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Table 1 Details of the 23 ATP7B variants retained, based on the three classifications of pathogenic, probably pathogenic and VUS

From: High genetic carrier frequency of Wilson’s disease in France: discrepancies with clinical prevalence

Chromosomal position/change

rs ID

Allele Count

Exon

Nucleotide

Protein

Protein Domain

Max ExAC MAF (%),

PhyloP

PP

MT

CARD

Allele Count (1394 total alleles),

Lariboisiere database allele count (1208 total alleles)

Classification

Ref

g.52549234 T > C

rs201738967

1

2

c.122A > G

p.Asn41Ser

European: 0.040%

2.63

D

DC

24.4

1

1

pathogenic

[14]

g.52535997A > G

rs186924074

2

6

c.1922 T > C

p.Leu641Ser

HMA

European: 0.078%

2.87

D

DC

27.4

2

1

pathogenic

[15]

g.52535985A > C

rs121907998

1

6

c.1934 T > G

p.Met645Arg

European: 0.021%

0.69

B

DC

14.09

1

11

pathogenic

13, [16]

g.52534281 T > C

1

Intron 7

c.2121 + 3A > G

donor splicing

site utilisation: − 100%

p.?

European: 0.000090%

0.69

DC

7.698

1

0

pathogenic

[17]

g.52532619A > G

rs760713333

1

8

c.2183A > G

p.Asn728Ser

P-Type ATPASe

Asian: 0.046%

3.43

D

DC

22.8

1

0

pathogenic

[18]

g. 52524268C > T

rs191312027

1

11

c.2605G > A

p.Gly869Arg

P-Type ATPASe

Asian: 0.023%

6.10

D

DC

34

1

1

pathogenic

[16]

g.52520559G > A

rs201061621

1

13

c.2921C > T

p.Thr974Met

P-Type ATPase

African: 0.033%

5.94

D

DC

28.8

1

0

pathogenic

11

g.52513198 T > C

rs200911496

1

17

c.3688A > G

p.Ile1230Val

P-Type ATPase

Asian: 0.012%

4.89

D

DC

24.9

1

1

pathogenic

11

g.52511409 T > C

rs565970531

1

Intron 19

c.4021 + 3A > G donor splicing site utilisation: − 100%

p.?

Asian: 0.2791%

1.17

DC

9.707

1

0

pathogenic

[19]

g.52509155G > A

rs181250704

4

21

c.4135C > T

p.Pro1379Ser

European: 0.18%

2.87

D

DC

28.5

4

0

pathogenic

[15]

g.52518403-52518403delinsG

1

14

c.3083-3085delinsG

p.Lys1028Serfs*40

P-Type ATPase

4.97 1.34 4.89

D

DC

1

1

pathogenic

this study

g.52524498C > G

rs181388674

1

10

c.2485G > C

p.Asp829His

P-Type ATPase

6.10

D

DC

32

1

0

Likely pathogenic

this study

g.52511803 T > C

1

18

c.3712A > G

p.Lys1238Glu

P-Type ATPase

4.81

D

DC

27.5

1

0

Likely pathogenic

this study

g.52511700G > C

1

18

c.3815C > G

p.Ser1272Cys

P-Type ATPase

5.86

D

DC

25.9

1

0

Likely pathogenic

this study

g.52534283G > A

rs751235573

1

Intron 7

c.2121 + 1G > A donor splicing site utilisation: −100%

p.?

European: 0.00090%

5.86

DC

25.6

1

0

Likely pathogenic

this study

g.52532611C > A

_

1

8

c.2191G > T

p.Val731Leu

P-Type ATPase

European: 0.0018%

6.02

D

DC

25.8

1

0

Likely pathogenic

this study

g.52513215C > A

rs532177115

1

17

c.3671G > T

p.Arg1224Leu

P-Type ATPase

African: 0.0102%

4.24

D

DC

34

1

0

Likely pathogenic

this study

g.52511739C > T

1

18

c.3776G > A

p.Gly1259Glu

P-Type ATPase

European: 0.0018%

3.11

D

DC

26.9

1

0

Likely pathogenic

this study

g.52508989G > A

rs60986317

9

21

c.4301C > T

p.Thr1434Met

African: 0.57%

1.09

D

PM

24,1

9

0

VUS

10

g.52542680A > G

rs138427376

1

4

c.1607 T > C

p.Val536Ala

HMA

Finland: 1.15%

0.45

B

PM

9.214

1

0

VUS

7, 11

g.52542666C > T

rs187046823

1

4

c.1621G > A

p.Glu541Lys

HMA

European: 0.019%

0.53

B

PM

5.930

1

0

VUS

7

g.52534410C > T

rs72552259

3

7

c.1995G > A

p.Met665Ile

European: 0.1685%

2.38

B

DC

24

3

0

VUS

7, [12]

g.52511626C > T

rs148399850

1

18

c.3889G > A

p.Val1297Ile

P-Type ATPase

Asian: 1.5%

1.13

B

DC

18.36

1

0

VUS

10, [13]

  1. PP Polypen-2: D for Damaging, B for Benign. MT MutationTaster DC for Disease Causing, PM for Polymorphism HMA Heavy metal associated domain, copper ion-binding. Ref: described in Human Gene Mutation Database (HGMD)