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Table 1 Novel nonsynonymous singleton mutations in EFR3A

From: Rare deleterious mutations of the gene EFR3A in autism spectrum disorders

Cohort

Exon

Amino acid changea

Chromosome

hg19

Reference

Variant

ID

Sex

Father

Mother

Sib

PhyloP

GERP

ConSurf

Crystal

Cases (n = 2,196)

SSC cases ( n = 705)

Β 

3

R70C

8

132957112

C

T

12093.p1

M

+

-

n/a

2.95617

5.73

βˆ’1.51

Deleterious

4

L118P

8

132958867

T

C

12610.p1

M

+

-

- F

3.21686

5.47

βˆ’0.73

Deleterious

7

G243A

8

132968104

G

C

11572.p1

M

-

+

+ F

6.387

5.64

βˆ’0.291

Benign

10

F338Sb

8

132982744

T

C

11379.p1

F

-

-

- F

4.58456

5.54

βˆ’1.107

Deleterious

15

I534T

8

132996411

T

C

11473.p1

M

-

+

+ F

4.78917

6.02

βˆ’0.113

n/a

15

I576_A577insIc

8

132996539

*

I:ATT

11577.p1

M

-

+

+ F

3.628

5.03

0.043

n/a

22

T785A

8

133015525

A

G

11808.p1

F

-

+

- F

3.02491

4.27

βˆ’0.312

n/a

SSC cases ( n = 452)

Β Β Β Β Β Β Β Β Β Β Β Β Β 

5

F123L

8

132962216

T

C

13507.p1

M

-

+

- M

4.86423

5.51

βˆ’1.377

Deleterious

7

G216Sfs*12d

8

132968022

*

I:TCGCATA

11027.p1

M

-

+

- M

6.995

6.07

βˆ’1.591

Deleterious

AASC cases ( n = 1039)

Β 

3

K50E

8

132957052

A

G

20094

M

n/a

5.32367

5.55

βˆ’1.59

Deleterious

9

A321S

8

132980647

G

T

00HI1409C

M

n/a

3.10583

5.51

βˆ’0.66

Benign

10

V337L

8

132982740

G

C

00HI1533A

M

n/a

6.32607

5.54

βˆ’0.986

Benign

14

D504G

8

132991604

A

G

06C57233

M

n/a

4.41785

5.06

βˆ’0.002

n/a

14

L508P

8

132991616

T

C

07C71126

M

n/a

4.19838

5.06

0.349

n/a

14

I510V

8

132991621

A

G

20072

M

n/a

2.07681

3.88

0.088

n/a

15

Q528R

8

132996393

A

G

98HI0204A

M

n/a

5.21937

6.02

0.08

n/a

17

M646V

8

132998507

A

G

08C73985A

M

n/a

2.13232

4.65

2.129

n/a

Controls (n = 3,389)

NINDS controls ( n = 912)

2

P14R

8

132952776

C

G

ND11540

M

n/a

5.86267

5.93

βˆ’1.264

Benign

NE controls ( n = 1,614)

Β 

5

R161*d

8

132962330

C

T

S19G8

M

n/a

6.995

6.07

βˆ’1.591

Deleterious

6

M194V

8

132966156

A

G

S16H7

F

n/a

5.34254

5.73

βˆ’0.985

Benign

9

E320D

8

132980646

G

T

S6G2

F

n/a

1.06245

2.3

βˆ’0.162

Benign

10

N354D

8

132982791

A

G

S6B11

M

n/a

0.272244

0.403

1.188

Benign

13

T451M

8

132991119

C

T

S4H5

M

n/a

2.72643

5.71

0.289

Benign

15

R532W

8

132996404

C

T

S1B3

F

n/a

0.659283

0.794

1.218

n/a

15

D570G

8

132996519

A

G

S15E2

F

n/a

5.21937

6.02

βˆ’0.169

n/a

AASC controls ( n = 863)

Β Β Β Β Β Β Β 

3

G55C

8

132957067

G

T

04C27095A

F

n/a

6.81431

5.73

βˆ’1.321

Benign

4

F100L

8

132958812

T

C

05C42103

M

n/a

4.82034

5.47

βˆ’0.879

Benign

8

D268G

8

132971858

A

G

05C42750

F

n/a

4.99605

5.64

0.396

Benign

Β 

15_16

? (5β€² splice site)d

8

132996549

T

C

05C45515

F

n/a

6.995

6.07

βˆ’1.591

n/a

  1. aAll mutations are single alleles, i.e., heterozygous.
  2. bF338S is the initial de novo mutation identified by whole-exome sequencing.
  3. cFor I576_A577insI, PhyloP, GERP and ConSurf scores were derived by averaging the scores of the adjacent positions.
  4. dThese mutations were assigned the maximum conservation scores found for any position in EFR3A.
  5. *Under the Reference column indicates absence of the insertion/deletion variant.
  6. AASC, ARRA Autism Sequencing Collaboration; F, female; GERP, genomic evolutionary rate profiling; M, male; n/a, not applicable; NE, northern European; NINDS, National Institute of Neurological Disorders and Stroke; PhyloP, phylogenetic P values; SSC, Simons Simplex Collection.