ABCMdb

PMID: 19028736

Aguirre-Lamban J, Riveiro-Alvarez R, Maia-Lopes S, Cantalapiedra D, Vallespin E, Avila-Fernandez A, Villaverde-Montero C, Trujillo-Tiebas MJ, Ramos C, Ayuso C
Molecular analysis of the ABCA4 gene for reliable detection of allelic variations in Spanish patients: identification of 21 novel variants.
Br J Ophthalmol. 2009 May;93(5):614-21. Epub 2008 Nov 21., [PubMed]

Sentences

No. Mutations Sentence Comment

31 ABCA4 p.Ile2047Asn Restriction assays The presence of one novel missense mutation (p.Ile2047Asn) was analysed in 100 control chromosomes by conventional PCR amplification, restriction enzyme digestion (37uC overnight) with TaqI and analyses of the restriction fragments in a 3% agarose gel. Login to comment 42 ABCA4 p.Cys2137Tyr ABCA4 p.Ala762Glu ABCA4 p.Ile2047Asn Three missense changes were detected (p.Ala762Glu, p.Ile2047Asn and p.Cys2137Tyr) in patients but not in the 100 ethnically matched control chromosomes. Login to comment 43 ABCA4 p.Ile2142Val We identified the heterozygous p.Ile2142Val change in one out of 100 control chromosomes. Login to comment 45 ABCA4 p.Gly1977Ser ABCA4 p.Trp1724Cys Moreover, two previously described mutations [c.4537delC and p.Trp1724Cys], not included in the array by the time of the screening, and one false negative [p.Gly1977Ser] were detected (1/62; 1.6%). Login to comment 47 ABCA4 p.Val552Ile Additionally, one novel change in exon 12 (p.Val552Ile) was found in one STGD patient by means of the dHPLC technique. Login to comment 55 ABCA4 p.Arg1129Leu Despite the high allelic heterogeneity and the large amount of novel ABCA4 variants detected in this screening, the p.Arg1129Leu mutation was found to be the most frequent disease-associated allele (5/62; 8%). Login to comment 62 ABCA4 p.Ala1598Asp In the patient belonging to family ARDM-197, the chip detected the p.Ala1598Asp mutation. Login to comment 64 ABCA4 p.Trp1724Cys Interestingly, the p.Trp1724Cys mutation was detected by dHPLC in this family. Login to comment 65 ABCA4 p.Gly1977Ser In contrast, the dHPLC technique led to the detection of the p.Gly1977Ser mutation in the patient from the family ARDM-183, but the chip did not detect it (false negative). Login to comment 68 ABCA4 p.Ala1598Asp As we currently confirm these results by sequencing, a false positive [p.Ala1598Asp] was identified. Login to comment 76 ABCA4 p.Gly1961Glu Moreover, both patients presented the p.Gly1961Glu mutation, which is considered an allele of moderate effect.7 Figure 1 Chromatograms showing differences between the wild-type (down) and mutated profile (up). Login to comment 80 ABCA4 p.Gly1961Glu ABCA4 p.Gly1961Glu ABCA4 p.Gly1961Glu ABCA4 p.Thr1019Met ABCA4 p.Thr1019Met ABCA4 p.Arg2107His ABCA4 p.Gly1977Ser ABCA4 p.Gly1977Ser ABCA4 p.Arg602Trp ABCA4 p.Arg1640Gln ABCA4 p.Leu2027Phe ABCA4 p.Ala1598Asp ABCA4 p.Pro1486Leu ABCA4 p.Thr901Ala ABCA4 p.Val931Met ABCA4 p.Arg1129Leu ABCA4 p.Arg1129Leu ABCA4 p.Arg1129Leu ABCA4 p.Arg1129Leu ABCA4 p.Arg1129Leu ABCA4 p.Cys2137Tyr ABCA4 p.Trp1724Cys ABCA4 p.Ala762Glu ABCA4 p.Val1433Ile ABCA4 p.Val1433Ile ABCA4 p.Ile156Val ABCA4 p.Ile2047Asn ABCA4 p.Arg1108His Clinical science Br J Ophthalmol 2009;93:614-621. doi:10.1136/bjo.2008.145193 Table 1 Clinical findings of the Spanish patients with Stargardt disease (STGD), autosomal recessive cone-rod dystrophy and autosomal recessive retinitis pigmentosa Pedigree Age (years) Age (years) of onset Visual acuity Diagnosis Allele 1 Allele 2 Segregation OD OS Nucleotide changes (exons) Amino acid change Nucleotide changes (exons) Amino acid change ARDM-135 42 24 0.4 0.6 STGD c.5882G.A(42) p.Gly1961Glu