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Table 2 The somatic cancer driver SNVs and small indels found in data analysis with Ingenuity Variant Analysis software

From: Whole exome sequencing of a single osteosarcoma case—integrative analysis with whole transcriptome RNA-seq data

Gene symbol

Chr number

Position

REF/ALT

Tumour zygosity

Effect on function

Control zygosity

Effect on function

dbSNP

SIFT function

Polyphen function

Transcript ID

Nucleotide change

Amino acid change

Gene region

Translation impact

SNVs

RGPD3 (includes others)

2

110585652

A/G

1/1

Loss

0/0

Normal

 

Damaging

Benign

NM_001037866.1,

c.2393A > G

p.E798G

Exonic

Missense

NM_001123363.3,

 

NM_005054.2,

 

NM_032260.2

 

PRDM9

5

23527251

C/T

1/1

Loss

0/0

Normal

 

Tolerated

Probably damaging

NM_020227.2

c.2054C > T

p.T685I

Exonic

Missense

FOXK1

7

4722436

A/G

1/1

Loss

0/0

Normal

 

Damaging

Benign

NM_001037165.1

c.497A > G

p.N166S

Exonic

Missense

CCZ1/CCZ1B

7

6841033

T/A

1/1

Loss

0/1

Normal

 

Tolerated

 

NM_198097.3

c.1228A > T

p.M410L

Exonic

Missense

PLATa

8

42044965

G/A

1/1

Normal

0/0

Normal

2020921

Tolerated

Benign

NM_033011.2/

c.352C > T/

p.R118W/

Exonic

Missense

       

NM_000930.3

c.490C > T

p.R164W

 

AGTPBP1a

9

88292495

C/T

1/1

Loss

0/1

Normal

 

Tolerated

Benign

NM_015239.2

c.292G > A

p.G98R

Exonic

Missense

SARDH

9

136597592

T/C

1/1

Loss

0/0

Normal

149002589

Tolerated

Benign

NM_001134707.1,

c.463A > G

p.I155V

Exonic

Missense

       

NM_007101.3

   

FAH

15

80472526

C/T

1/1

Normal

0/1

Normal

11555096

Damaging

Probably damaging

NM_000137.2

c.1021C > T

p.R341W

Exonic

Missense

CDC27

17

45266522

T/C

1/1

Loss

0/0

Normal

62077279

Damaging

Probably damaging

NM_001114091.1,

c.17A > G

p.E6G

Exonic

Missense

       

NM_001256.3

   

SBF1a

22

50893287

T/C

1/1

Loss

0/1

Normal

200488568

Tolerated

Benign

NM_002972.2

c.4768A > G

p.T1590A

Exonic

Missense

LRRC37A3a (includes others)

17

44632540

T/C

1/1

Gain

0/0

Normal

144051917

Activating

Benign

NM_001006607.2

c.4882 T > C

p.W1628R

Exonic

Missense

ARL17A

17

44632540

T/C

1/1

Gain

0/0

Normal

144051917

Activating

Benign

NM_001113738.1/

c.*2182A > G/

-/

3'UTR/

 
       

NM_016632.2

c.259 + 15585A > G

-

Intronic

LILRB3

19

54725835

G/C

1/1

Gain

0/0

Normal

201948566

Activating

Benign

NM_001081450.1,

c.523C > G

p.R175G

Exonic

Missense

        

NM_006864.2

   

Small indels

CTCFL

20

56073500

(N)103/T

1/1

Loss

0/0

Normal

   

NM_001269041.1/

c.*4_*105del(N)103/

 

3′ UTR/

 
     

NM_001269043.1/

c.1988 + 8_1988 + 109del(N)103/

Intronic/

     

NM_001269040.1/

c.*4_*105del(N)103/

3′ UTR/

     

NM_001269042.1/

c.*4_*105del(N)103/

3′ UTR/

     

NM_080618.3/

c.*4_*105del(N)103/

3′ UTR/

     

NM_001269046.1

c.*4_*105del(N)103

3′ UTR

PRR23C

3

138763627

GTGC/G

1/1

Loss

0/1

Normal

63140560

  

NM_001134657.1

c.-168_-166delGCA

 

5′ UTR

 

CDCA7L

7

21941867

CTTAG/C

1/1

Loss

0/0

Normal

   

NM_001127371.2/

c.*69_*72delCTAA/

 

3′ UTR/

 
      

NM_001127370.2/

c.*69_*72delCTAA/

 

3′ UTR/

       

3′ UTR

      

NM_018719.4

c.*69_*72delCTAA

 

ALK

2

29416029

G/GATTG

1/1

Loss

0/0

Normal

   

NM_004304.4

c.*60_*61insCAAT

 

3′ UTR

 

DSPP

4

88537081

CAGCAGCAAT/C

0/1

Loss

0/0

Normal

   

NM_014208.3

c.3268_3276delAGCAGCAAT

p.S1090_N1092del

Exonic

In-frame

RELA

11

65422086

CTC/CTGTAGT

0/1

Loss

0/0

Normal

   

NM_001145138.1/

c.1408delGinsACTAC/

p.E470fs*19

Exonic/

Frameshift/

     

NM_021975.3/

c.1417delGinsACTAC/

 

Exonic/

Frameshift/

     

NM_001243984.1/

c.1210delGinsACTAC/

 

Exonic/

Frameshift/

     

NM_001243985.1

c.1216-108delGinsACTAC

 

Intronic

-

  1. aThe expression pattern of these genes has changed in the tumour tissue compared to that in the control tissue.
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Human Genomics

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