Table 3 Detailed summary of CNVs

From: Importance of copy number variants in childhood apraxia of speech and other speech sound disorders

Variant location (hg19)

Size (bp)

Cytoband

Families with variant

Children carrying variant with persistent CAS

Number of children (probands and siblings) with variant

Replication in our independent SSD sample

LoF intolerant

Likely pathogenic or causal based on gene regulation disruption score

pHaplo(max)

pTriplo(max)

CNV ClinViewer (based on region)

Case reports or support from prior literature for CAS, SSD or other neuro diseases

Frequency

chr11:113059924-115271926

2212002

11q23.2-11q23.3 (E)

8139

1394

1

 

X

X

0.97

0.91

Uncertain

X

NR

chr6:49976443-52091444

2115001

6p12.3-6p12.2 (E)

33

135

1

 

X

X

0.99

0.99

Pathogenic

X

NR

chr2:163855968-165518209

1662241

2q24.3 (E)

8047

1124

1

 

X

X

0.96

0.96

Uncertain

X

NR

chr16:29581236-30197928

616692

16p11.2 (E)

12, 25

50, 107

2

E

X

X

0.6

0.99

Pathogenic

X

0.05%

chr22:16340236-17295468

955232

22q11.1 (E)

8107

1302a, 1304a

3

   

0.16

0.49

Uncertain

 

0.03%

chr2:97735774-97804498

68724

2q11.2 (E)

8055

1159

2

E

  

0.12

0.33

Uncertain

X

0.53%

chr16:20545972-20596528

50556

16p12.3 (E)

8049

1128

1

   

0.08

0.18

Uncertain

 

0.10%

chr4:3892602-4168684

276082

4p16.3 (E)

8060

 

1

   

-

-

Uncertain

X

0.44%

chr4:189241227-189512452

271225

4q35.2 (E)

74

410

2

E

  

-

-

Uncertain

X

0.02%

chr4:168808644-168993082

184438

4q32.3 (E)

8008

 

1

U

  

-

-

Uncertain

X

0.40%

chr8:137680264-137735693

55429

8q24.23 (E)

8055

1159

2

E

  

-

-

Benign

 

5.42%

chr2:164641142-164646533

5391

2q24.3 (E)

8107

1302a, 1304a

3

   

-

-

Benign

X

7.01%

chr12:85939000-86285088

346088

12q21.31 (U)

8055

1159

2

   

0.16

0.11

Uncertain

X

NR

chr10:45208524-45336137

127613

10q11.21 (U)

8066

1188

1

U

  

0.28

0.17

Uncertain

X

1.11%

chr2:133176490-133188129

11639

2q21.2 (U)

8061

1174

1

   

0.19

0.07

Uncertain

X

0.05%

chr5:59710570-59769304

58734

5q12.1 (U)

33

135

3

U

  

-

-

Uncertain

 

0.44%

chr7:17165709-17222842

57133

7p21.1 (U)

8130

 

1

   

-

-

Uncertain

X

0.05%

chr2:132718104-132979733

261629

2q21.2 (U)

8055

1159

1

E,U

  

-

-

Benign

X

0.98%

  1. E Deletion, U Duplication, * Unknown persistence, NR Not reported in dbGV; - under pHaplo and pTriplo indicates unavailable from Collins paper.
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