Figure S1. the Genotype and Phenotype of Patient W29-1

Supplementary information

Supplementary information includes Figure S1, S2 and S3; TablesS1, S2, S3, S4 and S5.

Figure S1. The genotype and phenotype of patient W29-1

A. Pedigree and mutations segregating within the family; B. Sequencing chromatograms of the family; C. ERG examination of the proband.

Figure S2. The genotype and phenotype of patient W83-1

A. Pedigree and mutations segregating within the family; B. Sequencing chromatograms of the proband; C. Fundus image of the proband.

Figure S3. The genotype and phenotype of patient W196-1

A. Pedigree and mutations segregating within the family; B. Sequencing chromatograms of the proband; C. TheY218C mutation is located in a highly conserved region; D. Fundus image of the proband.

Table S1. List of 164known retinal-disease genes.

Gene / Entrez Gene ID / Chromosome / Coding size (bp) / Exon No.
ABCA4 / 24 / 1 / 6822 / 48
ABCC6 / 368 / 16 / 4512 / 31
ADAM9 / 8754 / 8 / 2460 / 22
AHI1 / 54806 / 6 / 3591 / 26
AIPL1 / 23746 / 17 / 1155 / 6
ALMS1 / 7840 / 2 / 12504 / 23
ARL6 / 84100 / 3 / 561 / 7
ATXN7 / 6314 / 3 / 2838 / 12
BBS1 / 582 / 11 / 1782 / 17
BBS10 / 79738 / 12 / 2172 / 2
BBS12 / 166379 / 4 / 2133 / 1
BBS2 / 583 / 16 / 2166 / 17
BBS4 / 585 / 15 / 1560 / 16
BBS5 / 129880 / 2 / 1026 / 12
BBS9 / 27241 / 7 / 2559 / 20
BEST1 / 7439 / 11 / 1815 / 8
C1QTNF5 / 114902 / 11 / 732 / 2
C2orf71 / 338939 / 2 / 3867 / 2
CA4 / 762 / 17 / 939 / 8
CABP4 / 57010 / 11 / 828 / 6
CACNA1F / 778 / X / 5933 / 48
CACNA2D4 / 93589 / 12 / 3414 / 38
CC2D2A / 57545 / 4 / 4863 / 36
CDH23 / 64072 / 10 / 3345 / 22
CDH3 / 1001 / 16 / 2490 / 16
CDHR1 / 92211 / 10 / 2580 / 17
CEP290 / 80184 / 12 / 7440 / 53
CERKL / 375298 / 2 / 1545 / 13
CFH / 3075 / 1 / 3696 / 22
CHM / 1121 / X / 1962 / 15
CLN3 / 1201 / 16 / 1317 / 15
CLRN1 / 7401 / 3 / 738 / 4
CNGA1 / 1259 / 4 / 2280 / 9
CNGA3 / 1261 / 2 / 2085 / 7
CNGB1 / 1258 / 16 / 900 / 12
CNGB3 / 54714 / 8 / 2430 / 18
CNNM4 / 26504 / 2 / 2328 / 7
COL11A1 / 1301 / 1 / 5421 / 67
COL2A1 / 1280 / 12 / 4464 / 54
COL9A1 / 1297 / 6 / 2766 / 38
CRB1 / 23418 / 1 / 3885 / 10
CRX / 1406 / 19 / 900 / 3
CYP4V2 / 285440
285440 / 4 / 1578 / 11
DFNB31 / 25861 / 9 / 2724 / 12
DHDDS / 79947 / 1 / 1002 / 8
DMD / 1756 / X / 11058 / 79
EFEMP1 / 2202 / 2 / 1482 / 10
ELOVL4 / 6785 / 6 / 945 / 6
EYS / 346007 / 6 / 9435 / 40
FAM161A / 84140 / 2 / 2151 / 7
FLVCR1 / 28982 / 1 / 1668 / 10
FSCN2 / 25794 / 17 / 1479 / 5
FZD4 / 8322 / 11 / 1614 / 2
GNAT1 / 2779 / 5 / 18921 / 90
GNAT2 / 2780 / 1 / 1065 / 8
GPR98 / 84059 / 5 / 18921 / 90
GRK1 / 6011 / 13 / 2101 / 7
GRM6 / 2916 / 5 / 2634 / 10
GUCA1A / 2978 / 6 / 606 / 4
GUCA1B / 2979 / 6 / 603 / 4
GUCY2D / 3000 / 17 / 3312 / 18
HMCN1 / 83872 / 1 / 16908 / 107
IDH3B / 3420 / 20 / 702 / 6
IMPDH1 / 3614 / 7 / 1530 / 14
IMPG2 / 50939 / 3 / 3726 / 15
INPP5E / 56623 / 9 / 1935 / 10
INVS / 27130 / 9 / 3198 / 16
