Table 2 Position and consequence of non-synonymous sequence changes identified in iAMP21-ALL patients with and without 12q CN-LOH and/or deletion of the SH2B3 region

From: SH2B3 inactivation through CN-LOH 12q is uniquely associated with B-cell precursor ALL with iAMP21 or other chromosome 21 gain

Patient ID

12q CN-LOH

SH2B3 CN

Somatically acquired variants

Germ line variants

Nucleotide sequence change

Protein sequence change

Level

p.R262W AF C/T

Other variant (AF)

28

Yes

0

–

  

100/0%

 

25

Yes

2

c.1174C > T

p.R392Wa

49%

74/26%

 

78

Yes

0b

   

93/7%

 

44

Yes

2

c.1566dupC

p.E523Rfs

63%

100/0%

p.G451S (16%)

45

Yes

2

   

0/100%

 

88

Yes

2

c.1198_1199insCT

p.E400Afs

69%

12/88%

 

12

Yes

0

–

  

100/0%

 

3

No

0

–

  

49/51%

 

61

No

1

c.760T > G

p.C254G

52%

0/100%

 

61

No

1

c.763_773del

p.SSIQ255-258Gfs

50%

  

61

No

1

c.775_776delGA_insCG

p.E259R

51%

  

19

No

2

–

  

100/0%

 

75

No

2

–

  

100/0%

 

77

No

2

–

  

100/0%

 

81

No

2

–

  

100/0%

 

84

No

2

–

  

0/100%

 

76

No

2

–

  

0/100%

 
  1. areported as a rare germline variant (rs770836648)
  2. bBi-allelic loss of start codon through exon 2 deletion. AF (Allelic Frequency) of R262W C / T alleles indicates homozygosity when AF are 0/100 or 100/0. In heterozygous patients allelic bias, caused by CN-LOH or deletion, is indicated by the ration of C and T alleles for the R262W variant
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