Confirmed CNVs impacting genes known as a cause of inherited retinal disease
| Study ID | Gene | Zygosity | hg19 coordinates of implicated exons | Exons (n) | HGVS cDNA | Classification |
| Deletions | ||||||
| 15010656 | TRPM1 | Het | chr15:31294020–31369129 | 26 | NM_002420.5: c.(?_−1)_(*1_?)del | Likely pathogenic |
| 14016924 | PDE6B | Het | chr4:6 19 411–6 63 901 | 22 | NM_000283.3: c.(?_−1)_(*1_?)del | Likely pathogenic |
| 15000307 | MERTK | Het | chr2:112702532–112786446 | 17 | NM_006343.2: c.(482+1_483–1)_(3000+1_3001–1)del | Likely pathogenic |
| 15010972* | PCDH15 | Het | chr10:55826512–56424027 | 19 | NM_001142763.1: c.(?_−1)_(2235+1_2236–1)del | Likely pathogenic |
| 15012122 | KIF11 | Het | chr10:94389928–94413558 | 11 | NM_004523.3: c.(1305+1_1306–1)_(*1_?)del | Likely pathogenic |
| 15006709* | MERTK | Het | chr2:112656308–112733054 | 7 | NM_006343.2: c.(?_−1)_(1144+1_1145–1)del | Likely pathogenic |
| 084929 | RPE65 | Het | chr1:68895454–68915593 | 14 | NM_000329.2: c.(?_−1)_(*1_?)del | Likely pathogenic |
| 15005941 | USH2A | Het | chr1:216405290–216465717 | 5 | NM_206933.2: c.(1644+1_1645–1)_(2993+1_2994–1)del | Likely pathogenic |
| 15005265 | EYS | Het | chr6:65612001–65655812 | 4 | NM_001142800.1: c.(2259+1_2260–1)_(2846+1_2847–1)del | Likely pathogenic |
| 14015843 | CRB1 | Het | chr1:197390125–197397136 | 2 | NM_201253.2: c.(1171+1_1172–1)_(2676+1_2677–1)del | Likely pathogenic |
| 13011434* | EYS | Hom | chr6:64708964–64709081 | 1 | NM_001142800.1: c.(6725+1_6726–1)_(6834+1_6835–1)del | Likely pathogenic |
| 15005668* | CERKL | Het | chr2:182468559–182521738 | 2 | NM_001030311.2: c.(?_−1)_(481+1_482–1)del | Likely pathogenic |
| 15010867* | CNGB3 | Het | chr8:87655974–87656919 | 2 | NM_019098.4: c.(990+1_991–1)_(1178+1_1179–1)del | Likely pathogenic |
| 15005008* | NMNAT1 | Het | chr1:10035645–10035838 | 1 | NM_001297778.1: c.(115+1_116–1)_(299+1_300–1)del | Likely pathogenic |
| 12008422* | USH2A | Het | chr1:216172225–216173909 | 2 | NM_206933.2: c.(6325+1_6326–1)_(6657+1_6658–1)del | Likely pathogenic |
| 14017566 | CERKL | Het | chr2:182521491–182521738 | 1 | NM_001030311.2: c.(?_−1)_(238+1_239–1)del | Likely pathogenic |
| 15001263* | USH2A | Het | chr1:216011328–216011450 | 1 | NM_206933.2: c.(9258+1_9259–1)_(9371+1_9372–1)del | Likely pathogenic |
| 15004859* | RPGRIP1 | Het | chr14:21798403–21798551 | 1 | NM_020366.3: c.(3099+1_3100–1)_(3238+1_3239–1)del | Likely pathogenic |
| 13001147 | EYS | Het | chr6:64791745–64791900 | 1 | NM_001142800.1: c.(6424+1_6425–1)_(6571+1_6572–1)del | Likely pathogenic |
| 13006640 | LRP5 | Het | chr11:68178900–68179093 | 1 | NM_002335.2: c.(2318+1_2319–1)_(2503+1_2504–1)del | Likely pathogenic |
| 14010419 | CNGB1 | Hom | chr16:57937722–57946903 | 4 | NM_001297.4: c.(2304+1_2305–1)_(2794+1_2795–1)del | Likely pathogenic |
| 12014502 | CNGB1 | Hom | chr16:57937722–57946903 | 4 | NM_001297.4: c.(2304+1_2305–1)_(2794+1_2795–1)del | Likely pathogenic |
| 14020104 | MAK | Hom | chr6:10819114–10819178 | 1 | NM_001242957.2: c.(101+1_102–1)_(156+1_157–1)del | Likely pathogenic |