c.1029_1030insT(8) p.Asn344fsX NP ARDM-240 15 13 0.2 0.16 STGD c.5882G.A(42) p.Gly1961Glu c.2285C.A(15) p.Ala762Glu Yes ARDM-225 32 25 0.25 0.50 STGD c.5882G.A(42) p.Gly1961Glu c.6559C.T(48) p.Gln2187X Yes ARDM-164 21 11 NA STGD c.3386G.T(23) p.Arg1129Leu c.700C.T(6) p.Gln234X Yes ARDM-162 50 16 0.1 0.1 STGD c.3386G.T(23) p.Arg1129Leu ND ND Yes ARDM-198 27 19 0.1 0.1 STGD c.3386G.T(23) p.Arg1129Leu ND ND NP ARDM-125 31 9 0.3 0.4 STGD c.3211insGT(22) FS p.KNLFA1876dup Yes ARDM-158 24 9 0.2 0.2 STGD c.3211insGT(22) FS c.4537delC(30) p.Gln1513fsX1525 NP ARDM-165 40 30 NA STGD c.3211insGT(22) FS ND ND NP ARDM-167 49 23 0.05 0.05 STGD c.3211insGT(22) FS ND ND NP ARDM-146 32 13 0.06 0.1 STGD c.3056C.T(21) p.Thr1019Met c.6140T.A(44) p.Ile2047Asn Yes ARDM-40 46 9 0.1 0.1 STGD c.3056C.T(21) p.Thr1019Met c.3943C.T(27) p.Gln1315X Yes ARDM-90 26 8 Hand moving STGD c.5929G.A (43) p.Gly1977Ser IVS21-2A.T Yes ARDM-181 57 16 0.1 0.09 STGD c.3323G.A (22) p.Arg1108His IVS38+5G.A Yes ARDM-197 35 15 0.1 0.1 STGD c.4793C.A(34) (false +) p.Ala1598Asp (false +) c.5172G.T(36) p.Trp1724Cys Yes ARDM-183 63 55 0.150 0.175 STGD c.6079C.T(44) p.Leu2027Phe c.5929G.A(43) (false -) p.Gly1977Ser (false -) NP ARDM-38 35 6 0.01 0.02 STGD c.1804C.T(13) p.Arg602Trp c.4739delT(33) p.Leu1580fs Yes ARDM-163 48 32 0.01 0.32 STGD c.4457C.T(30) p.Pro1486Leu ND ND Yes ARDM-166 42 39 NA STGD c.6320G.A(46) p.Arg2107His ND ND Yes ARDM-222 26 23 NA STGD c.2791G.A(19) p.Val931Met ND ND NP ARDM-160 30 5 0.25 0.1 STGD ND ND ND ND Yes ARDM-173 49 7 NA STGD ND ND ND ND Yes ARDM-205 NA NA NA STGD c.4919G.A(35) p.Arg1640Gln ND ND NP ARDM-247 30 12 0.05 0.1 CRD c.3386G.T(23) p.Arg1129Leu c.6410G.A(47) p.Cys2137Tyr Yes ARDM-99 59 46 0.05 0.05 CRD c.4297G.A(29) p.Val1433Ile ND ND NP ARDM-131 27 15 0.9 0.7 CRD c.2701A.G(18) p.Thr901Ala ND ND Yes ARDM-100 28 4 0.2 0.16 CRD ND ND ND ND Yes ARDM-142 30 25 0.8 0.5 CRD ND ND ND ND Yes RP-773 38 20 0.05 0.05 RP c.33N86G.T(23) p.Arg1129Leu ND ND NP RP-959 53 10 0.1 0.1 RP c.466A.G(5) p.Ile156Val ND ND Yes RP-1058 37 6 0.2 0.6 RP c.4297G.A(29) p.Val1433Ile ND ND NP Twenty-seven out of 31 subjects were found to be compound heterozygous for mutations in the ABCA4 gene detected by microarray. Login to comment 96 ABCA4 p.Val552Ile Table 2 Synonymous and non-synonymous codon variants and intronic variants in the ABCA4 gene Exon Nucleotide change Sequence change Reference 3 c.264 A.T p.Gly88Gly This study IVS2-27G.A This study IVS3+26 A.G 9 15 18 IVS6-32 T.C 9 15 8 c.1029T.C p.Asn343Asn This study 10 c.1299A.G p.Glu433Glu This study 12 c.1654G.A p.Val552Ile This study IVS13+16G.A This study 19 c.2832A.G p.Pro944Pro This study 20 c.2964C.T p.Leu988Leu 18 23 c.3507G.A p.Gln1169Gln This study IVS28+43G.A 24 IVS43-16G.A 25 IVS48+39 T.A This study IVS48-3T.C 15 18 Novel changes are shown in bold. Login to comment 99 ABCA4 p.Arg1129Leu Clinical science Br J Ophthalmol 2009;93:614-621. doi:10.1136/bjo.2008.145193 The p.Arg1129Leu mutation was found to be the most frequent missense variant, representing 8% (5/62) of the total pathogenic alleles (table 1). Login to comment 100 ABCA4 p.Arg1129Leu ABCA4 p.Arg1129Leu ABCA4 p.Cys2137Tyr In previous studies of the Spanish population, the p.Arg1129Leu variant was identified as a major mutant allele which accounted for 24% of the STGD alleles.14 This variant has been postulated to have a moderately severe effect and has predominantly been associated with a STGD phenotype.14 In contrast, the prevalence of this mutation in patients from North America was less than 1%.15 Interestingly, we identified one 30-year-old patient (ARDM-247), double