Table 3

Genomic positions (build 36-Hg18), size, type and affected genes of the 26 rare copy number variations identified in patientsa

Chromosome

Cytoband

Start site

Size (bp)

CNV type

Gene Names

Patient


chr1

p31.1

76,801,602

550,723

del

ST6GALNAC3, ST6GALNAC5, PIGK

3

chr1

q44

243,610,556

153,230

del

KIF26B

16

chr1

p32.1

59,559,568

41,339

del

FGGY

15

chr2

p25.1

9,165,985

192,606

del

ASAP2

21

chr2

q22.2

143,463,273

300,408

dup

KYNU, ARHGAP15

7

chr2

q32.2

190,015,149

45,366

dup

WDR75

28

chr3

p24.3

18,759,412

635,060

dup

KCNH8, MIR4791

11

chr3

q28

193,405,249

135,458

dup

FGF12

1

chr4

q31.3

152,508,270

136,605

del

FAM160A1

29

chr6

p12.1

55,468,168

33,031

dup

HMGCLL1

30

chr9

p21.3

20,661,515

136,814

del

KIAA1797, MIR491

13

chr9

p24.1

5,130,196

168,153

del

INSL6, INSL4, RLN2

20

chr9

q31.3

111,832,790

340,164

del

PALM2-AKAP2, AKAP2, C9orf152, TXN, TXNDC8, SVEP1

22

chr10

p13

16,970,291

103,018

dup

CUBN

19

chr11

q12.3

62,290,497

38,091

dup

POLR2G, TAF6L, TMEM179B, TMEM223, NXF1

25

chr16

q23.3

81,315,382

136,618

del

CDH13

5

chr16

q11.2

45,058,042

198,742

dup

ANKRD26P1, SHCBP1, VPS35

6

chr17

q25.1

71,478,161

33,362

dup

ACOX1, TEN1, CDK3

5

chr18

q12.1

27,990,329

64,132

dup

MEP1B

18

chr21

q21.3

29,391,572

496,425

del

C21orf7, LINC00189, BACH1, GRIK1

8

chr21

q22.3

46,538,913

210,594

dup

YBEY, C21orf58, PCNT, DIP2A

12

chrX

q22.3

109,193,988

31,659

del

TMEM164, MIR3978

23

chrX

q25

126,971,799

88,694

del

ACTRT1

17

chrX

q13.1

68,398,248

639,366

dup

FAM155B, EDA

27

chrX

p22.31

6,499,677

1,592,274

dup

HDHD1, STS, VCX, PNPLA4

15

chrX

q13.3

75,294,586

88,796

dup

CXorf26

14


aCNV = copy number variation; del = deletion; dup = duplication.

Krepischi et al. Breast Cancer Research 2012 14:R24   doi:10.1186/bcr3109

Open Data