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Table 1 Combined rare damaging variants among Wnt/PCP genes in human NTD samples

From: Genetic analysis of Wnt/PCP genes in neural tube defects

Sample

Gene

Variant

Chr.

Positiona

Minor/major allele

Sex

Phenotypeb

SIFTc

PP2d

MAF in ExACe

NTD_27

CELSR2

p.Thr2026Met

1

109,810,233

T/C

M

SB

D

D

0.000009415

 

DVL3

p.Asp403Asn

3

183,885,376

A/G

  

D

P

NAf

NTD_39

CELSR2

p.Arg2480Cys

1

109,813,177

T/C

M

SB

D

D

0.00003766

 

FZD7

p.Leu383Gln

2

202,900,518

A/T

  

D

D

NA

NTD_122

CELSR2

p.Arg1990His

1

109,808,784

A/G

M

EC

D

P

0.0001318

 

CELSR3

p.Arg1194His

3

48,696,487

T/C

  

D

D

0.00002825

NTD_15

LRP6

p.Arg386Cys

12

12,334,194

A/G

F

AE,SB

D

D

0.000273

 

CELSR1

p.Arg714His

22

46,930,927

T/C

  

D

D

NA

NTD_56

CELSR2

p.Arg2626Cys

1

109,814,294

T/C

NA

SB

D

P

0.0004425

 

FZD5

p.Trp242Leu

2

208,632,739

A/C

  

D

D

NA

NTD_19

VANGL1

p.Arg207His

1

116,206,697

A/G

F

SB

D

D

0.00001883

 

CELSR1

p.Thr1086Met

22

46,929,811

A/G

  

D

D

0.0001318

  1. aPositions are given in bp from GRCh37
  2. bSB, spinabifida; EC, encephalocele; AE, anencephaly
  3. cSIFT predictions: D, deleterious
  4. dPolyPhen2 (PP2) predictions: D, probably damaging; P, possibly damaging
  5. eMAF from Exome Aggregation Consortium (ExAC) database
  6. fNot available