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Table 1 Summary of 43 patients carrying pathogenic and likely pathogenic mutations in known CCRD genes

From: Next-generation sequencing applied to a large French cone and cone-rod dystrophy cohort: mutation spectrum and new genotype-phenotype correlation

ID

Type

Consang.

Gene

NM

Allele State

Exon

cDNA

Protein

Coseg.

Conservation

Polyphen2

Sift

Mutation taster

References

High confidence

             

CIC00137

simplex

 

ABCA4

NM_000350.2

Ho

47

c.6394G>A

p.(E2132K)

+

Highly

Prd

D

Dc

Novel

CIC00765

Ar

+

ABCA4

NM_000350.2

Ho

47

c.6445C>T

p.(R2149*)

+

-

-

-

-

(Lewis et al. 1999) (rs61750654)

CIC03436

Ar

+

ABCA4

NM_000350.2

Ho

42

c.5892del

p.(G1965Efs*9)

Np

-

-

-

-

a

CIC04412

simplex

 

ABC4A

NM_000350.2

Het

34

c.4793C>A

p.(A1598D)

+

Weakly

Pd

T

Dc

(rs61750155) [9]

   

ABCA4

NM_000350.2

Het

28

c.4234C>T

p.(Q1412*)

+

-

-

-

-

(rs61750137) [9]

CIC04645

Ar

+

ABCA4

NM_000350.2

Ho

13

c.1924T>C

p.(F642L)

Np

Moderately

B

D

Dc

Novel, but c.1924T>A p.F642I in [80]

CIC05087

simplex

 

ABCA4

NM_000350.2

Ho

IVS 11

c.1554+1G>C

r.(spl?)

Np

Highly

-

-

-

Novel

CIC05853

simplex

+

ABC4A

NM_000350.2

Ho

22

c.3259G>A

p.E1087K

Np

Highly

Prd

D

Dc

(rs61751398) [81]

CIC05854

Ar

+

ABC4A

NM_000350.2

Ho

35

c.4919G>A

p.(R1640Q)

+

Highly

Prd

D

Dc

(rs61751403) [82]

CIC05989

simplex

 

ABC4A

NM_000350.2

Het

34

c.4837G>A

p.(D1613N)

+

Not

B

D

Dc

Novel

   

ABC4A

NM_000350.2

Het

10

c.1302del

p.(Q437Rfs*12)

+

-

-

-

-

Novel

   

ABCA4

NM_000350.2

Het

38

c.5318C>T

p.(A1773V)

+

Moderately

Prd

D

Dc

[83]

CIC06170

simplex

 

ABC4A

NM_000350.2

Het

44

c.6089G>A

p.(R2030Q)

+

Highly

Prd

D

Dc

(Lewis et al. 1999) (rs61750641)

   

ABC4A

NM_000350.2

Het

IVS 24

c.3607+3A>T

r.(spl?)

+

Moderately

-

-

-

Novel

   

ABCA4

NM_000350.2

Het

14

c.2034G>T

p.(K678N)

+

Highly

Prd

D

Dc

[84]

CIC06735

Ar

+

ABC4A

NM_000350.2

Ho

42

c.5892del

p.(G1965Efs*9)

Np

-

-

-

-

a

CIC06913

Ar

+

ABCA4

NM_000350.2

Ho

21

c.3056C>T

p.(T1019M)

+

Highly

Prd

D

Dc

(rs201855602) [85]

CIC04239

Ar

+

CDHR1

NM_033100.3

Ho

9

c.838C>T

p.(R280*)

Np

-

-

-

 

Novel

CIC06568

Ar

+

CERKL

NM_001030311.2

Ho

8

c.1090C>T

p.(R364*)

Np

-

-

-

-

Thesis (Sergouniotis P. 2012) b

CIC07299

simplex

+

PDE6C

NM_006204.3

Ho

2

c.542del

p.(A181Efs*13)

Np

-

-

-

-

Novel

CIC05218

Ar

+

PDE6C

NM_006204.3

Ho

IVS 10

c.1413+3A>T

r.(spl?)

Np

Not

-

-

-

Novel

CIC05563

Ad

 

SEMA4A

NM_022367.3

Het

4

c.302T>C

p.(I101T)

+

Moderately

Prd

D

Dc

Novel (rs149652495)

CIC07563

simplex

 

SEMA4A

NM_022367.3

Ho

3

c.241C>T

p.(R81*)

Np

-

-

-

-

Novel

CIC00324

Ad

 

GUCY2D

NM_000180.3

Het

13

c.2512C>T

p.(R838C)

+

Highly

Prd

D

Dc

(rs61750172) [10]

CIC03249

Ad

 

GUCY2D

NM_000180.3

Het

13

c.2512C>T

p.(R838C)

+

Highly

Prd

D

Dc

(rs61750172) [10]

CIC04347

Ad

 

GUCY2D

NM_000180.3

Het

13

c.2512C>T

p.(R838C)

+

Highly

Prd

D

Dc

(rs61750172) [10]

CIC04918

Ad

 

GUCY2D

NM_000180.3

Het

13

c.2512C>T

p.(R838C)

Np

Highly

Prd

D

Dc

(rs61750172) [10]

CIC06757

Ad

 

PRPH2

NM_000322.4

Het

1

c.514C>T

p.(R172W)

+

Moderately

Prd

D

Dc

(rs61755792) [86]

CIC03621

Ad

 

PRPH2

NM_000322.4

Het

1

c.1-c581+?del

-

+

-

-

-

-

Novel

CIC00535

Ad

 

PROM1

NM_006017.2

Het

10

c.1117C>T

p.(R373C)

+

Not

Pd

D

Dc

(rs137853006) [3]

CIC01196

simplex

 

PROM1

NM_006017.2

Ho

12

c.1354dup

p.(Y452Lfs*13)

+

-

-

-

-

[71]

CIC07045

simplex

 

PROM1

NM_006017.2

Ho

IVS 17

c.1984-1G>T

r.(spl?)

