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Table 2 Nucleotide variants found in the IDS gene

From: Analysis of long-term observations of the large group of Russian patients with Hunter syndrome (mucopolysaccharidosis type II)

Nucleotide change number

Nucleotide; protein change found

Type of nucleotide change

Exons of IDS gene

HGMD accession

Allele frequency (%) in presented cohort

Comments

1

c.103G>C; p.Asp35His

Missense

1

None

0.88

Novel (NC_000023.11:g.149505035C>G)

ClinVar accession SCV001450592

2

c.136G>T; p.Asp46Tyr

Missense

2

None

0.44

Novel (NC_000023.11:g.149504261C>A)

ClinVar accession SCV001450595

one another described in the same codon

3

c.136G>A; p.Asp46Asn

Missense

2

None

0.44

Novel (NC_000023.11:g.149504261C>T)

ClinVar accession SCV001450596

one another described in the same codon

4

c.160T>G; p.Tyr54Asp

Missense

2

CM981010

0.44

 

5

c.187A>G; p.Asn63Asp

Missense

2

CM960853

1.3

 

6

c.236C>A; p.Ala79Glu

Missense

2

CM981012

0.88

 

7

c.253G>A; p.Ala85Thr

Missense

3

CM960855

2.2

 

8

c.253G>T; p.Ala85Ser

Missense

3

CM981013

0.44

 

9

c.257C>T; p.Pro86Leu

Missense

3

CM950659

1.3

 

10

c.257C>G; p.Pro86Arg

Missense

3

CM930414

0.44

 

11

c.263G>A; p.Arg88His

Missense

3

CM960857

2.65

 

12

c.262C>T; p.Arg88Cys

Missense

3

CM950661

1.76

 

13

c.263G>T; p.Arg88Leu

Missense

3

CM981014

0.44

 

14

c.263G>C; p.Arg88Pro

Missense

3

CM970749

0.44

 

15

c.283A>T; p.Arg95Trp

Missense

3

None

0.44

Novel (NC_000023.11:g.149503447T>A)

ClinVar accession SCV001450598

three other described in the same codon

16

c.305T>G; p.Leu102Arg

Missense

3

CM981017

0.88

 

17

c.307T>G; p.Tyr103Asp

Missense

3

None

0.44

Novel (NC_000023.11:g.149503423A>C)

ClinVar accession SCV001450601

two other described in the same codon

18

c.325T>C; p.Trp109Arg

Missense

3

CM128183

0.88

 

19

c.359C>G; p.Pro120Arg

Missense

3

CM930417

0.44

 

20

c.395C>G; p.Ser132Trp

Missense

3

CM950663

0.88

 

21

c.403A>G; p.Lys135Glu

Missense

3

None

0.44

Novel (NC_000023.11:g.149503327T>C)

ClinVar accession SCV001450599

two other described in the same codon

22

c.476A>C; p.His159Pro

Missense

4

CM981026

0.44

 

23

c.512G>A; p.Cys171Tyr

Missense

5

None

0.44

Novel (NC_000023.11:g.149498303C>T)

ClinVar accession SCV001450602

one another described in the same codon

24

c.545T>C; p.Leu182Pro

Missense

5

CM981027

0.44

 

25

c.551G>T; p.Cys184Phe

Missense

5

CM960862

0.44

 

26

c.587T>C; p.Leu196Ser

Missense

5

CM981029

0.88

 

27

c.590C>T; p.Pro197Leu

Missense

5

None

1.76

Novel (NC_000023.11:g.149498225G>A)

ClinVar accession SCV001450603

28

c.593A>G; p.Asp198Gly

Missense

5

CM981030

0.44

 

29

c.671G>A; p.Gly224Glu

Missense

5

CM981031

0.44

 

30

c.697A>G; p.Arg233Gly

Missense

5

CM146285

1.3

 

31

c.776T>C; p.Leu259Pro

Missense

6

CM030889

0.44

 

32

c.795C>A; p.Asn265Lys

Missense

6

CM128190

0.88

 

33

c.795C>G; p.Asn265Lys

Missense

6

CM141180

0.44

 

