Table 3 Identified variants and scores of pathogenicity prediction tools

From: Comprehensive genetic exploration of selective tooth agenesis of mandibular incisors by exome sequencing

Gene

GenBank accession number

Substitution

Variant ID

MAF

PolyPhen2

GERP

     

HGVD

1000 Genomes

  

PAX9

NM_006194

c.398A>G

p.Asn133Ser

 

0

0

0.985

4.90

AXIN2

NM_004655

c.1250C>T

p.Ala417Val

 

0.0141

0.0032

0.001

−4.86

 

NM_004655

c.1807G>C

p.Ala603Pro

rs145353986

0.0492

0.0100

0.000

−2.26

 

NM_004655

c.1853A>G

p.Asp618Gly

 

0

0

0.028

3.95

 

NM_004655

c.2213C>T

p.Ser738Phe

rs139209450

0.0150

0.0032

0.004

1.02

EDA

NM_001005613

c.428G>C

p.Gly143Ala

rs61761321

0

0

0.364

4.82

 

NM_001005613

c.436G>T

p.Gly146Cys

 

0

0

Unknown

0.00

 

NM_001005609

c.555T>A

p.Asn185Lys

 

0

0

0.616

2.59

EDAR

NM_022336

c.319A>G

p.Met107Val

rs61761321

0.0485

0.0200

0.364

4.82

 

NM_022336

c.701G>T

p.Ser234Ile

 

0

0

0.201

1.23

 

NM_022336

c.1138A>C

p.Ser380Arg

rs146567337

0.0282

0.0100

0.978

5.18

 

NM_022336

c.1166G>C

p.Gly389Ala

 

0

0

0.888

4.91

 

NM_022336

c.1270G>A

p.Val424Met

 

0

0

0.888

4.91

WNT10A

NM_025216

c.511C>T

p.Arg171Cys

rs116998555

0.0158

0.0046

0.999

1.57

 

NM_025216

c.637G>A

p.Gly213Ser

rs147680216

0.0156

0.0046

0.988

4.41

 

NM_025216

c.874A>G

p.Ser292Gly

 

0.0040

0

0.001

2.25

 

NM_025216

c.909C>A

p.H303Gln

 

0.0132

0

0.999

3.93

BMP2

NM_001200

c.389G>A

p.R130Gln

 

0.0012

0

0.023

5.70

FAM65A

NM_001193522

c.137C>T

p.Pro46Leu

 

0.0068

0.0009

0.793

4.82

 

NM_001193522

c.148C>T

p.Pro50Ser

rs140402307

0.0037

0.0009

0.679

4.82

 

NM_001193522

c.1117C>A

p.Leu373Met

 

0.0014

0.0009

0.009

1.17

 

NM_001193522

c.1994C>T

p.Thr665Ile

rs28364801

0.0167

0.0018

0.212

2.30

 

NM_001193522

c.2542G>A

p.Glu848Lys

 

0

0

0.676

4.91

 

NM_001193522

c.2668C>T

p.Arg890Cys

rs61744916

0.0107

0.0600

0.038

1.96

 

NM_001193522

c.2734C>A

p.Arg912Ser

 

0

0

0.026

1.18

 

NM_001193522

c.2771G>A

p.Arg924His

rs145721165

0.0268

0.0032

0.983

5.15

NFATC3

NM_004555

c.244A>G

p.Ser82Gly

rs56326642

0.0215

0.0014

0.000

1.65

 

NM_004555

c.281A>C

p.Glu94Ala

rs3743736

0.0156

0.0018

0.963

5.57

 

NM_004555

c.1043C>T

p.Ala348Val

rs146091507

0.0156

0.0018

0.001

5.25

 

NM_004555

c.1279C>G

p.His427Asp

 

0

0

0.996

5.13

CDH23

NM_001171933

c.127G>A

p.Val43Ile

rs41281334

0.0248

0.0400

0.014

3.21

 

NM_001171933

c.141T>G

p.Asn47Lys

 

0

0

1

5.49

 

NM_001171930

c.1637G>C

p.Arg546Pro

 

0

0

0.976

0.49

 

NM_001171933

c.1681T>G

p.Phe561Val

rs3802707

0.0175

0.0014

0.011

3.09

 

NM_001171930

c.3179G>A

p.Arg1060Gln

 

0

0

1.000

5.49

 

NM_001171930

c.3352G>A

p.Gly1118Ser

 

0.0055

0

0.272

4.92

 

NM_001171930

c.3397G>A

p.Glu1133Lys

 

0

0

0.668

4.89

 

NM_001171930

c.3656G>A

p.Arg1219Gln

 

0

0

1.000

4.32

 

NM_001171930

c.4009G>A

p.Ala1337Thr

 

0

0

1.000

4.81

 

NM_022124

c.4135C>T

p.Arg1379Cys

 

0

0

0.028

0.91

 

NM_022124

c.4346G>A

p.Gly1449Asp

 

0

0

0.045

1.01

 

NM_022124

c.4762C>T

p.Arg1588Trp

rs137937502

0.0051

0.0018

1.000

3.24

 

NM_022124

c.5418C>G

p.Asp1806Glu

rs74145660

0.0918

0.0300

0.998

−5.31

 

NM_022124

c.5722G>A

p.Val1908Ile

 

0.0040

0

0.028

−0.78

 

NM_022124

c.6023G>T

p.Gly2008Val

 

0

0

0.045

1.01

  1. Abbreviations: GERP, Genomic Evolutionary Rate Profiling; HGVD, Human Genetic Variation database; MAF, minor allele frequency (based on 1000 Genomes allele frequencies for Japanese and European populations); PolyPhen2, Polymorphism Phenotyping v2.
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