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Table 3 Missense variants

From: Prevalence of PALB2 mutations in Australian familial breast cancer cases and controls

Exon

Nucleotide changea

Protein changea

dbSNP ID

First reported

1000 G MAFb

NHBLI GO ESP MAFc

ExACd

HAPS cases

(n = 997)e

FCC-ViP cases (n = 999)e

Controls

(n = 1998)e

CADD scaled

C score

Condel

PolyPhen2

SIFT

1

c.11C > T

p.Pro4Leu

rs45619737

Rahman (2007) [3]

.

0.00038

0.0000999

1

1

1

12.9

Deleterious

Probably damaging

Tolerated

2

c.53A > G

p.Lys18Arg

rs138789658

Tischkowitz (2008)

0.0032

0.00523

0.0000552

-

-

1

18.0

Deleterious

Possibly damaging

Deleterious

2

c.94C > G

p.Leu32Val

rs151316635

Teo (2013) [8]

.

0.00023

0.0000184

-

1

1

16.3

Deleterious

Possibly damaging

Deleterious

3

c.194C > T

p.Pro65Leu

rs62625272

Adank (2011) [26]

.

0.00015

0.00006

-

-

1

4.6

Neutral

Benign

Tolerated

4

c.232G > A

p.Val78Ile

.

Tischkowitz (2012) [39]

.

.

0.000325

 

2

 

0.4

Neutral

Benign

Tolerated

4

c.298C > T

p.Leu100Phe

rs61756147

Wong (2011) [9]

0.0005

0.00023

0.000037

-

-

2

10.3

Neutral

Probably damaging

Tolerated

4

c.344G > T

p.Gly115Val

rs145598272

Foulkes (2007) [34]

.

0.00015

0.0000921

1

-

1

6.5

Neutral

Benign

Tolerated

4

c.353 T > C

p.Ile118Thr

.

-

.

0.00008

0.000037

-

-

1

5.4

Neutral

Benign

Tolerated

4

c.400G > A

p.Asp134Asn

rs139555085

Zheng (2011)

0.0005

0.00184

0

  

1

4.8

Neutral

Benign

Tolerated

4

c.508A > G

p.Arg170Gly

.

-

.

.

.

-

-

1

4.4

Neutral

Benign

Tolerated

4

c.557A > T

p.Asn186Ile

.

-

.

.

.

-

-

1

13.1

Deleterious

Probably damaging

Deleterious

4

c.571C > G

p.Pro191Ala

.

-

.

.

.

-

-

1

9.4

Neutral

Probably damaging

Tolerated

4

c.629C > T

p.Pro210Leu

rs57605939

Rahman (2007) [3]

0.0174

0.02216

0.0000736

1

1

2

10.6

Deleterious

Probably damaging

Tolerated

4

c.899C > T

p.Thr300Ile

.

Ding (2011)

.

.

0

1

-

-

15.1

Deleterious

Probably damaging

Tolerated

4

c.656A > G

p.Asp219Gly

rs45594034

Rahman (2007) [3]

.

0.00015

0.000221

 

1

 

1.8

Neutral

Benign

Tolerated

4

c.740C > G

p.Thr247Arg

.

.

.

.

.

 

1

 

15.5

Deleterious

Probably damaging

Tolerated

4

c.925A > G

p.Ile309Val

rs3809683

Rahman (2007) [3]

0.0087

0.00970

0.0000184

4 (1)

-

-

0.5

Neutral

Benign

Tolerated

4

c.1010 T > C

p.Leu337Ser

rs45494092

Rahman (2007) [3]

0.0133

0.01424

0.0197

44 (1)

44

93 (1)

8.9

Deleterious

Probably damaging

Tolerated

4

c.1085 T > C

p.Leu362Pro

.

-

.

.

.

1

-

-

14.4

Deleterious

Probably damaging

Tolerated

4

c.1145G > T

p.Ser382Ile

.

Tischkowitz (2012) [39]

.

.

0.0000184

-

1

-

15.2

Deleterious

Possibly_damaging

Deleterious

4

c.1189A > T

p.Thr397Ser

.

Rahman (2007) [3]

.

0.00008

0.0000184

-

1

1

22.9

Deleterious

Possibly damaging

Deleterious

4

c.1250C > A

p.Ser417Tyr

rs45510998

Rahman (2007)

.

.

0.000203

-

-

1

20.6

Deleterious

Probably damaging

Deleterious

4

c.1478C > T

p.Pro493Leu

.

-

.

.

0.0000184

-

-

1

12.4

Neutral

Benign

Tolerated

4

c.1492G > T

p.Asp498Tyr

rs75023630

Phuah (2013) [38]

0.0014

.

0

-

-

1

16.2

Deleterious

Benign

Deleterious

4

c.1544A > G

p.Lys515Arg

.

Tischkowitz (2012) [39]

.

.

0.000037

-

1

-

16.2

Deleterious

Possibly damaging

Tolerated

4

c.1610C > T

p.Ser537Leu

rs142103232

-

.

0.00015

0.000166

-

1

-

11.2

Neutral

Possibly damaging

Tolerated

4

c.1676A > G

p.Gln559Arg

rs152451

Rahman (2007) [3]

0.1465

0.13483

0.0961

216 (9)

182 (11)

335 (10)

0.0

Neutral

Benign

Tolerated

5

c.1699C > T

p.His567Tyr

.

Tischkowitz (2012) [39]

.

