Skip to main content

Table 3 Damaging variations identified in the affected individuals and selected using different functional prediction tools

From: Family specific genetic predisposition to breast cancer: results from Tunisian whole exome sequenced breast cancer cases

Chromosome-Positiona

Locus

Gene

Reference sequence

Variant type

Coding change

Protein variation

Variant Id

Frequency

Prediction of variant effect

Conservation score PhastConsb

ClinVar

dbSNP

ExAC

SIFT

Polyphen2

Mutation taster

Align-GVGD

Chr1: 120056630

1p12

HSD3B1

NM_000862

Nonsynonymous

c.484G > T

p.A162S

rs997216232

N/A

Damaging

Probably Damaging

Disease causing

C65

0.995

N/A

Chr7:117232713

7q31

CFTR

NM_000492

Splicing

c.2490 + 2T > C

–

rs1057516216

N/A

–

–

Disease causing

–

0.998

Likely Pathogenic

Chr8: 27668533

8p21

PBK

NM_018492

Nonsynonymous

c.714G > C

p.W238C

rs774498834

8.265e−06

Damaging

Probably Damaging

Disease causing

C65

1

N/A

Chr10:7751028

10p14

ITIH2

NM_002216

Nonsynonymous

c.236C > A

p.S79Y

rs749149620

9.884e−05

Damaging

Probably Damaging

Disease causing

C65

1

N/A

Chr10:99238117

10q24

MMS19

NM_001289403

Nonsynonymous

c.292C > T

p.R98W

rs29001280

0.0015

Damaging

Probably Damaging

Disease causing

C65

1

N/A

Chr13:25671311

13q12

PABPC3

NM_030979

Frameshift deletion

c.975_979del

p V325 fs

rs371130768

8.237e−06

–

–

Disease causing

–

1

N/A

Chr16:4934532

16p13

PPL

NM_002705

Nonsynonymous

c.4124T > G

p.I1375S

N/A

N/A

Damaging

Probably Damaging

Disease causing

C65

1

N/A

Chr16:21011744

16p12

DNAH3

NM_017539

Nonsynonymous

c.6223C > T

p.P2075S

N/A

N/A

Damaging

Probably Damaging

Disease causing

C65

1

N/A

Chr16:67241867

16q22

LRRC29

NM_001004055

Stopgain

c.412C > T

p.R138X

rs776721799

8.582e−06

–

–

Disease causing

–

0.259

N/A

Chr17:46940292

17q21

CALCOCO2

NM_005831

Stopgain

c.1266T > A

p.C422X

N/A

N/A

–

–

Disease causing

–

0.999

N/A

Chr19: 53740406

19q13

ZNF677

NM_182609

Frameshift insertion

c.1573dupA

p.T525 fs

rs566714089

0.0038

–

–

Disease causing

–

–

N/A

Chr20: 4766902

20p13

RASSF2

NM_170774

Nonsynonymous

c.886C > T

p.R296 W

rs756486184

8.238e−06

Damaging

Probably Damaging

Disease causing

C65

0.998

N/A

  1. aGRCh37/hg19; b PhastCons values vary between 0 and 1 and reflect the probability that each nucleotide belongs to a conserved element, based on the multiple alignment of genome sequences of 46 different species (the closer the value is to 1, the more probable the nucleotide is conserved)
Back to article page

Journal of Translational Medicine

ISSN: 1479-5876

Contact us