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Table 4 Rare or novel mutations identified in candidate genes by association studies

From: Identification of sequence variants associated with severe microtia-astresia by targeted sequencing

Sample ID

Gene Symbol

Consequence

GenBank accession No.

Exon

Mutation

PopFreqMax in 1000GM, ESP6500 or gnomAD

SIFT_score

SIFT_Pred

Polyphen2_HDIV_score

Polyphen2_HDIV_pred

Phylop in vertebrate

HGMD

XH1790

DCHS1

nonsynonymous

NM_003737

exon2

c. 481C > T, p.R161C

0.00003335

0.069

T

1

D

−0.001

NR

XH1785

FREM2

nonsynonymous

NM_207361

exon22

c. 8689C > T, p.R2897C

.

0

D

1

D

0.871

NR

1552

*GBA

nonsynonymous

NM_001005741

Exon10

c. 1292A > G, p.N431S

0.00001657

0.169

T

0.962

D

0.991

DM?

1454

PLEC

nonsynonymous

NM_201378

exon31

c.5273C > T, p.A1758V

0.0001578

0.535

T

1

D

0.897

NR

1467

PLEC

nonsynonymous

NM_201378

exon32

c.11563G > A, p.G3855S

0.00002367

0.652

T

0

B

−2.741

NR

 

USH2A

nonsynonymous

NM_007123

exon6

c.1007A > G, p.N336S

.

0.048

D

0.218

B

0.991

NR

XH1582

PLEC

nonsynonymous

NM_000445

exon2

c. 115A > G, p.S39G

0.001536

0.381

T

0.002

B

0.991

NR

XH1535

POMT1

nonsynonymous

NM_001136114

exon16

c. 1428G > C, p.L476F

0.0001156

0.556

T

0.001

B

−0.043

NR

XH1546

POMT1

nonsynonymous

NM_001136114

exon16

c. 1428G > C, p.L476F

0.0001156

0.556

T

0.001

B

−0.043

NR

 

USH2A

nonsynonymous

NM_206933

exon42

c. 8420C > T, p.T2807I

.

0.065

T

0.998

D

0.917

NR

XH1563

GLI3

nonframeshift

NM_000168

exon15

c. 3107C > T, p.A1036V

0.00007006

0.016

D

0

B

0.897

NR

XH1594

GLI3

nonsynonymous

NM_000168

exon7

c. 857C > T, p.A286V

.

0.18

T

0.024

B

0.917

NR

 

*USH2A

nonsynonymous

NM_206933

exon63

c.12344G > A, p.R4115H

0.0005825

0.072

T

0.462

P

0.871

DM

1575

USH2A

nonsynonymous

NM_206933

exon27

c. 5389A > G, p.N1797D

.

1

T

0

B

−0.068

NR

1742

USH2A

nonsynonymous

NM_206933

exon57

c.11123C > T, p.P3708L

.

0.223

T

1

D

0.917

NR

XH1566

USH2A

nonsynonymous

NM_206933

exon55

c.10871A > G, p.Q3624R

.

0.271

T

0.012

B

0.079

NR

XH1579

*USH2A

nonsynonymous

NM_206933

exon63

c.13157 T > C, p.I4386T

.

0.006

D

0.978

D

1.062

DM

 

USH2A

nonsynonymous

NM_206933

exon56

c.10958A > G, p.N3653S

.

0.409

T

0.489

P

0.991

NR

 

USH2A

nonsynonymous

NM_007123

exon6

c. 1105G > A, p.V369 M

.

0.015

D

0.992

D

0.871

NR

  1. Notes: *indicates the mutation has been reported in HGMD database
  2. Abbreviations: SIFT: D Deleterious, T Tolerated; PolyPhen 2: D = Probably damaging, B Benign, P Possibly damaging; NR not reported, DM: “disease causing” mutation
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BMC Medical Genomics

ISSN: 1755-8794

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