Seven hundred and fifty-six patients (98%) had inherited retinal diseases (IRD), and the remaining 17 (2%) had other etiologies, such as optic atrophy (6) and coloboma (4). Four hundred and eighty-three patients (62%) had a diagnosis of non-syndromic retinitis pigmentosa (RP), 41 (5%) of early-onset severe retinal dystrophy (EOSRD), 40 (5%) of Stargardt disease, 39 (5%) of Usher syndrome, 38 (5%) of macular dystrophy (MD), 19 (2%) of cone-rod dystrophy (CORD), 19 (2%) of choroideremia (CHM), and the remaining patients had less frequent conditions (Fig. ​(Fig.22 and Supplementary Table 1).

TABLE S2 Description and classification of variants observed to change classifications over time or between laboratories depicted in Figure 4. Separate tabs are present for different types of variant classifications changes: (a) changes from uncertain to pathogenic or benign, (b) changes from pathogenic to uncertain or benign, (c) changes from benign to pathogenic, (d) changes without clear trend.

Table 1shows the age, sex, vision at the most recent visit, fluorescein angiographic findings, and clinical phenotype for 29 patients with a possible disease-causing mutation in the ABCRgene. Each of the 29 patients were from different pedigrees. However, the mother of patient 12 and the father of patient 29 were also found to have compound heterozygous sequence variations in the ABCRgene.

Screening of reported pathogenic variants in ABCA4 for Stargardt (STGD) The disease prevalence of STGD is estimated as 1 in 10000 individuals4. It has been estimated that about 70% of STGD patients carry variants in ABCA45. Therefore, this represents the scenario of a recessive disease with a relatively homogeneous genetic cause. We screened 945 reported pathogenic variants in ABCA4 genes collected in HGMD. Among them, 11 variants are likely benign, as their population AF in is higher than 0.7% (1/20000‾‾‾‾‾‾‾‾√)<math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M11"><mrow><mrow><mo>(</mo><mrow><msqrt><mrow><mn>1</mn><mo>/</mo><mn>20000</mn></mrow></msqrt></mrow><mo>)</mo></mrow></mrow></math>, the cutoff based on STGD disease prevalence, therefore were excluded from further analysis. The remaining 934 variants were subjected to our test model. As a result, 26 variants with the AF in the range of 0.46% to 0.03% were identified as likely benign (Binomial test1, Bonferroni correction p-value ≤ 0.05/934 and test2 Bonferroni correction p-value > 0.05/934) (Figure 3A).

To overcome these limitations, we designed a genotyping microarray (gene chip) for ABCR that includes all approximately 400 disease-associated and other variants currently described, enabling simultaneous detection of all known ABCR variants.

Thirty-Three Truncated and 98 Amino Acid–Changing Variants in the ABCA4 Gene

ABCA4STGD1H2128R

Additional file 2: All supplemental tables cited in the text. Enclosed data include data set meta-information, CAP scores for all drug-related genes, DRP scores for all drugs, CAP and DRP differences between populations, and a comparison between allele frequencies in the studied data set and CPIC guidelines. (XLSX 776 kb)13073_2017_502_MOESM2_ESM.xlsx (776K)GUID: B02AAF40-A613-411F-A471-357C45A33F82

Supplementary data. bjophthalmol-2018-312064supp004.pdf

To determine the overall CF for all AR-IRD–causing mutations in different subpopulations, we initially calculated CF for each of the 10,044 likely pathogenic variants in each subpopulation (SI Appendix, Tables S2 and S3).

In humans, clinical studies have implicated mutations in 19 of the 48 known ABC transporters in diseases such as cystic fibrosis and adrenoleukodystrophy.

STGD in 48 patients (55%) was explained by recessive ABCA4 mutations (supplemental table S2). Only 22 patients could be solved using previously known STGD causing mutations. However, we identified 35 novel mutations in ABCA4 contributing to the diagnosis of 25 STGD patients. This contained 10 novel mutations leading to amino acid substitutions already known to cause disease and mutations known to cause diseases other than STGD. In addition, we identified 13 novel nonsense mutations. The remaining 12 novel mutations are well justified, and novel mutations were either completely absent or extremely rare in controls.

Table S2. ABCA4 variant categorization:

We identified 1319 distinct causative variants (Supplementary Table S1) in 132 different genes (Table ​(Table3).3). The ten most commonly mutated genes were ABCA4 (n = 535 [26.3%]), USH2A (n = 228 [11.2%]), RPGR (n = 102 [5%]), CHM (n = 72 [3.5%]), RHO (n = 72 [3.5%]), MYO7A (n = 69 [3.4%]), CRB1 (n = 55 [2.7%]), RPE65 (n = 40 [2%]), RP1 (n = 37 [1.8%]), and GUCY2D (n = 34 [1.7%]) (Table ​(Table3,3, Fig. 2a). The other 122 genes had a lower contribution to IRDs. One hundred genes were mutated in 15 patients or less and were collectively responsible for disease pathogenesis in 18% of the solved cohort (Fig. 2a, Table ​Table3).3). Thirty-two genes were mutated in only one patient (Table ​(Table3).3). Mutations in the mitochondrial DNA accounted for 2.1% of the cohort and were implicated almost exclusively in the pathogenesis of LHON.

See Supplementary Table S2 for a complete genotypic glossary of the cohort.

See Supplementary Table S2 for a complete genotypic glossary of the cohort.