34

c.998C>T; p.Ser333Leu

Missense

7

CM920367

3.09

 

35

c.1004A>G; p.His335Arg

Missense

7

CM981045

0.44

 

36

c.1006G>C; p.Gly336Arg

Missense

8

CM970753

0.44

 

37

c.1019G>A; p.Gly340Asp

Missense

8

CM981048

1.3

 

38

c.1028G>A; p.Gly343Glu

Missense

8

None

0.44

Novel (NC_000023.11:g.149487077C>T)

ClinVar accession SCV001450616

39

c.1035G>C, p.Trp345Cys

Missense

8

CM950668

0.44

 

40

c.1034G>C; p.Trp345Ser

Missense

8

None

0.44

Novel (NC_000023.11:g.149487071C>G)

ClinVar accession SCV001450617

four other described in the same codon

41

p.1037C>T; p.Ala346Val

Missense

8

CM950669

1.3

 

42

c.1204G>A; p.Glu402Lys

Missense

9

CM167391

0.88

 

43

c.1295G>A; p.Cys432Tyr

Missense

9

CM981052

0.88

 

44

c.1402C>T; p.Arg468Trp

Missense

9

CM920369

2.2

 

45

c.1403G>A; p.Arg468Gln

Missense

9

CM930422

4.4

 

46

c.1411G>C; p.Asp471His

c.1418C>T; p.Pro473Leu

Missense

9

None

0.44

Novel

Novel

(NC_000023.11:g.[149482988C>G;149482981G>A]) ClinVar accession SCV001450627

47

c.1432G>T; p.Asp478Tyr

Missense

9

CM981054

0.44

 

48

c.1432G>A; p.Asp478Asn

Missense

9

BM1234454

0.44

 

49

c.1454T>G; p.Ileu485Arg

Missense

9

CM940967

0.88

 

50

c.1565T>C; p.Leu522Pro

Missense

9

HM971766

0.44

 

51

c.196C>T; p.Gln66Term

Nonsense

2

CM068304

0.44

 

52

c.361C>T; p.Gln121Term

Nonsense

3

CM128174

0.44

 

53

c.514C>T; p.Arg172Term

Nonsense

5

CM920366

2.65

 

54

c.598C>T p.Gln200Term

Nonsense

6

CM146284

0.88

 

55

c.800G>A; p.Trp267Term

Nonsense

6

CM050243

0.44

 

56

c.814C>T; p.Gln272Term

Nonsense

6

None

0.44

Novel (NC_000023.11:g.149496411G>A)

ClinVar accession SCV001450612

57

c.829C>T; p.Gln277Term

Nonsense

6

None

0.44

Novel (NC_000023.11:g.149496396G>A)

ClinVar accession SCV001450613

58

c.998C>A; p.Ser333Term

Nonsense

7

None

0.88

Novel (NC_000023.11:g.149490322G>T)

ClinVar accession SCV001450615

two other described in the same codon

59

c.1010G>A; p.Trp337Term

Nonsense

8

CM128194

0.88

 

60

c.1234G>T; p.Gly412Term

Nonsense

9

None

0.44

Novel (NC_000023.11:g.149483165C>A)

ClinVar accession SCV001450623

61

c.1288G>T; p.Glu430Term

Nonsense

9

CM146287

0.44

 

62

c.1327C>T; p.Arg443Term

Nonsense

9

CM920368

1.3

 

63

c.1340T>A; p.Leu447Term

Nonsense

9

None

0.44

Novel (NC_000023.11:g.149483059A>T)

ClinVar accession SCV001450625

64

c.1375G>T; p.Glu459Term

Nonsense

9

CM1719915

0.44

 

65

c.1445T>G; p.Leu482Term

Nonsense

9

CM981058

0.44

 

66

c.1608T>A; p.Tyr536Term

Nonsense

9

CM141189

0.44

 

67

IVS1 as A-G -2; c.104-2A>G

Splicing substitutions

 

CS982224

0.44

 

68

IVS2 ds G-C +1; c.240+1G>C

Splicing substitutions

 

CS050391

0.44

 