IQCB1 / 9657 / 3 / 1797 / 13
JAG1 / 182 / 20 / 3657 / 26
KCNJ13 / 3769 / 2 / 285 / 2
KCNV2 / 169522 / 9 / 1638 / 2
KLHL7 / 55975 / 7 / 501 / 5
LCA5 / 167691 / 6 / 2094 / 7
LRAT / 9227 / 4 / 693 / 2
LRP5 / 4041 / 11 / 4848 / 23
MAK / 4117 / 6 / 1872 / 13
MERTK / 10461 / 2 / 3000 / 19
MFRP / 83552 / 11 / 1740 / 13
MKKS / 8195 / 20 / 1713 / 4
MKS1 / 54903 / 17 / 1680 / 18
MTTP / 4547 / 4 / 2685 / 18
MYO7A / 4647 / 11 / 6648 / 48
NDP / 4693 / X / 402 / 2
NPHP1 / 4867 / 2 / 2202 / 20
NPHP3 / 27031 / 3 / 3993 / 27
NPHP4 / 261734 / 1 / 4281 / 29
NR2E3 / 10002 / 15 / 2102 / 8
NRL / 4901 / 14 / 741 / 2
NYX / 60506 / X / 1446 / 2
OAT / 4942 / 10 / 1320 / 9
OFD1 / 8481 / X / 3039 / 23
OPA1 / 4976 / 3 / 2883 / 28
OPA3 / 80207 / 19 / 543 / 2
OPN1LW / 5956 / X / 1095 / 6
OPN1MW / 2652 / X / 1095 / 6
OPN1SW / 611 / 7 / 1047 / 5
OTX2 / 5015 / 14 / 894 / 3
PANK2 / 80025 / 20 / 1713 / 7
PAX2 / 5076 / 10 / 1254 / 11
PCDH15 / 65217 / 10 / 5874 / 33
PDE6A / 5145 / 5 / 2583 / 22
PDE6B / 5158 / 4 / 2562 / 22
PDE6C / 5146 / 10 / 2577 / 22
PDE6G / 5148 / 17 / 264 / 3
PDZD7 / 79955 / 10 / 1554 / 9
PEX1 / 5189 / 7 / 3852 / 24
PEX7 / 5191 / 6 / 972 / 5
PGK1 / 5230 / X / 1254 / 11
PHYH / 5264 / 10 / 1017 / 9
PITPNM3 / 83394 / 17 / 2925 / 20
PRCD / 768206 / 17 / 165 / 3
PROM1 / 8842 / 4 / 2529 / 25
PRPF3 / 9129 / 1 / 2052 / 15
PRPF31 / 26121 / 19 / 1500 / 13
PRPF6 / 24148 / 20 / 2826 / 21
PRPF8 / 10594 / 17 / 7008 / 42
PRPH2 / 5961 / 6 / 1041 / 3
PXMP3 / 5828 / 8 / 918 / 1
RAX2 / 84839 / 19 / 555 / 2
RB1 / 5925 / 13 / 2787 / 27
RBP3 / 5949 / 10 / 3744 / 4
RBP4 / 5950 / 10 / 606 / 5
RD3 / 343035 / 1 / 588 / 2
RDH12 / 145226 / 14 / 951 / 7
RDH5 / 5959 / 12 / 957 / 4
RGR / 5995 / 10 / 762 / 6
RGS9 / 8787 / 17 / 2025 / 19
RGS9BP / 388531 / 19 / 708 / 1
RHO / 6010 / 3 / 1047 / 5
RIMS1 / 22999 / 6 / 5079 / 34
RLBP1 / 6017 / 15 / 954 / 7
ROM1 / 6094 / 11 / 1056 / 3
RP1 / 6101 / 8 / 6471 / 3
RP1L1 / 94137 / 8 / 7203 / 3
RP2 / 6102 / X / 1053 / 5
RP9 / 6100 / 7 / 666 / 6
RPE65 / 6121 / 1 / 1602 / 14
RPGR / 6103 / X / 3459 / 15
RPGRIP1 / 57096 / 14 / 3861 / 24
RPGRIP1L / 23322 / 16 / 3948 / 26
RS1 / 6247 / X / 675 / 6
SAG / 6295 / 2 / 1218 / 15
SDCCAG8 / 10806 / 1 / 2142 / 18
SEMA4A / 64218 / 1 / 1890 / 12
SLC24A1 / 9187 / 15 / 3300 / 9
SNRNP200 / 23020 / 2 / 6411 / 45
SPATA7 / 55812 / 14 / 1704 / 11
TIMM8A / 1678 / X / 294 / 2
TIMP3 / 7078 / 22 / 636 / 5
TMEM126A / 84233 / 11 / 588 / 4
TOPORS / 10210 / 9 / 2943 / 2
TRIM32 / 22954 / 9 / 1962 / 1
TRPM1 / 4308 / 15 / 4812 / 26
TSPAN12 / 23554 / 7 / 918 / 7
TTC8 / 123016 / 14 / 1548 / 15
TTPA / 7274 / 8 / 837 / 5
TULP1 / 7287 / 6 / 1629 / 15
UNC119 / 9094 / 17 / 723 / 5
USH1C / 10083 / 11 / 2700 / 27
USH1G / 124590 / 17 / 1386 / 2
USH2A / 7399 / 1 / 15609 / 71
VCAN / 1462 / 5 / 10191 / 14
WFS1 / 7466 / 4 / 2673 / 7
ZNF513 / 130557 / 2 / 1440 / 3
Total / 460787 / 2654

Table S2. List of 88possiblecandidate genes.

