ABCMdb

PMID: 26593885

Sciezynska A, Ozieblo D, Ambroziak AM, Korwin M, Szulborski K, Krawczynski M, Stawinski P, Szaflik J, Szaflik JP, Ploski R, Oldak M
Next-generation sequencing of ABCA4: High frequency of complex alleles and novel mutations in patients with retinal dystrophies from Central Europe.
Exp Eye Res. 2015 Nov 22;145:93-99. doi: 10.1016/j.exer.2015.11.011., [PubMed]

Sentences

No. Mutations Sentence Comment

5 ABCA4 p.Val552Ile Our data disprove the pathogenic status of p.V552I and provide more evidence against a causal role of four further ABCA4 variants as drivers of the phenotype under a recessive paradigm. Login to comment 7 ABCA4 p.Val2050Leu [(R152*; V2050L)]. Login to comment 9 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] complex allele, which represents an unusually high level of genetic homogeneity for ABCA4-related diseases. Login to comment 12 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] and/or a truncating ABCA4 mutation always resulted in an early disease onset. Login to comment 32 ABCA4 p.Cys1490Tyr ABCA4 p.Ala1773Val Some of them have a high prevalence in certain ethnic groups, such as p.C1490Y in South Africans (September et al., 2004), p.A1773V in Mexicans (Chacon-Camacho et al., 2013) and a number of other mutations specific for different European populations (Rivera et al., 2000; Valverde et al., 2006; Maugeri et al., 1999; Rosenberg et al., 2007), which underlines the need of genotyping patients of various ethnicities. Login to comment 72 ABCA4 p.Val552Ile Comparison of the odds ratio (OR) for STGD conferred by p.V552I vs. Login to comment 74 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] was performed by BresloweDay test and Tarone's test implemented in the SPSS software package (SPSS Inc. Chicago, IL, USA). Login to comment 80 ABCA4 p.Arg212His ABCA4 p.His423Arg ABCA4 p.Ser2255Ile Thorough search of the literature and four distinct population-derived exome/genome variant databases, including a database of the Polish population showed that four of the ABCA4 variants, i.e. p.R212H, p.H423R, c.6282&#fe;7G>A and p.S2255I have a high frequency (at least 3%) in the general population (Allikmets et al., 1997; Maugeri et al., 1999; Rivera et al., 2000). Login to comment 81 ABCA4 p.His423Arg Additionally, none of the ABCA4 variants occurred more often among patients than control subjects (p > 0.05) and p.H423R was found significantly less prevalent in patients than in control subjects. Login to comment 83 ABCA4 p.Val552Ile In the Polish population another ABCA4 variant, p.V552I, was found with an allele frequency of 1.01%. Login to comment 85 ABCA4 p.Leu541Pro ABCA4 p.Val552Ile Using a statistical approach we compared the OR for STGD associated with the p.V552I (ORp.V552I) with the ORp.[(L541P;A1038V)], conferred by a well-established pathogenic variant p. Login to comment 86 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] (see Section 3.2). Login to comment 87 ABCA4 p.Leu541Pro As we calculated, ORp.V552I &#bc; 1.08 with 95% confidence intervals (CI) from 0.24 to 4.85, while ORp.[(L541P;A1038V)] &#bc; 59.05 with CI from 22.85 to 152.61. Login to comment 89 ABCA4 p.Leu541Pro The statistical significance of the difference between ORp.V552I and ORp.[(L541P;A1038V)] is further supported by BresloweDay test (p &#bc; 5.87E-08) and Tarone's test (p &#bc; 6.02E-08). Login to comment 90 ABCA4 p.Val552Ile Using in silico prediction tools for missense variants, we found that p.V552I was assigned as benign (PolyPhen-2) and tolerated (SIFT) with respect to protein function (data not shown). Login to comment 92 ABCA4 p.Leu541Pro Identification of complex alleles and common ABCA4 mutations The most frequent ABCA4 mutation detected in more than 35% (33/92) of our patients was p.L541P. Login to comment 93 ABCA4 p.Ala1038Val Except for two patients the mutation was always accompanied by p.A1038V. Login to comment 95 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] complex allele is well established, co-occurrence of both changes within one haplotype has been verified for selected cases, in which family samples were available for the study. Login to comment 97 ABCA4 p.Val2050Leu [(R152*; V2050L)] is a novel one. Login to comment 99 ABCA4 p.Gly1961Glu ABCA4 p.Thr1253Met The third ABCA4 complex allele contained the previously reported p.T1253M present in cis with p.G1961E (Paloma et al., 2001). Login to comment 101 ABCA4 p.Gly1961Glu ABCA4 p.Gly1961Glu ABCA4 p.Thr1253Met [(T1253M; G1961E)] complex allele, the p.G1961E mutation was identified in 21 other unrelated probands, which makes it the second most frequent