69

IVS2 ds G-T +1; c.240+1G>T

Splicing substitutions

 

CS982227

0.44

 

70

IVS2 as C-G -9; c.241-9C>G

Splicing substitutions

 

None

0.88

Novel (NC_000023.11:g.149503498G>C)

ClinVar accession SCV001450634

71

IVS4 ds G-A +1; c.507+1G>A

Splicing substitutions

 

CS982228

0.88

 

72

IVS6 ds G-A +1; c.879+1G>A

Splicing substitutions

 

CS982229

0.44

 

73

IVS6 as A-G -2; c.880-2A>G

Splicing substitutions

 

CS930833

0.44

 

74

IVS7 ds T-G +2 c.1006+2T>G

Splicing substitutions

 

None

0.44

Novel (NC_000023.11:g.149490312A>C)

ClinVar accession SCV001450635

75

IVS7 as G-A -1; c.1007-1G>A

Splicing substitutions

 

CS120471

0.44

 

76

IVS8 as C-A -15; c.1181-15C>A

Splicing substitutions

 

CS013824

0.44

 

77

IVS8 ds C-T -59; c.1122C>T

Splicing substitutions

 

CS963080

5.75

 

78

c.118_120delCTT; p.Leu40del

Small deletion

2

None

0.44

Novel (NC_000023.11:g.149504277_149504279delAAG)

ClinVar accession SCV001450593

79

c.121_123delCTC p.Leu41del

Small deletion

2

CD941707

0.44

 

80

c.133delG; p.Asp45Metfs

Small deletion

2

None

0.44

Novel

(NC_000023.11:g.149504264delC)

ClinVar accession SCV001450594

81

c.248delT; p.Val83Glyfs

Small deletion

3

None

0.44

Novel (NC_000023.11:g.149503482delA)

ClinVar accession SCV001450597

82

c.305delT; p.Leu102Argfs

Small deletion

3

None

0.44

Novel (NC_000023.11:g.149503425delA)

ClinVar accession SCV001450600

83

c.404_405delAA; p.Lys135Serfs

Small deletion

3

None

0.44

Described

ClinVar accession VCV000499561.1

84

c.410_411delTT p.Phe137Serfs

Small deletion

3

CD012530

0.44

 

85

c.596_599delAACA; p.Lys199Argfs

Small deletion

5

CD941708

2.21

 

86

c.613delG; p.Ala205Profs

Small deletion

5

None

0.44

Novel (NC_000023.11:g.149498202delC)

ClinVar accession SCV001450604

87

c.625_627del TTG; p.Leu209del

Small deletion

5

None

0.44

Novel (NC_000023.11:g.149498188_149498190delCAA)

ClinVar accession SCV001450605

88

c.667_683del17; p.Val223Thrfs

Small deletion

5

CD982702

0.44

 

89

c.687delC; p.His229Glnfs

Small deletion

5

None

0.44

Novel (NC_000023.11:g.149498128delG)

ClinVar accession SCV001450606

90

c.715_721del7; p.Gln239Cysfs

Small deletion

6

None

0.44

Novel (NC_000023.11:g.149496504_149496510delACTTCTG) ClinVar accession SCV001450607

91

c.782delC; p.Pro261Leufs

Small deletion

6

CD982703

0.44

 

92

c.800_801delGG; p.Trp267Tyrfs

Small deletion

6

None

0.44

Novel (NC_000023.11:g.149496424_149496425delCC)

ClinVar accession SCV001450611

93

c.899_900delAC; p.Tyr300Phefs

Small deletion

7

None

0.44

Novel (NC_000023.11:g.149490420_149490421delGT)

ClinVar accession SCV001450614

94

c.908_909delCT; p.Ser303Cysfs

Small deletion

7

CD1412401

0.44

 

95

c.1077delG; p.Ile360Tyrfs

Small deletion

8

CD146296

0.44

 

96

c.1129delC; p.Leu377Phefs

Small deletion

8

None

0.44

Novel (NC_000023.11:g.149486976delG)

