ABCMdb

PMID: 15494742

Klevering BJ, Yzer S, Rohrschneider K, Zonneveld M, Allikmets R, van den Born LI, Maugeri A, Hoyng CB, Cremers FP
Microarray-based mutation analysis of the ABCA4 (ABCR) gene in autosomal recessive cone-rod dystrophy and retinitis pigmentosa.
Eur J Hum Genet. 2004 Dec;12(12):1024-32., [PubMed]

Sentences

No. Mutations Sentence Comment

3 ABCA4 p.Gly618Glu ABCA4 p.Glu161Lys ABCA4 p.Pro597Ser ABCA4 p.Arg24Cys Single-strand conformation polymorphism (SSCP) analysis and subsequent DNA sequencing revealed four novel missense mutations (R24C, E161K, P597S, G618E) and a novel 1-bp deletion (5888delG). Login to comment 43 ABCA4 p.Arg24Cys The presence of R24C (70C4T) was analyzed using HinfI restriction fragment analysis of PCR-amplified exon 2. Login to comment 45 ABCA4 p.Glu161Lys E161K (481G4A) was tested using MboII, which cuts the normal PCR product of exon 5 (240 nts) into three fragments (170, 40, 30 nts) and the mutant PCR product into two fragments (200 and 40 nts). Login to comment 46 ABCA4 p.Pro597Ser The P597S (1789C4T) mutation was analyzed using AlwI, which cuts the normal PCR product of exon 13 (280 nts) into fragments of 100, 90, 60, and 30 nts and the mutant PCR product into fragments of 160, 90, and 30 nts. Login to comment 47 ABCA4 p.Gly618Glu An amplification-refractory mutation-specific (ARMS) assay48 was performed to test G618E (1853G4A). Login to comment 54 ABCA4 p.Leu541Pro Although the segregation of the L541P and A1038 V mutations could not be tested in the respective families, we have grouped them as complex alleles, based on previous observations that these alterations invariably occur in cis configuration in German patients with CRD (Table 1).5,34 Indeed, all four patients carrying these variants (14488, 14752, 16242, and 16582) were from Germany. Login to comment 55 ABCA4 p.Gly618Glu ABCA4 p.Glu161Lys ABCA4 p.Pro597Ser ABCA4 p.Arg24Cys Likewise, the 2588C and 2828A variants are presumed to be located in the same allele since the 2588C allele in previous studies was always found together with 2828A (see Discussion).33,49 Next, we employed SSCP analysis and DNA sequencing in patients with one ABCA4 mutation and identified five novel ABCA4 mutations that were not present on the microarray, that is, R24C, E161K, P597S, G618E, and 5888delG. Login to comment 57 ABCA4 p.Ala1038Val ABCA4 p.Ala1038Val ABCA4 p.Ala1038Val ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro ABCA4 p.Leu541Pro ABCA4 p.Leu541Pro ABCA4 p.Leu541Pro ABCA4 p.Arg1640Trp ABCA4 p.Arg1640Trp Table 1 ABCA4 sequence variants in CRD patients CRD patient number Inheritance Allele 1 Allele 2 Mutations segregateNucleotide change Effect Nucleotide change Effect 12608 Isolated IVS38-10T4C Unknowna IVS38-10T4C Unknowna Yes 14488 Isolated 1622T4C; 3113C4T L541P; A1038V Not identified NA 14750 Isolated 4918C4T R1640W Not identified NA 14752 Isolated 1622T4C; 3113C4T L541P; A1038V IVS38-10T4C Unknowna ? Login to comment 59 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro ABCA4 p.Val767Asp 15428 Isolated 1622T4C; 3113C4T L541P; A1038V 2300T4A V767D ? Login to comment 60 ABCA4 p.Arg18Trp ABCA4 p.Arg24Cys 15429 Isolated 52C4T R18W 70C4T R24C ? Login to comment 61 ABCA4 p.Gly1961Glu ABCA4 p.Gly863Ala ABCA4 p.Gly863Ala ABCA4 p.Arg943Gln ABCA4 p.Arg943Gln 15680 Isolated 5882G4A G1961E Not identified NA 15730 Isolated 2588G4C; 2828G4A DG863/G863A; R943Q 2588G4C; 2828G4A DG863/G863A; R943Q ? Login to comment 62 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro ABCA4 p.Ala1794Asp ABCA4 p.Pro597Ser 16242 Isolated 1622T4C; 3113C4T L541P; A1038V Not identified NA 16243 Isolated 5381C4A A1794D 1789C4T P597S ? Login to comment 63 ABCA4 p.Ala1038Val ABCA4 p.Leu541Pro ABCA4 p.Glu1087Lys ABCA4 p.Glu161Lys 481G4A E161K 16569 Aut. rec. 3259G4A E1087K Not identified NA 16582 Isolated 1622T4C; 