Gene / Entrez Gene ID / Chromosome / Coding size (bp) / Exon No.
ABLIM2 / 84448 / 4 / 1938 / 21
ALDH1A2 / 8854 / 15 / 3606 / 13
ANKRD33 / 341405 / 12 / 1359 / 5
ARHGDIB / 397 / 12 / 606 / 5
ASCL1 / 429 / 12 / 711 / 1
ASH1L / 55870 / 1 / 8895 / 27
ATOH7 / 220202 / 10 / 459 / 1
ATP6V1B2 / 526 / 8 / 1536 / 14
BCAR1 / 9564 / 16 / 2751 / 7
BCL6 / 604 / 3 / 2121 / 8
BTG2 / 7832 / 1 / 477 / 2
CAMK1G / 57172 / 1 / 1431 / 11
CASZ1 / 54897 / 1 / 5280 / 18
CBLN4 / 140689 / 20 / 606 / 3
CCKBR / 887 / 11 / 1344 / 5
CCND1 / 595 / 11 / 888 / 5
CDK5R2 / 8941 / 2 / 1104 / 1
CHRNB4 / 1143 / 15 / 1497 / 6
CRB3 / 92359 / 19 / 363 / 4
DACH1 / 1602 / 13 / 2127 / 11
EGFLAM / 133584 / 5 / 3054 / 23
EP300 / 2033 / 22 / 7245 / 31
ETV5 / 2119 / 3 / 1533 / 12
EYA1 / 2138 / 8 / 1779 / 16
EYA2 / 2139 / 20 / 1617 / 15
EYA3 / 2140 / 1 / 1722 / 17
EYA4 / 2070 / 6 / 1920 / 19
FBXW4 / 6468 / 10 / 1239 / 9
FOXF1 / 2294 / 16 / 1140 / 2
FOXG1 / 2290 / 14 / 1470 / 1
FOXM1 / 2305 / 12 / 2406 / 7
FOXN2 / 3344 / 2 / 1296 / 5
FOXN4 / 121643 / 12 / 1554 / 9
FOXO3 / 2309 / 6 / 2022 / 2
FOXP1 / 27086 / 3 / 2040 / 16
FOXP2 / 93986 / 7 / 2223 / 17
FOXS1 / 2307 / 20 / 993 / 1
GABARAPL1 / 23710 / 12 / 354 / 4
GLI3 / 2737 / 7 / 4743 / 14
HDAC4 / 9759 / 2 / 3255 / 26
HES1 / 3280 / 3 / 843 / 4
IER5 / 51278 / 1 / 984 / 1
IKZF1 / 10320 / 7 / 1434 / 6
KAT2A / 2648 / 17 / 2514 / 18
LHX2 / 9355 / 9 / 1221 / 5
MAB21L2 / 10586 / 4 / 1080 / 1
MEIS1 / 4211 / 2 / 1173 / 12
MITF / 4286 / 3 / 1563 / 10
NEUROD1 / 4760 / 2 / 1071 / 1
NEUROG2 / 63973 / 4 / 819 / 1
NLK / 51701 / 17 / 1584 / 11
NR1D1 / 9572 / 17 / 1845 / 8
NR2E1 / 7101 / 6 / 1158 / 9
NR2F1 / 7025 / 5 / 1272 / 3
OTX1 / 5013 / 2 / 1065 / 3
PAX6 / 5080 / 11 / 1311 / 11
PIAS3 / 10401 / 1 / 1887 / 14
PITX3 / 5309 / 10 / 909 / 3
POU2F2 / 5452 / 19 / 1392 / 14
PPARG / 5468 / 3 / 1518 / 7
PRDM1 / 639 / 6 / 2478 / 7
RAC3 / 5881 / 17 / 579 / 6
RARA / 5914 / 17 / 1389 / 8
RARB / 5915 / 3 / 1347 / 8
RARG / 5916 / 12 / 1365 / 8
RAX / 30062 / 18 / 1041 / 3
RCVRN / 5957 / 17 / 603 / 3
RORB / 6096 / 9 / 1380 / 10
RXRA / 6256 / 9 / 1389 / 10
RXRB / 6257 / 6 / 1614 / 10
RXRG / 6258 / 1 / 1392 / 10
SIX1 / 6495 / 14 / 855 / 2
SIX3 / 6496 / 2 / 999 / 2
SIX6 / 4990 / 14 / 741 / 2
SLC7A14 / 57709 / 3 / 2316 / 7
SMARCD3 / 6604 / 7 / 1452 / 13
SOX1 / 6656 / 13 / 1176 / 1
SOX2 / 6657 / 3 / 954 / 1
SP1 / 6667 / 12 / 2358 / 6
SP4 / 6671 / 7 / 2355 / 6
TCF19 / 6941 / 6 / 1038 / 3
THRB / 7068 / 3 / 1386 / 8
TLL1 / 7092 / 4 / 3042 / 21
TREX1 / 11277 / 3 / 1110 / 1
TSHZ1 / 10194 / 18 / 3099 / 1
TSHZ2 / 128553 / 20 / 3105 / 2
TSHZ3 / 57616 / 19 / 3246 / 2
VSX2 / 338917 / 14 / 1086 / 5
Total / 154242 / 722

Table S3. List of 32 microRNAs.

