)

n/a

ID: 1 n/a missense [42]; EE: 1 DN missense [47]

M

Hemizygous

CNGA2

F385S

chrX:150912129

T

C

No

7.56

0.49

0.999 (Mis3)

n/a

ID: 5 n/a missense [42, 44]

M

Homozygous

NOP9

A161_E162insEE

chr14:24769850

*

I:AGGAGG

Yes

0.59

0.98

n/a

n/a

DD: 1 DN indel [49]

M

Hemizygous

ZXDA

V264L

chrX:57936065

C

A

Yes

-0.44

n/a

0.000 (Mis1)

n/a

ID: 1 DN, 1 n/a missense [42, 43]

M

Hemizygous

SPANXN2

L41F

chrX:142795555

C

A

No

-1.83

0.41

0.946 (Mis2)

n/a

ID: 1 n/a missense [42]

M

De novo

NAV2

R2046W

chr11:20122629

C

T

Yes

3.78

-1.56

1.000 (Mis3)

n/a

ASD: 2 DN missense [23]

F

Homozygous

ADAMTS18

S660N

chr16:77359816

C

T

Yes

4.90

-0.09

0.001 (Mis1)

F

De novo

BBS5

I76M

chr2:170344335

A

G

Yes

1.29

0.04

0.82 (Mis2)

Bardet-Biedl syndrome 5 (615983, AR)

Syndromic ID

F

De novo

NSD1

R964W

chr5:176639097

C

T

Yes

0.27

-1.55

0.997 (Mis3)

Sotos syndrome 1 (117550, AD), Beckwith-Wiedemann syndrome (130650, AD)

Syndromic ID and ASD

F

De novo

OGDHL

3′UTR deletion

chr10:50940935-50943068

*

CNV: deletion

Yes

5.43

-0.54

n/a

n/a

F

Hemizygous

TUBGCP5

T274S

chr15:22846945

A

T (paternal allele deleted)

Yes

8.29

-0.77

0.891 (Mis2)

n/a

ASD: 1 DN missense [23]; ID: 1 inh deletion [50]; EE: 1 inh deletion [50]; SCZ: 1 inh deletion [50]

M

De novo

ZNF236

L1599H

chr18:74659496

T

A

Yes

5.43

-1.53

0.999 (Mis3)

M

Hemizygous

SUPT20HL2

G472R

chrX:24330019

C

T

No

1.32

n/a

0.884 (Mis2)

M

Homozygous

PRKCSH

E314_E315del

chr19:11558343-11558348

*

D:GGAGGA

Yes

1.61

-0.89

n/a

Polycystic liver disease 1 (174050, AD)

M

Hemizygous

SUPT20HL2

P795A

chrX:24329050

G

C

No

-0.55

n/a

0.047 (Mis1)

n/a

M

Hemizygous

USP9X

A843G

chrX:41027363

C

G

Yes

7.62

-1.62

0.102 (Mis1)

Mental retardation, X-linked 99 (300919, XLR and 300968, XLD)

Syndromic ID and EE

M

Hemizygous

GATA1

A55T

chrX:48649679

G

A

Yes

1.06

-0.60

0.993 (Mis3)

Anemia (300835, XLR); Thrombocytopenia (314050, XLR and 300367, XLR)

M

Hemizygous

MTMR8

N265K

chrX:63564995

G

T

Yes

4.00

-0.77

1.000 (Mis3)

n/a

ASD: 1 DN missense [23], 1 hemizygous SS [51]; ID: 5 n/a missense [42, 44]

M

Hemizygous

DCX

M51V

chrX:110654052

T

C

Yes

0.66

-0.10

0.002 (Mis1)

Lissencephaly, X-linked (300067, XL)

Syndromic ID and EE

M

Hemizygous

CT47B1

L236P

chrX:120008818

A

G

No

-1.15

n/a

0.001 (Mis1)

n/a

ASD: 1 DN missense [23]; ID: 2 n/a missense [44]

M

Heterozygous

CLUL1

5′SS disruption

chr18:618107

G

A (paternal)

