Table S5.

Evaluation of 39 distinct polymorphisms previously identified by Sanger sequencing, LCA chip analysis and/or genomewide
SNP genotyping using the consolidation method of condensation.
HGVS
Gene

Exon

Mutation
nomenclature

NextGENe

Hom pol

mutation call

region

Heterozygous variants
Patient(s)
6 (Sanger,
LCA chip), 7
(LCA chip)
4, 9, 10
(Sanger)

Homozygous variants

Min
freq

Max
freq

Min
score

Patient(s)

Min
freq

Max
freq

Min
score

50 (7)

51.72
(6)

30

30

5, 6 (Sanger)

100

100

30

30

5, 6, 9
(Sanger)

97.09
(5)

100

30

30

100

100

30
25 (6)

AIPL1

E2

c.268G>C
(p.Asp90His)

c.268G>C (90D>H)

no

AIPL1

I2

c.277-10A>C (p.?)

c.277-10A>C

no

AIPL1

E3

c.300A>G (p.=)

c.300A>G (100L>L)

no

4, 10 (Sanger)

50 (4)

CEP290

E21

c.2055T>C (p.=)

c.2055T>C (685A>A)

no

5, 9 (Sanger)

65.85
(9)

50.94
(10)
52.08
(10)
66.67
(5)

CEP290

E22

c.2268G>A (p.=)

c.2268A>G (756S>S)

(A)AA

5 (Sanger)

37.93

37.93

14

CEP290

I25

c.2818-50G>C
(p.?)

c.2818-50G>C

no

CEP290

I30

c.3574-9del (p.?)

c.3574-9delT

8T

5 (Sanger)

17.02

17.02

29

CEP290

I35

c.4704+46del (p.?)

c.4704+46delT

7T

5 (Sanger)

19.35

19.35

29

CEP290

I38

c.5227-43G>A

no

CEP290

I41

c.5709+45G>C

no

5, 9 (Sanger)

48.48
(9)

CEP290

I47

c.6522+12_6522+13insT

8T

CEP290

I48

c.6645+67G>A

no

CEP290

I10

c.853-12_853-11insG

CEP290

I10

c.853-125_853-

c.5227-43G>A
(p.?)
c.5709+45G>C
(p.?)
c.6522+12dup
(p.?)
c.6645+67G>A
(p.?)
c.853-12_85311insG (p.?)
c.853-127_853-

40.48
(9)

4, 6, 9
(Sanger)
4, 6, 9
(Sanger)
4, 6, 9
(Sanger)
4, 6, 9
(Sanger)

100

100

83.02
(6)
87.18
(6)

94.92
(9)
100
(9)

9 (Sanger)

100

100

30

50 (5)

30

6, 9 (Sanger)

90.91
(6)

91.23
(9)

22 (6)

100

100

30

T*TT

5 (Sanger)

44.44

44.44

30

100

100

30

no

5 (Sanger)

29.03

29.03

30

82.35

100

30

4 (Sanger,
SNP chip), 9
(Sanger)
4, 6, 9
(Sanger)
4, 6, 9

30
29 (6)

HGVS
Gene

Exon

NextGENe

Hom pol
region

nomenclature
125dup (p.?)

mutation call
124insTAA

Mutation

Heterozygous variants
Min
Max
Patient(s)
freq
freq

Min
score

Homozygous variants
Min
Max
Patient(s)
freq
freq
(Sanger)
(9)
(6)

Min
score

CRB1

3'UTR

c.*28T>C (p.?)

c.*28T>C

no

4, 9 (Sanger)

48.28
(9)

50 (4)

30

CRB1

E6

c.1410G>A (p.=)

c.1410A>G (470L>L)

no

4, 5, 6, 9, 10
(Sanger)

100

100

30

CRB1

I1

c.71-12A>T (p.?)

c.71-12A>T

5T(A)3T

9, 10 (Sanger)

46.15
(10)

30

CRB1

I4

c.989-53T>G

c.989-53T>G

no

5, 9 (Sanger)

50 (5)

