Table 3 List of cases observed with pathogenic or likely pathogenic single nucleotide variation using WES

1

ASD-001

20

C

A

KCNQ2

(*602,235)

ENST00000359125.2

NM_172107.4

c.868G > T

p.Gly290Cys

Het

AD

De novo

Pathogenic

Developmental and epileptic encephalopathy 7

(#613,720);

2

ASD-003

7

G

A

FOXP2

(*605,317)

ENST00000408937.3

NM_148898.4

c.1549G > A

p.Ala517Thr

Het

AD

not Maternal ^a

Likely pathogenic

Speech-language disorder-1

(#602,081)

3

ASD-010

2

G

T

SCN2A

(*182,390)

ENST00000375437.2

NM_001040142.2

c.1552G > T

p.Glu518Ter

Het

AD

De novo

Pathogenic

Developmental and epileptic encephalopathy 11

(#613,721)

4

ASD-011

1

-

GGTCTGCA

ALDH4A1

(*606,811)

ENST00000375341.3

NM_003748.4

c.363_370dup

p.Arg124LeufsTer9

Comp het

AR

Maternal

Pathogenic

Hyperprolinemia, Type II

(#239,510)

C

G

c.658G > C

p.Ala220Pro

Paternal

Likely pathogenic

5

ASD-013

17

T

TC

SLC6A4

(*182,138)

ENST00000261707.3

NM_001045.6

c.1745dup

p.Thr583AsnfsTer23

Het

AD;

-

Maternal

Likely pathogenic

{Obsessive-compulsive disorder} (#164,230);

{Anxiety-related personality traits}

(#607,834)

6

ASD-016

X

CGGCG

-

MECP2

(*300,005)

ENST00000453960.2

NM_001110792.2

c.23_27del

p.Ala8GlufsTer32

Het

XLD

De novo

Pathogenic

Rett syndrome

(#312,750)

7

ASD-017

3

G

A

TBL1XR1

(*608,628)

ENST00000457928.2

NM_024665.7

c.679G > A

p.Asp227Asn

Het

AD

De novo

Likely pathogenic

Intellectual developmental disorder, autosomal dominant 41

(#616,944);

Pierpont syndrome

(#602,342)

8

ASD-020

X

-

C

MECP2

(*300,005)

ENST00000453960.2

NM_001110792.2

c.842dup

p.Arg282ProfsTer61

Het

XLD

De novo

Pathogenic

Rett syndrome

(#312,750)

9

ASD-022

3

G

A

CLCN2

(*600,570)

ENST00000265593.4

NM_004366.6

c.1550 C > T

p.Thr517Met

Het

AD

Paternal

Likely pathogenic

{Epilepsy, idiopathic generalized, susceptibility to, 11}

(#607,628)

10

ASD-034

5

-

NEUROG1

(*601,726)

ENST00000314744.4

NM_006161.3

c.228_231dup

p.Thr78Profs*122

Homo

UNK

Maternal and Paternal

Likely pathogenic

-

11

ASD-045

19

A

G

LRFN1

(*612,807)

ENST00000248668.4

NM_020862.2

c.176T > C

p.Val59Ala

Het

UNK

De novo

Likely pathogenic

-

12

ASD-046

7

C

T

CNTNAP2

(*604,569)

ENST00000361727.3

NM_014141.6

c.1634 C > T

p.Ala545Val

Het

AD

De novo

Likely pathogenic

{Autism susceptibility 15}

(#612,100)

13

ASD-047

18

G

A

TCF4

(*602,272)

ENST00000398339.1

NM_001243226.3

c.2182 C > T

p.Arg278Ter

Het

AD

De novo

Pathogenic

Pitt-Hopkins syndrome

(#610,954)

14

ASD-049

2

T

A

SCN2A

(*182,390)

ENST00000375437.2

NM_001040142.2

c.5311T > A

p.Tyr1771Asn

Het

AD

De novo

Likely pathogenic

Developmental and

epileptic

encephalopathy-11;

(#613,721);

Benign familial

neonatal-infantile

seizures-3;

(#607,745);

Episodic

ataxia type 9

(618,924)

15

ASD-053

5

G

T

CAMK2A

(*114,078)

ENST00000348628.6

NM_015981.4

c.884 C > A

p.Ala295Asp

Het

AD

De novo

Likely pathogenic

Intellectual developmental disorder, autosomal dominant 53

(#617,798)

16

ASD-054

X

C

T

KDM6A

(*300,128)

ENST00000377967.4

NM_021140.4

c.3730 C > T

p.Leu1244Phe

Hemi

XL

Maternal

Likely pathogenic

Kabuki syndrome 2

(#300,867)

17

ASD-057

X

G

C

MECP2

(*300,005)

ENST00000453960.2

NM_001110792.2

c.491 C > G

p.Pro164Arg

Het

XLD

De novo

Pathogenic

Rett syndrome

(#312,750)

18

ASD-058

17

G

T

MED13

(*603,808)

ENST00000397786.2

NM_005121.3

c.4802 C > A

p.Ser1601Ter

Het

AD

Maternal

Pathogenic

Intellectual developmental disorder, autosomal dominant 61

(#618,009)

19

ASD-064

X

G

A

MECP2

(*300,005)

ENST00000453960.2

NM_001110792.2

c.433 C > T

p.Arg145Cys

Het

XLD

De novo

Pathogenic

Rett syndrome

(#312,750)

20

ASD-067

X

G

A

MECP2

(*300,005)

ENST00000453960.2

NM_001110792.2

c.538 C > T

p.Arg180Ter

Mosaic, somatic variant

XLD

De novo; post-zygotic event

Pathogenic

Rett syndrome

(#312,750)

21

ASD-072

X

T

G

NLGN3

(*300,336)

ENST00000358741.3

NM_181303.1

c.2222T > G

p.Leu741Arg

Hemi

XL

De novo

Likely pathogenic

{Autism susceptibility, X-linked 1}

(#300,425)

22

ASD-074

9

C

T

RORB

(*601,972)

ENST00000376896.3

NM_006914.4

c.202 C > T

p.Gln68Ter

Het

AD

Paternal (affected father)

Pathogenic

{Epilepsy, idiopathic generalized, susceptibility to, 15}

(#618,357)

23

ASD-080

17

C

T

NF1

(*613,113)

ENST00000358273.4

NM_001042492.3

c.2041 C > T

p.Arg681Ter

Het

AD

De novo

Pathogenic

Neurofibromatosis, type 1;

(#162,200) Neurofibromatosis-Noonan syndrome

(#601,321)

24

ASD-082

7

G

A

AUTS2

(*607,270)

ENST00000342771.4

NM_015570.4

c.1531G > A

p.Gly511Arg

Het

AD

De novo

Likely pathogenic

Intellectual developmental disorder, autosomal dominant 26

(#615,834)

25

ASD-084

2

C

T

LMAN2L

(*609,552)

ENST00000377079.4

NM_001142292.2

c.773G > A

p.Arg258His

Hom

AR

Maternal & Paternal

Likely pathogenic

? Intellectual developmental disorder, autosomal recessive 52

(#616,887)

26

ASD-085

5

G

A

ALDH7A1

(*107,323)

ENST00000409134.3

NM_001182.5

c.1232 C > T

p.Pro411Leu

Hom

AR

Maternal & Paternal

Likely pathogenic

Epilepsy, pyridoxine-dependent

(#266,100)

27

ASD-105

X

G

A

MECP2

(*300,005)

ENST00000453960.2

NM_001110792.2

c.952 C > T

p.Arg318Cys

Het

XL

De novo

Pathogenic

Autism susceptibility, X-linked 3

(#300,496)