microRNAs / Chromosome / Location
hsa-mir-9-1 / 1 / 207975197-207975284
hsa-mir-181b-1 / 1 / 220291499-220291583
hsa-mir-181a-1 / 11 / 568089-568198
hsa-mir-29c / 11 / 64658827-64658911
hsa-mir-194-1 / 15 / 79502130-79502213
hsa-mir-210 / 15 / 89155056-89155165
hsa-mir-194-2 / 15 / 89911248-89911337
hsa-mir-184 / 19 / 13985513-13985622
hsa-mir-7-2 / 19 / 13985689-13985825
hsa-mir-9-3 / 19 / 4770682-4770791
hsa-mir-181c / 2 / 56216085-56216194
hsa-mir-181d / 2 / 56227849-56227930
hsa-mir-7-3 / 2 / 56210102-56210211
hsa-mir-216a / 22 / 20020662-20020743
hsa-mir-216b / 5 / 87962671-87962757
hsa-mir-217 / 6 / 33175612-33175721
hsa-mir-185 / 7 / 129414532-129414609
hsa-mir-9-2 / 7 / 129414745-129414854
hsa-mir-219-1 / 7 / 130135952-130136045
hsa-mir-96 / 7 / 99691183-99691266
hsa-mir-183 / 7 / 99691616-99691697
hsa-mir-335 / 7 / 129410223-129410332
hsa-mir-25 / 9 / 127454721-127454830
hsa-mir-106b / 9 / 127455989-127456077
hsa-mir-182 / 9 / 131154897-131154993
hsa-mir-181a-2 / 9 / 21512114-21512184
hsa-mir-181b-2 / 9 / 73424891-73425000
hsa-mir-219-2 / 9 / 86584663-86584772
hsa-mir-31 / X / 85158641-85158712
hsa-mir-204 / 1 / 207975197-207975284
hsa-mir-7-1 / 1 / 220291499-220291583
hsa-mir-361 / 11 / 568089-568198

Table S4. Phenotypic and genotypic information in ninety-nine IRD patients.