disease-causing ABCA4 change in our patients. Login to comment 102 ABCA4 p.Gln1412* The third most frequent ABCA4 mutation is p.Q1412*, which was identified in 10 patients (Table 2, Supplementary Tables S1 and S2). Login to comment 108 ABCA4 p.Met448Lys Three of them, including p.M448K (deemed pathogenic by only one algorithm) were detected in two unrelated patients each, which strongly supports their pathogenic potential. Login to comment 109 ABCA4 p.Trp821Arg The p.W821R mutation resulting from c.2461T>A transversion was previously reported by Lewis et al. (1999), however in both of our patients thymine at position c.2461 was not substituted by adenine but by cytosine (c.2461T>C). Login to comment 124 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] correlated with AO in the direction unexpected for a non-truncating variant (Spearman R &#bc; 0.24, p &#bc; 0.019), suggesting that the effect of p. Login to comment 125 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] was a strong one, more similar to truncating than the non-truncating variants. Login to comment 127 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] thus creating a group of "strong" mutations. Login to comment 130 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] is shown in Fig. 2. Login to comment 139 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] allele, was present in more than 33.7% (31/92) of our patients, which corresponds to at least one fourth (37/143) of all alleles with an identified mutation. Login to comment 141 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] allele frequency of 20.1% (37/184) in our cohort is higher than the 14% (10/70) reported in Hungarian Table 1 Frequency of common ABCA4 variant alleles identified in the study compared with control subjects of European origin. Login to comment 142 ABCA4 p.Arg212His ABCA4 p.Val552Ile ABCA4 p.His423Arg ABCA4 p.Ser2255Ile ABCA4 variant Patients Controls Present study ZGM 1000 Genomes ESP6500 ExAC c.635G>A 2.17% 3.82% 5.17% 3.41% 3.79% p.R212H (4/184) (45/1178) (52/1006) (293/8600) (2791/73,710) p &#bc; 0.39 p &#bc; 0.09 p &#bc; 0.48 p &#bc; 0.34 c.1268A>G 20.11% 29.90% 29.13% 30.94% 29.66% p.H423R (37/184) (354/1184) (293/1006) (2661/8600) (22,085/74,456) p < 0.01 p < 0.0001 p < 0.0001 p < 0.0001 c.6282&#fe;7G>A 4.89% 7.84% 5.86% 6.78% 5.92% splice site mutation (9/184) (93/1186) (59/1006) (583/8600) (4378/74,008) p &#bc; 0.18 p &#bc; 0.73 p &#bc; 0.39 p &#bc; 0.67 c.6764G>T 2.17% 4.41% 4.57% 4.65% 3.77% p.S2255I (4/184) (52/1178) (46/1006) (400/8600) (2802/74,338) p &#bc; 0.23 p &#bc; 0.16 p &#bc; 0.16 p &#bc; 0.35 c.1654G>A 1.09% 1.01% 0.10% 0.37% 0.37% p.V552I (2/184) (12/1188) (1/1006) (32/8600) (273/74,448) p &#bc; 1 p &#bc; 0.06 p &#bc; 0.34 p &#bc; 0.32 ZGM: exome data for the Polish population; 1000 Genomes: 1000 Genomes Project (http://www.1000genomes.org/); ESP6500: NHLBI GO Exome Sequencing Project (http:// evs.gs.washington.edu/EVS/); ExAC: Exome Aggregation Consortium (http://exac.broadinstitute.org/); The number of variant and total alleles detected is given in brackets. Login to comment 147 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] (37/184) (5/1178) p < 0.0001 c. Login to comment 149 ABCA4 p.Val2050Leu [(R152*; V2050L)] (8/184) (1/1172) p < 0.0001 c. Login to comment 151 ABCA4 p.Gly1961Glu ABCA4 p.Thr1253Met [(T1253M; G1961E)] (1/184) x x ZGM: exome data for the Polish population; The number of mutant and total alleles detected is given in brackets; x e no ABCA4 diseases-associated variant detected. Login to comment 158 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] has been so far regarded as a founder mutation of mostly German origin (Hargitai et al., 2005; Rivera et al., 2000). Login to comment 160 ABCA4 p.Ala1038Val ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro ABCA4 p.Leu541Pro [(L541P; A1038V)] allele among our patients was paralleled by a relatively high frequency of p.L541P- and p.A1038V-containing alleles in the Polish population. Login to comment 161 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro To dissect the pathogenic potential of p.L541P and p.A1038V, both mutations were examined independently. Login to comment 163 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro Subsequent functional studies in transgenic frogs have demonstrated that the ABCA4 protein processing is affected by p.L541P but not by p.A1038V. Login to comment 164 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro A mislocalization of the p.L541P mutant in the rod inner segments and correct localization of p.A1038V to rod outer segments were