Yes

6.04

0.66

n/a

n/a

M

Hemizygous

BCOR

F1023L

chrX:39930395

G

C

Yes

8.97

-3.03

0.999 (Mis3)

Microphthalmia, syndromic 2 (300166, XLD)

Syndromic ID

M

Hemizygous

BEX2

Y97C

chrX:102564711

T

C

Yes

0.78

0.64

0.046 (Mis1)

n/a

ASD: 1 n/a missense [52]; ID: 1 n/a missense [42]; SCZ: 1 n/a missense [52]

M

Hemizygous

VSIG1

Q88R

chrX:107304707

A

G

Yes

1.19

-0.18

0.856 (Mis2)

n/a

ASD: 2 hemizygous SS [51]; ID: 1 n/a missense [44]

M

Hemizygous

SRPK3

R619Q

chrX:153050929

G

A

Yes

7.69

-0.33

1.000 (Mis3)

n/a

ID: 7 n/a missense [42, 44, 53]

M

Hemizygous

USP9Y

R122X

chrY:14837084

C

T

Yes

2.63

n/a

n/a

Spermatogenic failure, Y-linked, 2 (415000, YL)

M

Homozygous

KIAA2018

Q1472del

chr3:113376112-113376114

*

D:GCT

Yes

3.58

-0.71

n/a

n/a

ASD: 1 DN nonsense, 4 n/a missense [22]; EE: 1 DN missense [47]; SCZ: 1 DN missense [54]

M

Homozygous

BRIP1

V193I

chr17:59924512

C

T

Yes

-0.69

-0.64

0.000 (Mis1)

Breast cancer, early-onset (114480, AD); Fanconi anemia, complementation group J (609054, AR)

M

Hemizygous

PDK3

K410Q

chrX:24557261

A

C

Yes

2.44

0.13

0.001 (Mis1)

Charcot-Marie-Tooth disease, 6 (300905, XLD)

M

Hemizygous

ARSF

R386Q

chrX:3021857

G

A

Yes

6.00

0.36

0.999 (Mis3)

n/a

ASD: 1 n/a nonsense [51]; ID: 4 n/a missense, 3 n/a indel, 2 n/a SS [42, 44]

M

Hemizygous

ALAS2

V193I

chrX:55047546

C

T

Yes

3.26

0.13

0.803 (Mis2)

Anemia, sideroblastic, 1 (300751, XLR); Protoporphyria, erythropoietic (300752, XLD)

M

Hemizygous

STARD8

3 bp deletion

chrX:67938303-67938305

*

D:AAG

Yes

3.59

0.74

n/a

n/a

ID: 2 n/a missense, 1 n/a indel [42, 44]

M

Hemizygous

CXorf57

R545T

chrX:105882817

G

C

Yes

6.24

-0.40

1.000 (Mis3)

n/a

ID: 2 n/a missense [42, 44]

M

Hemizygous

ALG13

S891F

chrX:110980084

C

T

Yes

4.77

-1.00

0.986 (Mis3)

Epileptic encephalopathy, early infantile, 36 (300884, XLD)

Syndromic ID and EE

F

Homozygous

RAD51C

T287A

chr17:56798128

A

G

Yes

5.16

0.11

0.988 (Mis3)

Fanconi anemia, complementation group O (613390, AR)

F

Homozygous

SHANK3

G277R

chr22:51117800

G

A

Yes

1.95

n/a

0.002 (Mis1)

Phelan-McDermid syndrome (606232, DN); Schizophrenia 15 (613950, DN)

Syndromic ID, ASD, EE, SCZ

M

Homozygous

DAP3

G5E

chr1:155679584

G

A

Yes

1.86

-0.22

0.890 (Mis2)

n/a

ASD: 1 DN missense [23]

M

Hemizygous

ENOX2

E12K

chrX:129843232

C

T

Yes

-0.35

-0.43

0.000 (Mis1)

n/a

ID: 1 hemizygous, 1 n/a missense [42, 55]