Patient ID / Sex / Age / Diagnosis / Onset age / BCVA / Family history / Gene
W5-1 / M / 34 / RP / 14 / 0.5/0.5 / AR / EYS
W10-1 / M / 36 / RP / 6 / 0.3/0.3 / XL / RPGR
W33-1 / M / 31 / RP / 21 / HM/HM / S / CRB1
W34-1 / F / 30 / RP / 5 / FC/HM/ / S* / CRB1
W37-1 / F / 29 / RP / 6 / 0.4/0.4 / S / USH2A
W132-1 / M / 12 / RP / 5 / 0.16/0.2 / XL / RP2
W55-1 / F / 40 / RP / 20 / 0.25/0.5 / S / SNRNP200
W115-1 / F / 20 / RP / 10 / 0.12/0.12 / S / RPE65
W119-1 / M / 40 / RP / 20 / HM/HM / S* / RP1
W127-1 / F / 48 / RP / 20 / 0.2/0.04 / AR / EYS
W131-1 / F / 60 / RP / 20 / LP/NLP / AR* / USH2A
W146-1 / M / 32 / RP / 5 / 0.6/0.6 / S* / CNGA1
W155-1 / F / 39 / RP / 30 / 0.1/0.06 / S / CYP4V2
W156-1 / M / 27 / RP / 15 / 0.3/0.1 / S / CERKL
W159-1 / M / 34 / RP / 20 / 0.5/0.4 / AR* / EYS
W171-1 / F / 37 / RP / 20 / FC/FC / S* / EYS
W172-1 / F / 38 / RP / 27 / 0.1/0.4 / AR / CYP4V2
W177-1 / F / 48 / RP / 10 / LP/LP / AR / RP1
W214-1 / M / 49 / RP / 35 / FC/FC / S* / CNGB1
W286-1 / M / 43 / RP / 20 / FC/0.05 / S / EYS
W106-1 / M / 23 / RP / 5 / HM/HM / S* / RP1
W139-1 / F / 32 / RP / 15 / 0.4/0.5 / AR* / PDE6A
F67-1 / F / 26 / RP / 5 / FC/FC / AR / MERTK
F5-1 / F / 36 / RP / 26 / 0.8/0.8 / AD / RHO
F7-1 / M / 34 / RP / 15 / HM/0.01 / AR / USH2A
F9-1 / M / 22 / RP / 6 / 0.08/0.09 / XL / RP2
F10-1 / M / 23 / RP / 5 / 0.25/0.2 / AR / RLBP1
F11-1 / M / 48 / RP / 41 / 0.4/0.4 / S / EYS
F12-1 / M / 67 / RP / 20 / 0.07/0.08 / S / PRPF31
F23-1 / F / 25 / RP / 20 / 0.12/0.1 / S / ABCA4
F25-1 / M / 48 / RP / 10 / 0.12/0.15 / XL / RPGR
F29-1 / M / 26 / RP / 6 / 0.5/0.5 / S / USH2A
F31-1 / M / 20 / RP / 10 / 0.8/0.8 / S / RLBP1
F33-1 / M / 21 / RP / 15 / 0.2/0.2 / S / PROM1
F35-1 / M / 43 / RP / 13 / 0.2/0.2 / S / EYS
F39-1 / M / 54 / RP / 40 / HM/FC / AR / CERKL
H2-1 / M / 59 / RP / 41 / LP/LP / AD / PRPF31
H3-1 / F / 34 / RP / 20 / 1/1.2 / S / MAK
H4-1 / F / 43 / RP / 39 / 0.08/0.08 / S / PRPF31
H12-1 / F / 57 / RP / 43 / 0.06/0.06 / AR / USH2A
S4-1 / M / 23 / RP / 5 / 0.4/0.5 / S / PITPNM3
S7-1 / M / 50 / RP / 10 / LP/0.1 / S / PDE6B
S11-1 / F / 38 / RP / 5 / 0.04/0.01 / S / RHO
W76-1 / M / 47 / RP / 20 / 0.1/0.3 / S / CYP4V2
W83-1 / F / 67 / RP / 10 / FC/FC / S / RHO
W84-1 / M / 32 / RP / 20 / 0.5/0.3 / S / PDE6B
W136-1 / F / 42 / RP / 32 / 0.8/0.7 / AD / TOPORS
W59-1 / M / 43 / RP / 20 / 0.3/0.4 / S / SNRNP200
W67-1 / F / 37 / RP / 10 / 0.8/0.6 / S / PDE6B
W69-1 / M / 35 / RP / 20 / HM/HM / S* / CYP4V2
W82-1 / F / 43 / RP / 22 / 0.5/0.5 / S / EYS
W86-1 / M / 25 / RP / 15 / 0.6/0.6 / S / EYS
W89-1 / M / 35 / RP / 32 / 0.2/0.2 / S / RPGR
W90-1 / F / 44 / RP / 30 / 0.4/0.15 / AD / RHO
W92-1 / M / 41 / RP / 21 / 0.1/0.08 / AD / PROM1
W93-1 / F / 10 / RP / 5 / FC/0.3 / S / CRB1
W13-1 / M / 63 / RP / 41 / 0.15/0.2 / AR / EYS
W50-1 / M / 30 / RP / 25 / LP/LP / AR / CYP4V2
W74-1 / F / 62 / RP / 22 / 0.25/0.25 / AD / PRPF6
W75-1 / M / 31 / RP / 20 / 0.2/0.2 / S* / EYS
W78-1 / M / 31 / RP / 20 / 0.3/0.4 / S* / MERTK
W99-1 / M / 60 / RP / 20 / LP/LP / AR / USH2A
W44-1 / F / 49 / RP / 5 / 0.04/0.04 / AD / PRPF6
W181-1 / F / 18 / RP / 5 / 0.12/0.1 / S / USH2A
W32-1 / M / 22 / RP / 15 / 0.5/0.6 / S / USH2A
W11-1 / M / 24 / Usher / 14 / 0.3/0.3 / AR / USH1C
W31-1 / M / 28 / Usher / 16 / 0.4/0.6 / S / USH2A
W124-1 / M / 26 / Usher / 5 / 0.15/0.4 / S / USH2A
W130-1 / M / 41 / Usher / 5 / HM/HM / S* / USH2A
W133-1 / M / 36 / Usher / 5 / FC/FC / S* / USH2A
W176-1 / M / 45 / Usher / 30 / 0.5/0.4 / AR* / USH2A
W272-1 / M / 52 / Usher / 10 / FC/0.6 / AR / USH2A
W197-1 / F / 30 / Usher / 20 / 0.4/0.25 / S / USH2A
H9-1 / F / 47 / Usher / 33 / 0.08/0.08 / AR / CLRN1
W56-1 / M / 41 / Usher / 5 / HM/HM / S / USH2A
W1-1 / M / 8 / LCA / 4 / FC/FC / S / CRB1
W141-1 / F / 4 / LCA / 1 / ND / S / CRB1
W290-1 / F / 3 / LCA / 1 / ND / S / CRB1
W138-1 / M / 7 / LCA / 5 / 0.4/0.5 / S / RPE65
W169-1 / M / 2 / LCA / 1 / ND / S / CEP290
W105-1 / F / 4 / LCA / 1 / LP/LP / S / AIPL1
W152-1 / M / 31 / CRD / 20 / 0.12/0.1 / S* / CDHR1
W154-1 / M / 10 / CRD / 6 / 0.3/0.25 / S / CACNA1F
F14-1 / F / 22 / CRD / 10 / 0.1/0.1 / S / CRX
W72-1 / M / 37 / CRD / 20 / FC/FC / AR* / KCNV2
W58-1 / M / 42 / CRD / 20 / 0.3/LP / S / CACNA2D4
W96-1 / M / 56 / CRD / 10 / FC/FC / S / CACNA1F
W111-1 / F / 27 / Stargardt / 10 / 0.06/0.08 / S / ABCA4
W205-1 / M / 48 / Stargardt / 18 / LP/LP / AR / PROM1
W140-1 / M / 14 / Stargardt / 10 / 0.16/0.16 / S / ABCA4
W142-1 / M / 43 / Stargardt / 30 / 0.16/0.1 / AD / PROM1
W149-1 / M / 34 / Stargardt / 5 / 0.05/0.05 / S / ABCA4
W9-1 / M / 40 / BCD / 30 / 0.04/0.04 / S / CYP4V2
W15-1 / M / 41 / BCD / 21 / HM/HM / AR* / CYP4V2
W20-1 / M / 48 / BCD / 25 / 0.07/HM / AR / CYP4V2
W129-1 / M / 10 / CSNB / 5 / 0.2/0.3 / S / PDE6B
F8-1 / F / 44 / CSNB / 5 / 0.2/0.15 / AD / PDE6B
W196-1 / F / 35 / RP / 10 / LP/LP / S / AHI1
W29-1 / F / 9 / ESCS / 5 / 0.4/0.8 / S* / NR2E3

