Background
Methods
Subjects and clinical investigation
Molecular genetic analysis
Design of the microdroplet-based PCR primer library
RainDance target enrichment and NGS sequencing
Variant detection
Determination of pathogenic variants
Validation of mutations by Sanger sequencing and segregation
Results
Patients
Evaluation and validation of the novel RD gene panel
Variant filtering and annotation
Identification of known and novel mutations
Clinical correlations
Sample ID | Clincial Diagnosis | Family Inheritance | Candidate Gene(s) | Transcript | Nucleotide Change | Amino Acid Change | Genotypes (Sanger confirmed) | HGMD or dbSNP IDs | References (or in silico Analysis) | |
---|---|---|---|---|---|---|---|---|---|---|
RD13–01 | CRD | Autosomal dominant |
GUCA1A
| NM_000409.3 | c.296A > G | p.Y99C | Heterozygous | CM980960 | [26] | |
RD1–07 | RP | Autosomal dominant |
PRPF31
| NM_015629.3 | c.220C > T | p.Q74* | Heterozygous | CM063073 | [27] | |
RD20–06 | CRD | Autosomal dominant |
PRPH2
| NM_000322.4 | c.514C > T | p.R172W | Heterozygous | CM930639 | [28] | |
RD20–07 | CRD | Autosomal dominant |
PRPH2
| NM_000322.4 | c.514C > T | p.R172W | Heterozygous | CM930639 | [28] | |
RD2–01 | RD | Autosomal dominant |
RGR
| NM_001012720.1 | c.824dupG | p.I276N*77 | Heterozygous | CI993291 | [16] | |
RD11–03 | RP | Autosomal dominant |
RHO
| NM_000539.3 | c.574dup | p.Y192Lfs*139 | Heterozygous | novel | (predicted as pathogenic) | |
RD14–07 | RP | Autosomal dominant |
TOPORS
| NM_005802.4 | c.2474dupA | p.Y825* | Heterozygous | CSI075704 | [29] | |
RD10–02 | OCMD | Autosomal dominant |
RP1L1
| NM_178857.5 | c.133C > T | p.R45W | Heterozygous | CM105618 | [20] | |
RD5–08 | RP | Autosomal recessive |
CERKL
| NM_001030311.2 | c.1045_1046del | p.M349Vfs*20 | Heterozygous | Novel (predicted as pathogenic) | ||
c.316C > T | p.R106C | Heterozygous | Novel | (predicted as likely pathogenic) | ||||||
RD14–08 | RP | Autosomal recessive |
USH2A
| NM_206933.2 | c.2276G > T | p.C759F | Heterozygous | CM001372 | [30] | |
c.4108G > C | p.V1370 L | Heterozygous | novel | (predicted as pathogenic) | ||||||
RD20–08 | RP | Autosomal recessive |
USH2A
| NM_206933.2 | c.2299delG | p.E766Sfs*21 | Heterozygous | CD982997 | [9] | |
c.2276G > T | p.C759F | Heterozygous | CM001372 | [30] | ||||||
RD20–05 | CSNB | X-linked |
CACNA1F
| NM_005183.3 | c.2576 + 1G > A | IVS20 + 1G > A | Hemizygous | novel | (predicted as pathogenic) | |
RD6–08 | CHM | X-linked |
CHM
| NM_000390.2 | c.49 + 2dupT | IVS1 + 2dupT | Hemizygous | CI137323 | [31] | |
RD12–02 | RP | X-linked |
RPGR
| NM_000328.2 | c.1088_1089delinsA | p.V363Dfs*18 | Hemizygous | novel | (predicted as pathogenic) | |
RD4–04 | RP | Sporadic |
ABCA4
| NM_000350.2 | c.1804C > T | p.R602W | Homozygous | CM990025 | [32] | |
RD6–01 | RP | Sporadic |
BBS1
| NM_024649.4 | c.1169 T > G | p.M390R | Homozygous | CM021489 | [33] | |
RD12–06 | RP | Sporadic |
CERKL
| NM_001030311.2 | c.481 + 2 T > G | IVS2 + 2 T > G | Homozygous | CS140556 | [7] | |
RD5–05 | RP | Sporadic |
CRB1