30

CRB1
CRB1

I3
I3

c.849-35T>C
c.849-62T>G

no
no

10 (Sanger)
4 (Sanger)

45.16
50

30
30

4, 6 (Sanger)
/

100
/

100
/

30
/

CRX

I2

c.100+12C>T

no

10 (Sanger)

75

75

30

GUCY2D

E12

c.2345T>A (782L>H)

no

1, 4, 7, 8 (LCA
chip)

37.04
(1)

57.83
(7)

30

10 (Sanger,
LCA chip)

100

100

30

GUCY2D

I13

c.2576+37G>T

no

10 (Sanger)

100

100

30

GUCY2D

I13

c.2577-31C>T

CC(C)CC

10 (Sanger)

100

100

30

GUCY2D

c.741C>T (247H>H)

no

10 (Sanger)

98.85

98.85

30

c.*197G>C (p.?)

c.*197G>C

no

4 (Sanger)

100

100

30

c.-6051_194delTGGGAGC
c.574C>T (192L>L)

4 (Sanger)

88.42

88.42

30

no

4 (Sanger)

100

100

30

IQCB1

I10

c.986+143A>G

no

5 (SNP chip)

33.33

33.33

MERTK

I12

c.1786+180C>A

no

4 (SNP chip)

57.89

57.89

24

5 (SNP chip)

100

100

29

RDH12

E7

c.482G>A (161R>Q)

no

5 (Sanger)

100

100

30

RPE65

E10

c.1056G>A (352E>E)

no

10 (Sanger)

100

100

30

RPE65

I12

c.1338+20A>C

no

10 (Sanger)

100

100

30

RPE65

I12

c.-147_-142del
(p.?)
c.574C>T (p.=)
c.986+143A>G
(p.?)
c.1786+180C>A
(p.?)
c.482G>A
(p.Arg161Gln)
c.1056G>A (p.=)
c.1338+20A>C
(p.?)
c.1339-39T>C
(p.?)

no

IQCB1

E3
3'
UTR
5'
UTR
E7

c.849-35T>C (p.?)
c.849-62T>G (p.?)
c.100+12C>T
(p.?)
c.2345T>A
(p.Leu782His)
c.2576+37G>T
(p.?)
c.2577-31C>T
(p.?)
c.741C>T (p.=)

39.13
(9)
45.71
(9)
45.16
50

c.1339-39T>C

no

5 (Sanger)

41.18

41.18

30

IQCB1
IQCB1

HGVS
Gene

Exon

RPE65
RPE65
RPGRIP
1
RPGRIP
1
RPGRIP
1

I6
I2
18
4
I6

Mutation
nomenclature
c.644-33C>G
(p.?)
c.95-18G>A (p.?)
c.3097G>C
(p.Glu1033Gln)
c.574A>G
(p.Lys192Glu)
c.907-16_90714del (p.?)

NextGENe

Hom pol

mutation call
c.644-33C>G
c.95-18G>A

region
no
no

c.3097G>C (1033E>Q)

no

c.574A>G (192K>KE)

(A)AA

c.907-16_907-14delAAT

4(AAT)

Heterozygous variants
Min
Max
Patient(s)
freq
freq
9 (Sanger)
64.44 64.44
5 (Sanger)
45.71 45.71
8 (LCA chip)

66.67

66.67

1, 6, 10 (LCA
chip)
2, 10 (LCA
chip)

48.15
(1)
21.43
(2)

60.53
(6)
29.21
(10)

Min
score
30
30
30
28 (6)
30

Homozygous variants
Min
Max
Patient(s)
freq
freq
5 (Sanger)
100
100
/
/
/
1, 4, 5, 6,
100
100
(LCA chip)
2, 3, 4, 5, 7, 8 77.59
100
(LCA chip)
(3)
/

Min
score
23
/
30
30

The following variants were not included in this table as they were not present in the NextGENe mutation report:
c.907-16_907-14del (RPGRIP1, patients 5 and 6) and c.2818-50G>C (CEP290, patient 5). Abbreviations used: E:
exon; I: intron; hom pol: homopolymeric; freq: frequency; min: minimal; max: maximal; UTR: untranslated region.