3113C4T L541P; A1038V IVS38-10T4C Unknowna ? Login to comment 64 ABCA4 p.Gly65Glu 16583 Isolated 194G4A G65E 768G4T Splice site ? Login to comment 65 ABCA4 p.Gly863Ala ABCA4 p.Gly863Ala ABCA4 p.Arg943Gln ABCA4 p.Arg943Gln ABCA4 p.Val1433Ile ABCA4 p.Gly618Glu 16697 Isolated 2588G4C; 2828G4Ab DG863/G863A; R943Q 1853G4A; 4297G4A G618E; V1433I Yes 16755 Isolated 2588G4C; 2828G4A DG863/G863A; R943Q Not identified NA 16887 Isolated 768G4T Splicing IVS38-10T4C Unknowna Yes 17906 Aut. rec. 768G4T Splicing Not identified NA a Mutation which is presumed to be in linkage disequilibrium with unknown pathologic ABCA4 mutation. Login to comment 77 ABCA4 p.Val1433Ile ABCA4 p.Gly618Glu In family members of patient 16697, the 2588C; 2828A variants segregated from the G618E; V1433I mutations. Login to comment 101 ABCA4 p.Asp2177Asn ABCA4 p.Asp2177Asn ABCA4 p.Ala1038Val ABCA4 p.Gly863Ala ABCA4 p.Leu541Pro ABCA4 p.Val2050Leu ABCA4 p.Arg943Gln Likewise, the known Table 2 ABCA4 sequence variants in RP patients RP patient number Inheritance Allele 1 Allele 2 Nucleotide change Effect Nucleotide change Effect 9304 Aut. Rec. 2588G4C; 2828G4Aa DG863/G863A; R943Q 5888delG R1963fs 9444 Aut. Rec. 6529G4A D2177N Not identified 9545 Isolated 6529G4A D2177N Not identified 14753 Isolated 1622T4C; 3113C4T L541P; A1038V Not identified 17597 Isolated 6148G4C V2050L Not identified a Polymorphic variants 4203A, 5603 T, and 5682C also present. Login to comment 114 ABCA4 p.Val2050Leu ABCA4 p.Val1433Ile For two conservative missense mutations (V1433I and V2050L), the pathologic nature can be questioned. Login to comment 131 ABCA4 p.Asp2177Asn In two RP patients, we identified the D2177N mutation heterozygously. Login to comment 132 ABCA4 p.Asp2177Asn The D2177N mutation has never been found in patients with STGD1 but was found to be associated with age-related macular degeneration at a statistically significant level.25 As shown by Sun et al,50 this mutation, contrary to other mutations, results in increased ATP hydrolysis when compared to the wild-type protein. Login to comment 133 ABCA4 p.Asp2177Asn These data do not allow us to draw a definitive conclusion regarding the pathologic nature of D2177N. Login to comment 143 ABCA4 p.Gly1961Glu ABCA4 p.Asp2177Asn ABCA4 p.Ala1038Val ABCA4 p.Gly863Ala ABCA4 p.Leu541Pro ABCA4 p.Arg18Trp ABCA4 p.Arg1640Trp ABCA4 p.Val2050Leu ABCA4 p.Val767Asp ABCA4 p.Glu1087Lys ABCA4 p.Arg943Gln ABCA4 p.Ala1794Asp ABCA4 p.Val1433Ile ABCA4 p.Gly618Glu ABCA4 p.Gly65Glu ABCA4 p.Glu161Lys ABCA4 p.Pro597Ser ABCA4 p.Arg24Cys Given this clinical presentation and the fact that homozygous null mutations were not found Table 5 Functional assessment of missense (A) and splice site (B) mutations (A) Missense mutation Nature of amino-acid change Effect on ABCR functionRef R18W Nonconservative Unknown R24C Nonconservative Unknown; adjacent to first transmembrane domain G65E Nonconservative Unknown E161K Nonconservative Unknown L541P Conservative Decreased ATP binding and ATPase activity50 P597S Nonconservative Unknown G618E Nonconservative Unknown V767D Nonconservative Decreased ABCR expression10 G863A Nonconservative Decreased ATPase activity50, 51 R943Q Nonconservative Decreased ATPase activity51 A1038V Conservative Decreased ATP binding and ATPase activity50 E1087K Nonconservative Decreased ATP binding50 V1433I Conservative Unknown R1640W Nonconservative Unknown A1794D Nonconservative Introduction charged aa in 10th transmembrane domain G1961E Nonconservative Decreased ATP binding and ATPase activity 50 V2050L Conservative Unknown D2177N Nonconservative Increased ATPase activity50 (B) Splice site mutation Effect on mRNARef Predicted effect on ABCR protein 768G4T Nonsense-mediated decay33 No protein IVS36+2T4C Unknown Truncation of exon 36 resulting in V1673fs? 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