| NM_201253.2 | c.3983C > A | p.A1328D | Heterozygous | rs762975680 | (predicted as likely pathogenic) | |
RD4–06 | RP | Sporadic |
EYS
| NM_001142800.1 | c.2259 + 1G > A | IVS14 + 1G > A | Heterozygous | CS150721 | [34] | |
c.6137G > A | p.W2046* | Heterozygous | novel | (predicted as pathogenic) | ||||||
RD6–07 | RP | Sporadic |
EYS
| NM_001142800.1 | c.8473_8474insT | p.V2804 fs | Heterozygous | novel | (predicted as pathogenic) | |
c.1153 T > G | p.C385G | Heterozygous | Novel |
(predicted as unlikely pathogenic)
| ||||||
RD12–05 | RP | Sporadic |
EYS
| NM_001142800.1 | c.6416G > A | p.C2139Y | Heterozygous | CM102730 | [25] | |
c.7868G > A | p.G2623E | Heterozygous | novel | (predicted as likely pathogenic) | ||||||
RD15–04 | RP | Sporadic |
EYS
| NM_001142800.1 | c.2975G > T | p.C992F | Homozygous | rs566917467 | (predicted as pathogenic) | |
RD13–05 | CRD | Sporadic |
GUCY2D
| NM_000180.3 | c.2375C > T | p.P792L | Heterozygous | rs763774686 | (predicted as pathogenic) | |
RD11–08 | RP | Sporadic |
IMPDH1
| NM_000883.3 | c.931G > A | p.D311N | Heterozygous | CM020283 | [35] | |
RD15–03 | RP | Sporadic |
IMPDH1
| NM_000883.3 | c.931G > A | p.D311N | Heterozygous | CM020283 | [35] | |
RD5–04 | RP | Sporadic |
RHO
| NM_000539.3 | c.68C > A | p.P23H | Heterozygous | CM900197 | [36] | |
RD13–02 | RP | Sporadic |
RHO
| NM_000539.3 | c.68C > A | p.P23H | Heterozygous | CM900197 | [36] | |
RD12–08 | RP | Sporadic |
RHO
| NM_000539.3 | c.561 T > G | p.C187W | Heterozygous | novel | (predicted as pathogenic) | |
RD12–07 | RP | Sporadic |
RHO
| NM_000539.3 | c.936 + 1G > T | IVS4 + 1G > T | Heterozygous | CS920776 | [37] | |
RD14–06 | RD | Sporadic |
PRPH2
| NM_000322.4 | c.514C > T | p.R172W | Heterozygous | CM930639 | [28] | |
RD12–03 | RP/LCA | Sporadic |
RPE65
| NM_000329.2 | c.886dup | p.R296Kfs*7 | Homozygous | CI107001 | [38] | |
RD12–01 | RP | Sporadic |
RPGR
| NM_000328.2 | c.197A > G | p.Q66R | Hemizygous | novel | (predicted as pathogenic) | |
RD6–05 | MD | Sporadic |
TIMP3
| NM_000362.4 | c.29 T > A | p.L10H | Heterozygous | Novel | (predicted as pathogenic) | |
RD20–03 | CSNB | Sporadic |
TRPM1
| NM_002420.5 | c.1197G > A | p.P421= | Heterozygous | CS097758 | [25] | |
c.215A > G | p.Y72C | Heterozygous | CM097760 | [25] | ||||||
RD6–04 | CSNB | Sporadic |
TRPM1
| NM_002420.5 | c.2947_2948delGCinsAT | p.A983I | Heterozygous | Novel | (predicted as pathogenic) | |
c.3125 T > G | p.L1042R | Heterozygous | Novel | (predicted as likely pathogenic) | ||||||
RD5–07 | RP | Sporadic |
USH2A
| NM_206933.2 | c.2276G > T | p.C759F | Homozygous | CM001372 | [30] | |
RD14–02 | RP | sporadic |
USH2A
| NM_206933.2 | c.11411del | p.P3804Lfs*13 | Heterozygous | CD149996 | [39] | |
c.8431C > A | p.P2811T | Heterozygous | rs111033529 | (predicted as likely pathogenic) | ||||||
RD11–04 | RP | Sporadic |
USH2A
| NM_206933.2 | c.13335_13347delinsCTTG | p.E4445_S4449delinsDL | Heterozygous | CX104126 | [40] | |
Additional affected family members
| ||||||||||
RD14–04 | CRD | Autosomal dominant |
GUCA1A
