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Table 3 New variants detected by NGS-based targeted sequencing in all patients

From: Next-generation-based targeted sequencing as an efficient tool for the study of the genetic background in Hirschsprung patients

Patient

Gene

Chr position

ID

Changes

MAF

In silico prediction

1

ECE1

1:g.21573855 A > G

rs1076669

c.1013C > T/p.Thr338Ile

0.04

- / -

 

ECE1

1:g.21551614 G > A

rs3026905

c.2004 + 129C > T

0.02

-

2

GFRA3

5:g.137588322 C > T

-

c.*335 G > A

<0.01

Low activity region

 

RET

10:g.43600210delGCACAGTCA

rs546164092

c.625 + 2134delGCACAGTCA

0.004

Enhancer

 

RET

10:g.43600325delCC

rs144431581

c.625 + 2244delCC

>0.05

Enhancer

 

GFRA1

10:g.117884822 T > A

-

c.665A > T/p.Gln222Leu

<0.01

- / +

3

SEMA3D

7:g.84651849 G > T

rs141893504

c.1272C > A/p.His424Gln

<0.01

+ / +

 

GFRA1

10:g.118030415 A > T

rs8192662

c.253 T > A/p.Tyr85Asn

0.02

+ / +

 

EDNRB

13:g.78493201 C > T

-

c.-51-442 C > T

<0.01

Promoter

 

GDNF

5:g.37835932 G > A

-

c.-26-1008 G > A

-

-

4

ECE1

1:g.21564631 C > T

rs141146885

c.1376G > A/p.Ser459Asn

<0.01

- / -

5

PHOX2B

4:g.41749629 A > G

rs191239994

c.242-76 T > C

<0.01

Enhancer

 

SEMA3C

7:g.80378343 T > A

rs201228749

c.1713A > T/p.Ala571Ala

-

New splicing site

 

GFRA2

8:g.21640172 C > T

-

c.280C > T/p.Arg94Cys

<0.01

+ / +

6

PHOX2B

4:g.41747630 G > A

rs186778106

c.*194C > A

0.01

Enhancer

 

NRG1

8:g.32406656 C > T

rs148585725

c.100 + 312C > T

0.01

Promoter /CTCF binding site

 

NRG1

8:g.32617713C > T

rs79223941

c.1086-5C > T

0.01

-

7

NRG1

8:g.32611970 G > T

rs74942016

c.772G > T/p.Val258Leu

0.02

+ / +

8

GFRA1

10:g.118030415 A > T

rs8192662

c.253 T > A/p.Tyr85Asn

0.02

+ / +

10

NRG1

8:g.32611970 G > T

rs74942016

c.772G > T/p.Val258Leu

0.02

+ / +

 

ECE1

1:g.21571475 G > A

rs28368004

c.1242 + 7C > T

0.01

CTCF binding site

 

GFRA1

10:g.118031734 G > C

rs45568534

c.-193C > G

0.01

Enhancer

11

EDNRB

13:g.78492763 G > C

-

c.*988C > G

-

Predicted promoter

 

NTF3

12:g.5541624 C > G

rs71578945

c.18 + 116C > G

<0.01

Enhancer

  1. Description of all new variants found in this study, except for patient 9, who was not found to carry any new additional variant by NGS
  2. In silico prediction: amino acidic changes (− / −) benign for SIFT and Polyphen; (− / +) damaging in one; (+ / +) damaging in both
  3. Non-coding regions evaluated by the ENCODE project database
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BMC Medical Genetics

ISSN: 1471-2350

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