M, male; F, female; RP, retinitis pigmentosa; Usher, Usher Syndrome; LCA, Leber congenital amaurosis; CRD, cone-rod dystrophy; BCD, Bietti crystalline dystrophy; CSNB, congenital stationary night blindness; ESCS, enhanced Scone syndrome;BCVA, best corrected visual acuity; HM, hand movement; FC, fingers count, LP, light perception; NLP, no light perception; AR, autosomal recessive; AD, autosomal dominant; XL, X-linked; S, simplex;asterisk indicates the consanguineous families.

Table S5. Mutations identified in ninety-nine IRD patients.

Patient / Gene / Mutation / Type a / Segb / Prediction c / Frequency d / Reference
PolyPhen-2 / SIFT / Hapmap / 1K
W10-1 / RPGR / c.2006G>A, p.W669X / Hemi / Yes / ND / ND / None / None / Novel
W33-1 / CRB1 / c.2480G>A, p.G827E
c.137delA / Hetero
Hetero / Yes
Yes / Damaging
ND / Tolerated
ND / None
None / None
None / Novel
Novel
W34-1 / CRB1 / c.3676G>T, p.G1226X / Homo / Yes / ND / ND / None / None / 1
W37-1 / USH2A / c.7068T>G, p.N2356K
c.5752G>A, p.E1918K / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Tolerated
Tolerated / Rare
None / Rare
None / 2
Novel
W132-1 / RP2 / c.884-1G>C / Hemi / Yes / ND / ND / None / None / 3
W55-1 / SNRNP200 / c.1614T>G, p.I538M / Hetero / Yes / Damaging / Damaging / None / None / Novel
W115-1 / RPE65 / c.311G>A, p.G104D
c.272G>A, p.R91Q / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Damaging
Tolerated / None
None / Rare
Rare / Novel
4
W119-1 / RP1 / c.380G>A, p.W127X / Homo / Yes / ND / ND / None / None / Novel
W127-1 / EYS / c.6557G>A, p.G2186E
c.9186_9187delCA / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / 5
Novel
W131-1 / USH2A / c.6908C>T, p.S2303F
c.15562A>G, p.S5188G / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Damaging
Tolerated / None
Rare / None
Rare / Novel
6
W146-1 / CNGA1 / c.1271G>A, p.R424Q / Homo / Yes / Damaging / Tolerated / Rare / Rare / 7
W155-1 / CYP4V2 / c.1091-2A>G
c.810delT / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / Rare
Rare / Rare
Rare / 8
Novel
W156-1 / CERKL / c.451T>G, p.W151G
c.758delT / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / Novel
9
W159-1 / EYS / c.7492G>C, p.A2498P / Homo / Yes / Damaging / Damaging / None / None / Novel
W171-1 / EYS / c.7609G>A, p.A2537T
c.7949C>T, p.S2650F / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Damaging
Damaging / Rare
None / Rare
None / Novel
Novel
W172-1 / CYP4V2 / c.1091-2A>G
c.810delT / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / Rare
Rare / Rare
Rare / 8
Novel
W177-1 / RP1 / c.3223G>T, p.E1075X
c.254_255insC / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / None
None / None
None / Novel
Novel
W214-1 / CNGB1 / c.1631C>T, p.P544L / Homo / Yes / Damaging / Tolerated / Rare / Rare / Novel
W286-1 / EYS / c.6416G>A, p.C2139Y
c.8150delA / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / Rare
None / Rare
None / 5
Novel
W106-1 / RP1 / c.678delA / Homo / Yes / ND / ND / None / None / Novel
W139-1 / PDE6A / c.357delT / Homo / Yes / ND / ND / None / None / Novel
F67-1 / MERTK / c.1691-1G>A / Homo / Yes / ND / ND / None / None / Novel
F5-1 / RHO / c.1030C>T, p.Q344X / Hetero / Yes / ND / ND / None / None / 10
F7-1 / USH2A / c.13010C>T ,p.T4337M
c.8559-2A>G / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / 11
12
F9-1 / RP2 / c.358C>T, p.R120X / Hemi / Yes / ND / ND / None / None / 13
F10-1 / RLBP1 / c.282delC / Homo / Yes / ND / ND / None / None / Novel
F11-1 / EYS / c.2510G>T, p.C837F
c.8107G>T, p.E2703X / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / Novel
Novel
F12-1 / PRPF31 / c.910C>T, p.R304C / Hetero / Yes / Damaging / Damaging / None / None / Novel
F23-1 / ABCA4 / c.1531C>T, p.R511C
c.6479+1G>C / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / 14
14
F25-1 / RPGR / c.935-2A>G / Hemi / Yes / ND / ND / None / None / Novel
F29-1 / USH2A / c.13010C>T, p.T4337M
c.11389+1G>C / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / 11
Novel
F31-1 / RLBP1 / c.282delC / Homo / Yes / ND / ND / None / None / Novel