| NM_000409.3 | c.296A > G | p.Y99C | Heterozygous | CM980960 | [26] | |
RD2–02 | RD | Autosomal dominant |
RGR
| NM_001012720.1 | c.824dupG | p.I276N*77 | Heterozygous | CI993291 | [16] | |
RD10–02 | OCMD | Autosomal dominant |
RP1L1
| NM_178857.5 | c.133C > T | p.R45W | Heterozygous | CM105618 | [20] | |
RD10–06 | OCMD | Autosomal dominant |
RP1L1
| NM_178857.5 | c.133C > T | p.R45W | Heterozygous | CM105618 | [20] | |
RD15–02 | RP | Autosomal recessive |
CERKL
| NM_001030311.2 | c.1045_1046del | p.M349Vfs*20 | Heterozygous | Novel | (predicted as pathogenic) | |
c.316C > T | p.R106C | Heterozygous | Novel | (predicted as likely pathogenic) | ||||||
RD20–02 | RP | Autosomal recessive |
USH2A
| NM_206933.2 | c.2299delG | p.E766Sfs*21 | Heterozygous | CD982997 | [9] | |
c.2276G > T | p.C759F | Heterozygous | CM001372 | [30] |
Inconclusive genotypes
Sample ID | Clincial Diagnosis | Family Inheritance | Candidate Gene(s) | Transcript | Nucleotide Change | Amino Acid Change | Genotypes (Sanger confirmed) | HGMD or dbSNP IDs | References (or in silico Analysis) | |
---|---|---|---|---|---|---|---|---|---|---|
RD1–12 | CRD | Sporadic |
C2orf71
| NM_001029883.2 | c.1514G > A | p.W505* | Heterozygous | CM1511740 | [15] | |
C2orf71
| c.3266dup | p.S1090Ifs*17 | Heterozygous | Novel | (predicted as pathogenic | |||||
BBS4
| NM_033028.4 | c.1375C > T | p.Q459* | Heterozygous | Novel | (predicted as pathogenic) | ||||
TYRP1
| NM_000550.2 | c.1557 T > G | p.Y519* | Heterozygous | CM135790/rs41302073 | [41] | ||||
GUCA1A
| NM_000409.3 | c.149C > T | p.P50L | Heterozygous | CM012969/rs104893968 | [13] | ||||
RD11–05 | RP | Sporadic |
GUCA1A
| NM_000409.3 | c.149C > T | p.P50L | Heterozygous | CM012969/rs104893968 | [13] | |
RD14–05 | RP | Sporadic |
TRPM1
| NM_002420.5 | c.1192 T > C | p.W398R | Heterozygous | Novel | (predicted as pathogenic) | |
TRPM1
| c.3914G > A | p.R1305H | Heterozygous | rs13380059 |
(predicted as unlikely pathogenic
| |||||
RD11–06 | RP | Sporadic |
GUCY2D
| NM_000180.3 | c.1724C > T | p.P575L | Heterozygous | CM023932/rs28743021 | [14] | |
TYR
| NM_000372.4 | c.1217C > T | p.P406L | Heterozygous | CM910385/rs104894313 | [42] | ||||
TYRP1
| NM_000550.2 | c.1261 + 1G > A | IVS9 + 1G > A | Heterozygous | rs140365820 | (predicted as pathogenic) | ||||
Insufficient for clinical correlation
| ||||||||||
RD4–05 | RP | Sporadic |
EYS
| NM_001142800.1 | c.6138G > A | p.W2046* | Heterozygous | Novel | (predicted as pathogenic) | |
RD11–02 | RP | Sporadic |
EYS
| NM_001142800.1 | c.5677_5681del | p.Y1893Rfs*12 | Heterozygous | Novel | (predicted as pathogenic) | |
RD4–03 | RP | Sporadic |
FLVCR1
| NM_014053.3 | c.1546C > T | p.R516* | Heterozygous | rs538343832 | (pathogenic but likely incidental) | |
RD14–03 | RP | sporadic |
ABCA4
| NM_000350.2 | c.5714 + 5G > A | IVS40 + 5G > A | Heterozygous | CS982057 | [43] | |
USH2A
| NM_206933.2 | c.8600C > T | p.S2867 L | Heterozygous | rs145468090 | (predicted as pathogenic) | ||||
USH2A
| c.10552G > A | p.V3518I | Heterozygous | rs75397806 |
(predicted as unlikely pathogenic)
| |||||