heterozygous for the p.Arg1129Leu and p.Cys2137Tyr alleles, who presented a CRD phenotype. Login to comment 101 ABCA4 p.Cys2137Tyr This p.Cys2137Tyr change was located more towards the amino terminus. Login to comment 102 ABCA4 p.Arg1129Leu ABCA4 p.Cys2137Tyr Moreover, in other study, the results showed that the changes located in this zone appear to result in altered processing of the protein and to be associated with an earlier onset of disease.16 The p.Cys2137Tyr change in combination with the p.Arg1129Leu allele produced a CRD phenotype. Login to comment 103 ABCA4 p.Cys2137Tyr Therefore, we speculate that the novel p.Cys2137Tyr variant could be a severe allele which is modifying the patient`s phenotype. Login to comment 104 ABCA4 p.Gly1961Glu The second most prevalent missense disease-associated allele was p.Gly1961Glu (3/62; 4.8%), presenting a lower frequency than other European populations.10 This mutation was found in three STGD patients, two of them presenting at least one putative null mutation (c.1030insT and p.Gln2187X), who presented symptoms at the age of 24-25 years. Login to comment 105 ABCA4 p.Gly1961Glu Thus, we could suspect a moderate effect for the p.Gly1961Glu allele, as previously reported.7 In relation to null alleles, the most frequent mutation was c.3211insGT, identified in four independent STGD families out of 31 (6.4%). Login to comment 112 ABCA4 p.Arg212Cys Interestingly, Paloma et al19 described one CRD case, compound heterozygous for the c.3211insGT and p.Arg212Cys variants, showing symptoms at the age of 9. Login to comment 113 ABCA4 p.Arg212Cys Interestingly, Paloma et al19 described one CRD case, compound heterozygous for the c.3211insGT and p.Arg212Cys variants, showing symptoms at the age of 9. Login to comment 123 ABCA4 p.Val1433Ile In these cases, the total inactivation of the splice site is unlikely, although these changes could alter the splicing of corresponding exon, creating cryptic sites, thus producing a longer protein.21 In two patients diagnosed as having arCRD and arRP phenotypes respectively, we identified the missense p.Val1433Ile mutation, located in the second transmembrane domain. Login to comment 124 ABCA4 p.Val1433Ile In these cases, the total inactivation of the splice site is unlikely, although these changes could alter the splicing of corresponding exon, creating cryptic sites, thus producing a longer protein.21 In two patients diagnosed as having arCRD and arRP phenotypes respectively, we identified the missense p.Val1433Ile mutation, located in the second transmembrane domain. Login to comment 125 ABCA4 p.Ile156Val Family RP-959 was previously analysed by the genotyping microarray, and the p.Ile156Val allele was detected.20 This variant has been associated with the STGD phenotype. Login to comment 126 ABCA4 p.Ile156Val Family RP-959 was previously analysed by the genotyping microarray, and the p.Ile156Val allele was detected.20 This variant has been associated with the STGD phenotype. Login to comment 137 ABCA4 p.Val552Ile Given an estimated prevalence of STGD (1:10 000), the Hardy-Weinberg equilibrium would indicate that the heterozygous state can be expected in about 1/50.24 So many variants, such as p.Val552Ile, could be really a mutation found in normal population. Login to comment 138 ABCA4 p.Val552Ile Given an estimated prevalence of STGD (1:10 000), the Hardy-Weinberg equilibrium would indicate that the heterozygous state can be expected in about 1/50.24 So many variants, such as p.Val552Ile, could be really a mutation found in normal population. 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