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Table 1 De novo mutations in Hirschsprung disease probands

From: Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes

Trio

Phenotype

Gene

De novo mutation

Type

MAF (dbSNP137/ESP6500/ExAC)a

1

L, F

RET

3splicing9 + 1

Splicing

N/N/N

  

RBM25

c.474C > T:p.L158L

Synonymous

N/N/N

2

L, F

RET

c.2511_2519delCCCTGGACC:p.S837fs

Frameshift

N/N/N

  

COL6A3

c.3327C > T:p.H1109H

Synonymous

4.2E-4 (rs114845780)/N/1.2E-4

3

L, F

RET

c.1818_1819insGGCAC:p.Y606fs

Frameshift

N/N/N

4

L, F

DAB2IP

c.2339C > T:p.T780Mb

Missense

N/N/2.8E-3

  

ISG20L2

c.961G > A:p.G321R

Missense

N/N/N

  

MED26

c.675C > T:p.A225A

Synonymous

N/N/N

  

NCLN

c.496C > T:p.Q166Xb

Nonsense

N/N/N

  

NUP98

c.5207A > G:p.N1736S

Missense

N/N/N

  

VEZF1

c.584C > T:p.S195F

Missense

N/N/N

  

ZNF57

c.570C > T:p.D190D

Synonymous

N/N/N

5

L, F

RET

c.1761delG :p.G588fs

Frameshift

N/N/N

  

SCUBE3

c.1493A > T:p.N498I

Missense

N/N/N

6

L, M

AFF3

c.1975G > C:p.V659L

Missense

N/N/N

  

PLEKHG5

c.2628G > T:p.T876T

Synonymous

N/N/9.1E-6

7

L, M

KDM4A

c.26A > G:p.N9S

Missense

N/N/N

8

L, M

MAP4

c.3351C > T:p.G1117G

Synonymous

N/N/9.2E-6

9

L, F

RET

c.1858 T > C:p.C620R

Missense

0 (rs77316810)/N/N

10

TCA, M

CKAP2L

c.555_556delAA:p.E186fs

Frameshift

N/2E-5/2.5E-5

11

L, F

RET

c.409 T > G:p.C137G

Missense

N/N/N

  

HMCN1

c.10366G > A:p.A3456T

Missense

N/N/N

  

TUBG1

c.699 T > C:p.S233S

Synonymous

N/N/8.2E-6

12

L, F

CCR2

c.848 T > A:p.L283Q

Missense

N/N/N

  

DENND3

c.1921delT:p.K640fs

Frameshift

N/N/N

13

L, F

RET

c.1710C > A:p.C570X

Nonsense

N/N/N

14

L, F

RET

c.526_528delGCA:p.R175del

Non-frameshift

N/N/N

  

TBATA

c.157C > T:p.R53C

Missense

N/N/4.1E-5

  1. Genes in bold indicate patients carrying de novo RET mutations. Underlines genes are genes giving a HSCR-like phenotype in zebrafish.
  2. F female, L long-segment HSCR, M male, TCA total colonic aganglionsis
  3. aMinor allele frequency (MAF) in dbSNP137, ESP database or ExAC database, with “N” standing for no data available.
  4. bMosaic mutation