RD15–01 | RP | Autosomal recessive |
ABCA4
| NM_000350.2 | c.4685 T > C | p.I1562T | Heterozygous | CM970013 | [44] | |
RPGRIP1
| NM_020366.3 | c.1753C > T | p.P585S | Heterozygous | CM111852 | [45] | ||||
LRP5
| NM_002335.3 | c.4574C > T | p.A1525V | Heterozygous | CM078457 | [46] | ||||
RD6–06 | RP | sporadic |
CNGB1
| NM_001297.4 | c.2957A > T | p.N986I | Heterozygous | CM111413/rs201162411 | (predicted as likely pathogenic) | |
MYO7A
| NM_000260.3 | c.1132C > T | p.R378C | Heterozygous | rs199818783 | (predicted as likely pathogenic) | ||||
RD6–02 | RP | Sporadic |
RIMS1
| NM_014989.5 | c.3027 T > C | p.= | Heterozygous | Novel | (predicted as affecting splicing) | |
LCA5
| NM_181714.3 | c.2050G > C | p.A684P | Heterozygous | rs745875716 |
(predicted as unlikely pathogenic)
|
Sample ID | Clincial Diagnosis | Family Inheritance | Candidate Gene(s)
| Transcript | Nucleotide Change | Amino Acid Change | Genotypes (Sanger confirmed) | HGMD or dbSNP IDs | References (or in silico Analysis) | |
---|---|---|---|---|---|---|---|---|---|---|
RD11–03 | RP | Autosomal dominant |
RHO
| NM_000539.3 | c.574dup | p.Y192Lfs*139 | Heterozygous | Novel | (predicted as pathogenic) | |
CNGA3
| NM_001298.2 | c.1810C > T | p.Q604* | Heterozygous | Novel | (predicted as pathogenic) | ||||
RD20–07 | CRD | Autosomal dominant |
PRPH2
| NM_000322.4 | c.514C > T | p.R172W | Heterozygous | CM930639 | [28] | |
CERKL
| NM_001030311.2 | c.847C > T | p.R283* | Heterozygous | CM040509/rs121909398 | [47] | ||||
RD14–08 | RP | Autosomal recessive |
USH2A
| NM_206933.2 | c.2276G > T | p.C759F | Heterozygous | CM001372 | [30] | |
USH2A
| c.4108G > C | p.V1370 L | Heterozygous | Novel | (predicted as pathogenic) | |||||
GUCY2D
| NM_000180.3 | c.2950 T > C | p.C984R | Heterozygous | Novel | (predicted as pathogenic) | ||||
RD12–02 | XLRP | X-linked |
RPGR
| NM_000328.2 | c.1088_1089delinsA | p.V363Dfs*18 | Hemizygous | Novel | (predicted as pathogenic) | |
CACNA1F
| NM_005183.3 | c.1619 T > C | p.F540S | Hemizygous | Novel | (predicted as pathogenic) | ||||
TMEM67
| NM_153704.5 | c.1387C > T | p.R463* | Heterozygous | CM110634 | [48] | ||||
RD12–01 | RP | Sporadic |
RPGR
| NM_000328.2 | c.197A > G | p.Q66R | Hemizygous | Novel | (predicted as pathogenic) | |
TYR
| NM_000372.4 | c.721G > A | p.A241T | Heterozygous | CM145799 | (DM?)/rs538081629 | [49] | |||
RD13–02 | RP | Sporadic |
RHO
| NM_000539.3 | c.68C > A | p.P23H | Heterozygous | CM900197 | [36] | |
ABCA4
| NM_000350.2 | c.1610G > A | p.R537H | Heterozygous | CM032805 | [50] | ||||
RD12–07 | RP | Sporadic |
RHO
| NM_000539.3 | c.936 + 1G > T | IVS4 + 1G > T | Heterozygous | CS920776 | [37] | |
TYRP1
| NM_000550.2 | c.1354A > G | p.M452 V | Heterozygous | CM081465 | [51] | ||||
RD13–08 | Achromatopsia | Sporadic |
CNGB3
| NM_019098.4 | c.1148delC | p.T383Ifs*13 | Heterozygous | CD001927 | [52] | |
ABCA4
| NM_000350.2 | c.6089G > A | p.R2030Q | Heterozygous | CM990070/rs61750641 | [53] | ||||
RPGRIP1
| NM_020366.3 | c.1767G > T | p.Q589H | Heterozygous | CM057749/rs34067949 | [45] |