F33-1 / PROM1 / c.1824delT / Homo / Yes / ND / ND / None / None / Novel
F35-1 / EYS / c.8012T>A, p.L2671X
c.704G>A, p.W235X / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / None
None / None
None / Novel
Novel
F39-1 / CERKL / c.547A>T, p.I183F
c.1404delA / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / Novel
15
H2-1 / PRPF31 / c.629delC / Hetero / Yes / ND / ND / None / None / Novel
H3-1 / MAK / c.552G>C, p.W184C / Homo / Yes / Damaging / Damaging / None / None / Novel
H4-1 / PRPF31 / c.1305T>A, p.Y435X / Hetero / Yes / ND / ND / None / None / Novel
H12-1 / USH2A / c.15017C>T, p.T5006M
c.4307C>T, p.P1436L / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Tolerated
Damaging / None
None / None
None / Novel
Novel
S4-1 / PITPNM3 / c.2233G>A, p.G745R / Hetero / Yes / Damaging / Damaging / None / None / Novel
S7-1 / PDE6B / c.1669C>T, p.H557Y
c.167_171del5bp / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / 7
Novel
S11-1 / RHO / c.403C>T, p.R135W / Hetero / Yes / Damaging / Damaging / None / None / 7
W76-1 / CYP4V2 / c.694C>T, p.R232X
c.810delT / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / None
Rare / None
Rare / 16
Novel
W83-1 / RHO / c.628G>T, p.V210F / Hetero / Yes / Damaging / Damaging / None / None / 17
W84-1 / PDE6B / c.1133G>A, p.W378X / Homo / Yes / ND / ND / None / None / Novel
W136-1 / TOPORS / c.2598_2609del11bp / Hetero / Yes / ND / ND / None / None / Novel
W59-1 / SNRNP200 / c.1631T>C, p.M544T / Hetero / Yes / Damaging / Damaging / None / None / Novel
W67-1 / PDE6B / c.1219G>A, p.G407R
c.1712C>T, p.T571M / Hetero
Hetero / Yes
Yes / Damaging
Tolerated / Damaging
Damaging / Rare
None / Rare
None / Novel
Novel
W69-1 / CYP4V2 / c.958C>T, p.R320X
c.810delT / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / None
Rare / None
Rare / 18
Novel
W82-1 / EYS / c.7492G>C, p.A2498P
c.8244_8245insT / Hetero
Hetero / Yes
Yes / Damaging
ND / Tolerated
ND / None
None / None
None / Novel
Novel
W86-1 / EYS / c.6416G>A, p.C2139Y
c.8392delG / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / Rare
None / Rare
None / 5
Novel
W89-1 / RPGR / c.2377C>T, p.Q793X / Hemi / Yes / ND / ND / None / None / Novel
W90-1 / RHO / c.403C>T, p.R135W / Hetero / Yes / Damaging / Damaging / None / None / 7
W92-1 / PROM1 / c.1117C>T, p.R373C / Hetero / Yes / Damaging / Damaging / None / Rare / 19
W93-1 / CRB1 / c.1831T>C, p.S611P
c.1576C>T, p.R526X / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / 1
1
W13-1 / EYS / c.3489T>A, p.N1163K
c.2644T>C, p.F882L / Hetero
Hetero / Yes
Yes / Damaging
Tolerated / Tolerated
Damaging / Rare
Rare / Rare
Rare / 20
Novel
W29-1 / NR2E3 / c.290G>A, p.R97H / Homo / Yes / Damaging / Damaging / None / None / 21
W50-1 / CYP4V2 / c.1027T>G, p.Y343D
c.694C>T, p.R232X / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / Novel
16
W74-1 / PRPF6 / c.514C>T, p.R172W / Hetero / Yes / Damaging / Damaging / None / None / Novel
W75-1 / EYS / c.6416G>A, p.C2139Y / Homo / Yes / Damaging / Damaging / Rare / Rare / 5
W78-1 / MERTK / c.1690+1G>A / Homo / Yes / ND / ND / None / None / Novel
W99-1 / USH2A / c.9469C>T, p.Q3157X
c.2802T>G, p.C934W / Hetero
Hetero / Yes
Yes / ND
Damaging / ND
Damaging / None
Rare / None
Rare / 22
23
W44-1 / PRPF6 / c.551A>G, p.D184G / Hetero / Yes / Damaging / Damaging / None / None / Novel
W181-1 / USH2A / c.15562A>G, p.S5188G
c.2617G>A, p.G873R / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Tolerated
Tolerated / Rare
None / Rare
None / 6
Novel
W32-1 / USH2A / c.9259G>A, p.V3087I
c.100_101insT / Hetero
Hetero / Yes
Yes / Tolerated
ND / Tolerated
ND / Rare
None / Rare
None / Novel
Novel
W11-1 / USH1C / c.463C>T, p.R155X
c.311G>A, p.G104D / Hetero
Hetero / Yes
Yes / ND
Damaging / ND
Damaging / None
None / None
None / 24
25
W31-1 / USH2A / c.5581G>A, p.G1861S
c.4576G>A, p.G1526R / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Damaging
Tolerated / None
None / None
None / 22
Novel
W124-1 / USH2A / c.5581G>A, p.G1861S
c.15427C>T, p.R5143C / Hetero