ClinVar accession SCV001450618

97

c.1191delC; p.Met398Trpfs

Small deletion

9

None

0.44

Novel (NC_000023.11:g.149483208delG)

ClinVar accession SCV001450620

98

c.1214_1220del7; p.Ser405Phefs

Small deletion

9

None

0.44

Novel (NC_000023.11:g.149483179_149483185delAAAAGAG)

ClinVar accession SCV001450621

99

c.1221delT; p.Ser409Argfs

Small deletion

9

None

0.44

Novel (NC_000023.11:g.149483178delA)

ClinVar accession SCV001450622

100

c.1353_1357delGTACC; p.Tyr452Profs

Small deletion

9

None

0.44

Novel (NC_000023.11:g. 149483042_149483046delGGTAC)

ClinVar accession SCV001450626

101

c.1426_1437 del12 p.476_479delAsnSerAspLys

Small deletion

9

None

0.44

Novel (NC_000023.11:g.149482962_149482973delCTTGTCAGAATT)

ClinVar accession SCV001450629

102

c.1431delT; p.Asp478Thrfs

Small deletion

9

None

0.44

Novel (NC_000023.11:g.149482968delA)

ClinVar accession SCV001450628

103

c.1438_1442delCCGAG;p.Pro480Phefs

Small deletion

9

None

0.44

Novel (NC_000023.11:g.149482957_149482961delCTCGG) ClinVar accession SCV001450630

104

c.1466delG p.Val489Alafs

Small deletion

9

CD146297

0.44

 

105

c.776_777dupTA; p.Pro260Tyrfs

Small insertions/duplications

6

None

0.44

Novel (NC_000023.11:g.149496448_149496449dupTA)

ClinVar accession SCV001450608

106

c.801_802insG; p.Met268Aspfs

Small insertions/duplications

6

None

0.44

Novel (NC_000023.11:g.149496423_149496424insC)

ClinVar accession SCV001450610

107

c.1151_1152 insTGCGACCCTTT; p.Phe384Leufs

Small insertions/duplications

8

None

0.44

Novel (NC_000023.11:g.149486954_149486955 insTGCGACCCTTT)

ClinVar accession SCV001450619

108

c.1239_c.1240insCT; p.Ala414Leufs

Small insertions/duplications

9

None

0.44

Novel (NC_000023.11:g.149483159_149483160insAG)

ClinVar accession SCV001450624

109

c.1491_1492dupTA; p.Arg498Ileufs

Small insertions/duplications

9

None

0.44

Novel (NC_000023.11:g.149482909_149482910dupTA)

ClinVar accession SCV001450631

110

c.104-1_104delGAinsT

Small indels

2

None

0.44

Novel (NC_000023.11:g.149504293_149504294delTCinsA) ClinVar accession SCV001450632

111

c.240 +2_c.240+3insTCCCAGA

Small indels

Intron 2

None

0.44

Novel (NC_000023.11:g.149504154_149504155insTCCCAGA) ClinVar accession SCV001450633

112

c.786_787delGGinsC; p.Ala263Profs

Small indels

6

None

0.44

Novel (NC_000023.11:g.149496438_149496439delCCinsG) ClinVar accession SCV001450609

113

gDNA level exons 1–3 deletion

Gross deletions

  

0.88

 

114

gDNA level exons 1–4 deletion

Gross deletions

  

0.44

 

115

gDNA level exons 1–7 deletion

Gross deletions

  

0.44

 

116

gDNA level exons 1–7 deletion

Gross deletions

  

0.44

 

117

gDNA level exon 4 deletion

Gross deletions

  

0.44

 

118

cDNA level del incl. ex 5–6

Gross deletions

 

CG984375

0.44

 

119

gDNA level exon 7 deletion

Gross deletions

  

0.44

 

120

Complete IDS del

Gross deletions

  

3.5

 

121

Recomb. between in. 7 and seq. distal of ex. 3 in IDS-2 without exons deletion

Complex rearrangements

 

CP973598

6.19

 

122

Recomb. between in. 7 and seq. distal of ex. 3 in IDS-2 with 4–7 exons deletion

Complex rearrangements

  

1.32