detected. Login to comment 165 ABCA4 p.Leu541Pro The results suggested that p.L541P is the major disease-causing mutation as it prevents the ABCA4 protein from reaching its proper physiological compartment and produces a functionally null allele (Wiszniewski et al., 2005). Login to comment 167 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] had a strong impact on the age of disease onset in our patients. Login to comment 170 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] was almost three times earlier (7.8 vs. 23.7 years) than in patients with other missense or with no detectable ABCA4 mutations (data not shown). Login to comment 172 ABCA4 p.Val2050Leu [(R152*; V2050L)] was of immense importance for making a proper molecular diagnosis. Login to comment 173 ABCA4 p.Val2050Leu ABCA4 p.Arg152* A patient carrying exclusively p.R152* and p.V2050L, could have been easily misinterpreted as a compound heterozygote. Login to comment 174 ABCA4 p.Val2050Leu ABCA4 p.Arg152* Co-occurrence of p.R152* and p.V2050L has been previously noted in Polish patients (M. Krawczynski, unpublished data) and now the existence of the novel complex allele has been definitely confirmed. Login to comment 191 ABCA4 p.Arg1129Leu For instance, the most prevalent disease-associated allele p.R1129L in Spanish (Riveiro-Alvarez et al., 2013) Fig. 2. Login to comment 193 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] and/or truncating mutations (standard error (SE), confidence interval (CI), number of patients (n)). Login to comment 195 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] and/or truncating mutations on disease age of onset (AO). Login to comment 197 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] and/or truncating mutations One p. Login to comment 198 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] and/or truncating mutations Two p. Login to comment 199 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro [(L541P; A1038V)] and/or truncating mutations Total no. Login to comment 201 ABCA4 p.Asn965Ser of patients Early 13 (50%) 27 (60%) 21 (100%) 61 Late 13 (50%) 18 (40%) 0 (0%) 31 Early &#fe; late 26 45 21 92 or p.N965S in Danish patients (Rosenberg et al., 2007) have not been detected in any of our patients. Login to comment 202 ABCA4 p.Gly1961Glu One of the major ABCA4 mutations identified among patients from different population is the p.G1961E (Cella et al., 2009) that was found in Slovenian (Jaakson et al., 2003), Italian (Fumagalli et al., 2001; Jaakson et al., 2003), German (Rivera et al., 2000), Dutch (Jaakson et al., 2003) and Spanish (Valverde et al., 2006) patients with an allele frequency ranging from 21% to 6.5%, respectively. Login to comment 203 ABCA4 p.Gly1961Glu The frequency of the p.G1961E-carrying allele, the second most common mutation in Polish patients (12.5%), fits almost exactly in the middle of the range. Login to comment 205 ABCA4 p.Val552Ile In our study p.V552I was regarded as a non-pathogenic variant. Login to comment 207 ABCA4 p.Val552Ile In the German population the p.V552I-containing alleles were detected in control individuals (0.5%) but not in STGD patients (Rivera et al., 2000). Login to comment 208 ABCA4 p.Val552Ile Given the prevalence of p.V552I in Spanish, Polish and German populations, this variant should represent one of the major ABCA4 mutations among the respective patient groups. Login to comment 209 ABCA4 p.Gly1961Glu As it is clearly not the case, among the most frequent ABCA4 mutations are p.G1961E and p. Login to comment 210 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro ABCA4 p.Val552Ile ABCA4 p.Arg1129Leu [(L541P; A1038V)] in the German and Polish patients, and p.R1129L in the Spanish patients, the data cast considerable doubt on the pathogenic potential of p.V552I. Login to comment 211 ABCA4 p.Val552Ile We have detected p.V552I in two patients (STGD and CRD) and in both cases the accompanying second ABCA4 mutation was lacking. Login to comment 212 ABCA4 p.Val552Ile It is interesting to know that in other publications p.V552I was also identified as a solitary ABCA4 mutation (Eisenberger et al., 2013; Michaelides et al., 2007), which was not sufficient for a molecular diagnosis of an ABCA4-associated disease. Login to comment 213 ABCA4 p.Val552Ile Finally, comparison of the OR for STGD associated with the p.V552I with the OR for p. Login to comment 214 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro ABCA4 p.Val552Ile [(L541P; A1038V)] showed a strong statistically significant difference indicating that p.V552I is either non-pathogenic or has a very low penetrance. Login to comment