Hetero / Yes
Yes / Damaging
Tolerated / Damaging
Damaging / None
Rare / None
Rare / 22
22
W130-1 / USH2A / c.9469C>T, p.Q3157X / Homo / Yes / ND / ND / None / None / 22
W133-1 / USH2A / c.4576G>A, p.G1526R / Homo / Yes / Damaging / Tolerated / None / None / Novel
W176-1 / USH2A / c.8559-2A>G / Homo / Yes / ND / ND / None / None / 12
W272-1 / USH2A / c.8559-2A>G
c.8917_8918delCT / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / None
None / None
None / 12
Novel
W197-1 / USH2A / c.9801C>G, p.C3267W
c.802G>A, p.G268R / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Damaging
Damaging / None
None / None
None / Novel
26
H9-1 / CLRN1 / c.149C>A, p.S50X
c.253+6T>C / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / None
None / None
None / Novel
Novel
W56-1 / USH2A / c.2209C>T, p.R737X
c.8603delA / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / None
None / None
None / 23
22
W1-1 / CRB1 / c.455G>A, p.C152Y
c.1985C>A, p.S662X / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / 27
Novel
W141-1 / CRB1 / c.1841G>T, p.G614V
c.3442T>C, p.C1148R / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Damaging
Damaging / None
None / None
None / 28
Novel
W290-1 / CRB1 / c.1148G>A, p.C383Y
c.2498G>A, p.G833D / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Damaging
Damaging / Rare
None / Rare
None / Novel
29
W138-1 / RPE65 / c.917C>T, p.T306I
c.912C>A, p.Y304X / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / None
None / Novel
Novel
W169-1 / CEP290 / c.451C>T, p.R151X
c.4195-1G>C / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / None
None / None
None / 30
Novel
W105-1 / AIPL1 / c.421C>T, p.Q141X / Homo / Yes / ND / ND / None / None / Novel
W152-1 / CDHR1 / c.1117C>T, p.Q373X / Homo / Yes / ND / ND / None / None / Novel
W154-1 / CACNA1F / c.2932C>T, p.R978X / Hemi / Yes / ND / ND / None / None / Novel
F14-1 / CRX / c.790G>A, p.V264M / Hetero / Yes / Damaging / Damaging / None / None / Novel
W72-1 / KCNV2 / c.1284_1287delTGTC / Homo / Yes / ND / ND / None / None / Novel
W58-1 / CACNA2D4 / c.2120G>A, p.R707H / Homo / Yes / Damaging / Tolerated / None / None / Novel
W96-1 / CACNA1F / c.1464G>T, p.E488D / Hemi / Yes / Damaging / Tolerated / None / None / Novel
W111-1 / ABCA4 / c.5584G>C, p.G1862R
c.1804C>T, p.R602W / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Damaging
Damaging / None
None / None
None / Novel
14
W205-1 / PROM1 / c.436C>T, p.R146X
c.1229_1230delCT / Hetero
Hetero / Yes
Yes / ND
ND / ND
ND / None
None / None
None / Novel
Novel
W140-1 / ABCA4 / c.2894A>G, p.N965S / Homo / Yes / Damaging / Damaging / None / Rare / 31
W142-1 / PROM1 / c.1117C>T, p.R373C / Hetero / Yes / Damaging / Damaging / None / Rare / 19
W149-1 / ABCA4 / c.2894A>G, p.N965S
c.6479+4A>G / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
None / Rare
None / 31
Novel
W9-1 / CYP4V2 / c.992A>C, p.H331P
c.1091-2A>G / Hetero
Hetero / Yes
Yes / Damaging
ND / Damaging
ND / None
Rare / None
Rare / 8
8
W15-1 / CYP4V2 / c.1091-2A>G / Homo / Yes / ND / ND / Rare / Rare / 8
W20-1 / CYP4V2 / c.992A>C, p.H331P / Homo / Yes / Damaging / Damaging / None / None / 8
W129-1 / PDE6B / c.1624C>T, p.R542W / Hetero / Yes / Damaging / Damaging / None / None / Novel
F8-1 / PDE6B / c.1811C>T, p.T604I / Hetero / Yes / Damaging / Damaging / None / None / 7
W5-1 / EYS / c.9368A>C, p.N3123T
c.6416G>A, p.C2139Y / Hetero
Hetero / Yes
Yes / Tolerated
Damaging / Damaging
Damaging / None
Rare / None
Rare / Novel
5
W196-1 / AHI1 / c.653A>G, p.Y218C
c.3257A>G, p.E1086G / Hetero
Hetero / Yes
Yes / Damaging
Damaging / Damaging
Damaging / None
Rare / None
Rare / Novel
32

a Mutation type: Hetero, heterozygous; Homo, homozygous; Hemi, hemizygous. bSeg, co-segregation. c Prediction of functional effects of missense mutations by using PolyPhen-2 and SIFT. ND, nonsense, frameshift or splice site mutations are not detected. d Allele frequencies: none, absent in the database; rare, less than 0.01.

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