| 15010966 | BBS2 | Het | chr16:56544766–56545201 | 2 | NM_031885.3: c.(345+1_346–1)_(534+1_535–1)del | Likely pathogenic |
| 14017272 | BBS4 | Het | chr15:73015130–73017001 | 2 | NM_033028.4:c.(405+1_406–1)_(587+1_588–1)del | Likely pathogenic |
| 14021329 | CDH3 | Het | chr16:68721410–68725834 | 2 | NM_001793.5:c.(1570+1_1571–1)_(2002+1_2003–1)del | Likely pathogenic |
| 15010313 | CLN3 | Het | chr16:28497663–28497976 | 2 | NM_001042432.1:c.(460+1_461–1)_(677+1_678–1)del | Likely pathogenic |
| 14016318 | GRM6 | Het | chr5:178413126–178413759 | 1 | NM_000843.3:c.(1500+1_1501)_(2124+1_2125–1)del | Likely pathogenic |
| 13009597† | IDH3B | Het | chr20:2639084–10394167 | 17 | NM_006899.4:c.(?_−1)_(*1_?)del | Likely pathogenic |
| MKKS | NM_018848.3:c.(?_−1)_(*1_?)del | |||||
| 14009753 | NPHP1 | Het | chr2:110881363–110962550 | 20 | NM_000272.3:c.(?_−1)_(*1_?)del | Likely pathogenic |
| 13013491 | RGR | Het | chr10:86008662–86008804 | 1 | NM_002921.3:c.(236+1_237–1)_(370+1_371–1)del | Uncertain significance |
| 043844 | FSCN2 | Het | chr17:79502074–79502239 | 1 | NM_001077182.2:c.(826+1_827–1)_(983+1_984–1)del | Uncertain significance |
| 14020099 | RP1L1 | Het | chr8:10473951–10480716 | 2 | NM_178857.5:c.(?_−1)_(751+1_752–1)del | Uncertain significance |
| Duplications | ||||||
| 10003406 | USH2A | Het | chr1:215914713–215933190 | 4 | NM_206933.2: c.(11048+1_11 049–1)_(11711+1_11 712–1)dup | Likely pathogenic |
| 13018538‡ | EYS | Hom | chr6:65016859–65016980 | 1 | NM_001142800.1: c.(6078+1_6079–1)_(6191+1_6192–1)dup | Likely pathogenic |
| 14001342 | EYS | Het | chr6:64694272–64709081 | 2 | NM_001142800.1: c.(6725+1_6726–1)_(7055+1_7056–1)dup | Uncertain significance |
| 14017670‡ | PRPF31 | Hom | chr19:54621654–54628040 | 7 | NM_015629.3: c.(?_−1)_(855+1_856–1)dup | Uncertain significance |
| 15007281 | BBS5 | Het | chr2:170336059–170361097 | 12 | NM_152384.2:c.(?_−1)_(*1_?)dup | Uncertain significance |
| 15009450† | RP9 BBS9 | Het | chr7:33134841–33185981 | 7 | NM_203288.1:c.(?_−1)_(*1_?)dup NM_198428.2:c.(?_−1)_(112+1_113–1_?)dup | Uncertain significance |
| 13009597† | ZNF513 C2orf71 EFEMP1 FAM161A | Het | chr2:27600408–62081181 | 23 | NM_144631.5:c.(?_−1)_(*1_?)dup NM_001029883.2:c.(?_−1)_(*1_?)dup NM_001039348.2:c.(?_−1)_(*1_?)dup NM_001201542.1: c.(?_−1)_(*1_?)dup | Uncertain significance |
| 14015751 | NPHP1 | Het | chr2:110881363–110962550 | 20 | NM_000272.3:c.(?_−1)_(*1_?)dup | Likely benign |
| 14018818 | NPHP1 | Het | chr2:110881363–110962550 | 20 | NM_000272.3:c.(?_−1)_(*1_?)dup | Likely benign |
| 15008560 | NPHP1 | Het | chr2:110881363–110962550 | 20 | NM_000272.3:c.(?_−1)_(*1_?)dup | Likely benign |
| 15010871 | CYP4V2 | Het | chr4:187112973–187131800 | 20 | NM_207352.3:c.(?_−1)_(*1_?)dup | Likely benign |
*CNV events reported previously in Ellingford et al,14 Ellingford et al7 or Carss et al18 through alternative techniques and analysis strategies.
†Four copies confirmed.
‡CNV event impacts multiple genes.
Het, heterozygous; hom, homozygous.