0.00008

0.000094

-

-

1

0.9

Neutral

Benign

Tolerated

5

c.1931G > A

p.Gly644Glu

.

-

.

.

.

-

-

1

16.0

Deleterious

Probably damaging

Deleterious

5

c.2014G > C

p.Glu672Gln

rs45532440

Rahman (2007) [3]

0.0142

0.02324

0.0278

64 (1)

68 (4)

123 (1)

11.4

Neutral

Possibly damaging

Tolerated

5

c.2106A > G

p.Ile702Met

.

-

.

.

0.0000184

1

-

-

11.1

Neutral

Probably damaging

Tolerated

5

c.2135C > T

p.Ala712Val

rs141458731

Dansonka-Meiszkowska (2010)

0.0014

0.00062

0.00039

-

-

1

12.2

Neutral

Benign

Tolerated

5

c.2200A > T

p.Thr734Ser

rs45543843

Rahman (2007) [3]

.

.

0.0000368

-

-

3

25.3

Deleterious

Possibly damaging

Deleterious

5

c.2228A > G

p.Tyr743Cys

rs141749524

-

0.0009

.

0.0000184

1

-

-

8.5

Neutral

Benign

Tolerated

5

c.2289G > C

p.Leu763Phe

.

Phuah (2013) [38]

.

.

0

2

-

-

15.5

Neutral

Probably damaging

Tolerated

5

c.2360C > T

p.Thr787Ile

rs201042302

-

0.0005

.

0

-

1

-

9.7

Neutral

Probably damaging

Tolerated

5

c.2417C > T

p.Pro806Leu

rs45464991

Rahman (2007) [3]

.

0.00008

0.000037

-

1

1

0.5

Neutral

Benign

Tolerated

7

c.2590C > T

p.Pro864Ser

rs45568339

Rahman (2007) [3]

0.0018

0.00239

0.00396

6

10

19

12.0

Neutral

Benign

Tolerated

7

c.2606C > G

p.Ser869Cys

.

.

.

.

0.0000184

 

1

 

19.9

Deleterious

Probably damaging

Deleterious

7

c.2674G > A

p.Glu892Lys

rs45476495

Rahman (2007) [3]

.

0.00008

0.000092

1

2

-

20.8

Deleterious

Possibly damaging

Deleterious

8

c.2755G > A

p.Val919Ile

.

-

.

.

.

-

-

1

15.7

Neutral

Benign

Tolerated

8

c.2794G > A

p.Val932Met

rs45624036

Rahman (2007) [3]

0.0009

0.00431

0.00869

15

8

23

18.3

Deleterious

Probably damaging

Tolerated

8

c.2816 T > G

p.Leu939Trp

rs45478192

Rahman (2007) [3]

0.0009

0.00154

0.0015

2

3 (1)

8

20.9

Deleterious

Probably damaging

Deleterious

9

c.2993G > A

p.Gly998Glu

rs45551636

Rahman (2007) [3]

0.0105

0.01785

0.0213

42

46 (2)

92 (1)

22.7

Deleterious

Probably damaging

Deleterious

10

c.3054G > C

p.Glu1018Asp

rs183489969

Tischkowitz (2012) [39]

0.0009

.

0

1

-

1

16.4

Deleterious

Possibly damaging

Deleterious

10

c.3106G > C

p.Val1036Leu

.

-

.

.

0.000037

-

1

-

13.3

Neutral

Benign

Tolerated

11

c.3128G > C

p.Gly1043Ala

.

Hellebrand (2011) [36]

0.0009

.

0.000037

1

-

-

20.9

Deleterious

Probably damaging

Deleterious

11

c.3146 T > C

p.Met1049Thr

rs138273800

-

.

0.00008

.

-

1

-

18.0

Deleterious

Probably damaging

Deleterious

12

c.3307G > A

p.Val1103Met

rs201657283

Casadei (2011) [29]

.

0.00015

0.0000184

-

1

-

13.0

Neutral

Benign

Tolerated

13

c.3366C > A

p.Asp1122Glu

.

.

.

.

.

-

 

1

16.0

Neutral

Possibly damaging

Tolerated

13

c.3367G > A

p.Val1123Met

  

.

.

.

-

1

-

18.7

Deleterious

Probably damaging

Deleterious

13

c.3428 T > A

p.Leu1143His

rs62625284

Balia (2010)

.

0.00008

0.00031

2

-

-

20.0

Deleterious

Possibly damaging

Tolerated

13

c.3448C > T

p.Leu1150Phe

  

.

.

.

-

1

-

15.5

Deleterious

Possibly damaging

Deleterious

13

c.3449 T > G

p.Leu1150Arg

rs45566737

 

.

.

0.0000368

-

1

-

18.2

Deleterious

Possibly damaging

Deleterious

  1. HAPS Hunter Area Pathology Service, FCC Familial Cancer Centre, ViP Variants in Practice
  2. aVariant positions are reported in reference to NCBI RefSeq NM_024675.3 (mRNA) and NP_078951.2 (protein)
  3. bMinor allele frequency (MAF) reported in the 1000 Genomes (1000 G) cohort Phase 1
  4. cMAF reported in the Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) [46] (data release ESP6500SI-V2)
  5. dMAF reported in ExAC [45] from non-Finnish Europeans, excluding individuals in the database who were part of The Cancer Genome Atlas and therefore known to have had cancer
  6. eNumber of individuals carrying the variant. Where applicable, the number of homozygous carriers is indicated in parentheses
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Breast Cancer Research

ISSN: 1465-542X

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