Np

Highly

-

-

-

Novel (rs373680665)

CIC06642c

Ad

 

PROM1

NM_006017.2

Het

1

c.7dup

p.(L3Pfs*28)

+

-

-

-

-

Novel

CIC06698c

Ad

 

PROM1

NM_006017.2

Het

1

c.7dup

p.(L3Pfs*28)

+

-

-

-

-

Novel

CIC04945

simplex

 

PROM1

NM_006017.2

Het

23

c.2383T>C

p.(W795R)

+

Highly

Prd

D

Dc

Novel

   

PROM1

NM_006017.2

Het

IVS 13

c.1579-1G>C

r.(spl?)

+

Highly

-

-

-

Novel

CIC04965

Ad

 

CRX

NM_000554.4

Het

4

c.608_609del

p.(S203Ffs*32)

+

-

-

-

-

Novel

CIC3750

simplex

 

CRX

NM_000554.4

Het

3

c.121C>T

p.(R41W)

+

Highly

Prd

D

Dc

(rs104894672) [70]

CIC06321

simplex

+

RPGRIP1

NM_020366.3

Ho

14

c.2021C>A

p.(P674H)

+

Highly

Prd

T

Dc

Novel

CIC00190

simplex

 

AIPL1

NM_014336.4

Het

5

c.769C>T

p.(L257F)

+

Moderately

Prd

D

Dc

Novel

   

AIPL1

NM_014336.4

Het

5

c.767T>G

p.(I256S)

+

Moderately

B

D

Dc

Novel

Lower confidence d

             

CIC00162

Ar

 

ABCA4

NM_000350.2

Het

31

c.4546_4547del

p.(Q1516Afs*38)

+

-

-

-

-

Novel

   

ABCA4

NM_000350.2

Het

16

c.2463G>A

p.(W821*)

+

-

-

-

-

Novel

CIC05987

Ar

 

ABC4A

NM_000350.2

Het

22

c.3295T>C

p.(S1099P)

+

Highly

Pd

D

Dc

(rs61750119) [87]

   

ABC4A

NM_000350.2

Het

22

c.3322C>T

p.(R1108C)

Np

-

-

-

-

[88]

CIC06694

simplex

 

ABC4A

NM_000350.2

Het

IVS36

c.5196+1G>A

r.(spl?)

Np

-

-

-

-

[62]

   

ABC4A

NM_000350.2

Het

22

c.3322C>T

p.(R1108C)

Np

-

-

-

-

[86]

CIC02712

simplex

+

PDE6C

NM_006204.3

Het

10

c.1325T>A

p.(M442K)

Np

Moderately

Pd

D

Dc

Novel

   

PDE6C

NM_006204.3

Het

10

c.1375C>G

p.(Q459E)

 

Weakly

B

T

Dc

Novel

CIC00597

simplex

 

GUCY2D

NM_000180.3

Het

14

c.2747T>C

p.(I916T)

+

Moderately

Prd

D

Dc

[89]

CIC06352

simplex

 

GUCA1A

NM_000409.3

Het

3

c.149C>T

p.(P50L)

Np

Moderately

B

T

Dc

(rs104893968) [90]

CIC07188

simplex

 

PROM1

NM_006017.2

Het

12

c.1354dup

p.(Y452Lfs*13)

Np

-

-

-

-

[71]

   

PROM1

NM_006017.2

Het

IVS 12

c.1454+2>C

r.(spl?)

Np

Highly

-

-

-

Novel

CIC03241

simplex

 

CRX

NM_000554.4

Het

4

c.564dup

p.(A189Rfs*47)

+

-

-

-

-

Not clear if same mutation as in [69]

CIC07569

simplex

 

CRX

NM_000554.4

Het

IVS 3

c.252+1G>A

r.(spl?)

Np

Highly

-

-

-

Novel

  1. Ar: autosomal recessive; Ad: autosomal dominant; Het: heterozygous; Ho: homozygous; Consang.: Consanguinity; Coseg.: Cosegregation; Np: Not possible; B: Benign; T: Tolerated; Prd: Proabably damaging, Pd: Possible disease causing; D: Damaging; Dc: Dicease causing
  2. a personal communication B. Puech
  3. b Sergouniotis P. (2012). Genotype and phenotypic heterogeneity in autosomal recessive retinal disease. Ph.D.Thesis. Institute of Ophthalmology, University College London, United Kingdom
  4. c sibling patients. Only one of the 2 siblings (CIC06642) was considered for the mutation prevalence analysis
  5. d these mutations were considered pathogenic with lower confidence because biallelism could not be demonstrated by cosegregation analysis