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Table 4 Results of the ASD-NGS panel

From: Mitochondrial dysfunction and autism: comprehensive genetic analyses of children with autism and mtDNA deletion

Patient ID

Gene

Mutation

Zygosity

Inheritance

Clinical relevance

Polyphen2

Patients with ASD and mtDNA deletion (N = 10)

 P1

FOXP2

A280T

HET

AD

Uncertain significance

0.99

 P2

RAI1

V1565M

HET

AD

Uncertain significance

0.845

AUTS2

L433P

HET

AD

Uncertain significance

1

 P3

TSC2

K22N

HET

AD

Uncertain significance

1

CHD7

Fs

HET

AD

Pathogenic [38]

n/d

 P4

RELN

L496P

HET

AD/AR

Uncertain significance

0.98

KATNAL2

R1382S

HET

AR/AD

Uncertain significance

0.99

 P6

ZNF804A

A1108T

HET

n/d

Uncertain significance

1

 P7

RAI1

G1070R

HET

AD

Uncertain significance

0.99

 P8

DHCR7

W119*

HET

AR

Pathogenic

n/d

NHS

R409Q

HET

XLD

Uncertain significance

1

 P10

PDE10A

P477A

HOM

AR/AD

Uncertain significance

0.99

Patients with ASD and without mtDNA deletion (N = 7)

 C-ASD1

SHANK2

A1129P

HET

n/d

Uncertain significance

0.86

 C-ASD2

PON3

S820N

HET

n/d

Uncertain significance

1

NRXN1

S820N

HET

AR

Uncertain significance

0

CNTNAP2

Y716C

HET

n/d

Uncertain significance

0.9

 C-ASD3

SCN2A

L577I

HET

AD

Uncertain significance

0

 C-ASD4

NLGN4X

Q89H

HET

XLD

Uncertain significance

0.99

 C-ASD6

GNA14

Y287C

HET

n/d

Uncertain significance

1

Healthy controls (N = 6)

 C-H1

ZNF804A

A1108T

HET

n/d

Uncertain significance

1

NIPBL

R765K

HET

AD

Uncertain significance

0.001

 C-H2

ZNF804A

A1108T

HET

n/d

Uncertain significance

1

 C-H3

RELN

A150V

HET

AD/AR

Uncertain significance

0.974

Patient ID

SIFT

MT

dbSNP

ExAC

1000 Genome/ EUR AF

 

Patients with ASD and mtDNA deletion (N = 10)

 P1

0.23

D

n/d

0.000008278

n/d

 

 P2

0.02

P

rs368106957

0.0001819

0.0002/0

 

n/d

D

n/d

0.0002025

n/d

 

 P3

0.42

P

n/d

n/d

n/d

 

n/d

D

n/d

n/d

n/d

 

 P4

0.02

D

n/d

n/d

n/d

 

0.14

P

rs148791504

0.0009651

0.0016/n/d

 

 P6

0.16

P

rs112183442

0.02529

0.0158/0.0457

 

 P7

0.01

D

rs370633684

0.0004679

0.0004/0.00077

 

 P8

0.12

P

rs11555217

0.0007

n/d

 

0.31

P

n/d

0.00002282

n/d

 

 P10

1

P

rs61733392

0.004515

0.0024/0.006

 

Patients with ASD and without mtDNA deletion (N = 7)

 C-ASD1

0.29

D

rs377255888

0.00004137

n/d

 

 C-ASD2

0

D

rs139856535

0.002787

0.0016/n/d

 

0.33

D

rs80293130

0.0002235

0.0002/n/d

 

0.18

D

n/d

0.00008303

n/d

 

 C-ASD3

0.91

D

n/d

n/d

n/d

 

 C-ASD4

0.1

D

n/d

n/d

n/d

 

 C-ASD6

1

D

rs61755085

0.001506

0.0014/0.004

 

Healthy controls (N = 6)

 C-H1

0.16

P

rs112183442

0.02529

0.0158/0.0457

 

0.64

D

rs185678374 

0.0005529

0.0004/n/d

 

 C-H2

0.16

P

rs112183442

0.02529

0.0158/0.0457

 

 C-H3

0.01

n/d

n/d

0.000008245

n/d

 
  1. The detected rare variants of the 10 mtdel-ASD cases, in ASD patients without a mtDNA deletion, and in healthy controls are presented (only pathogenic, likely pathogenic variations and variations with uncertain significance variations are shown)
  2. P mtdel-ASD patient, non-mtdel-ASD ASD patient without mtDNA deletion, MD patient with mitochondrial disease, H healthy control individual, HET heterozygous, AR autosomal recessive, AD autosomal dominant, n/d no data, SIFT sorting intolerant from tolerant prediction database, MT mutation t@ster prediction database, D disease causing according to mutation t@ster prediction, P polymorphism according to mutation t@ster prediction, ExAC allele frequency data from exome aggregation consortium, 1000 Genomes allele frequency data from 1000 Genomes project, EUR AF allele frequency in the European Super Population of the 1000 Genomes project
  3. *The symbol of the non sense mutation in protein level