ABCMdb

PMID: 18246475

Karjalainen MK, Haataja R, Hallman M
Haplotype analysis of ABCA3: association with respiratory distress in very premature infants.
Ann Med. 2008;40(1):56-65., [PubMed]

Sentences

No. Mutations Sentence Comment

59 ABCA3 p.Glu292Val Selection of SNPs, haplotype prediction, and data analysis Intronic SNPs with a validated minor allele frequency (MAF) >0.1 among Caucasians and all coding SNPs (cSNPs) indicated in the dbSNP database (http://ncbi.nih.gov/SNP/) within the ABCA3 gene in the NCBI entry NT_037887, a novel intronic SNP (320-17GwA) and 875AwT (E292V) were initially screened. Login to comment 81 ABCA3 p.Glu292Val Additionally, a novel SNP (320-17GwA) and a single-base change (875AwT) corresponding to a glutamine-to-valine substitution at amino acid position 292 (E292V) were included in the analysis, as this position has been reported to be frequently mutated in infants suffering from ILD (22). Login to comment 90 ABCA3 p.Leu101Pro ABCA3 p.Glu292Val ABCA3 p.Gln1591Pro ABCA3 p.Leu1552Pro ABCA3 p.Val839Phe SNP rs149532 (corresponding to residue S1372S) was rare (MAF50.02) in our population, and it was thus excluded from further analysis, together with the nonpolymorphic cSNPs (rs28936412, 875AwT, rs13332760, rs28936690, and rs28936691, corresponding to residues L101P, E292V, V839F, L1552P, and Q1591P, respectively). Login to comment 94 ABCA3 p.Leu101Pro ABCA3 p.Glu292Val ABCA3 p.Gln1591Pro ABCA3 p.Leu1552Pro ABCA3 p.Val839Phe SNP No. or position a Alleles (major/minor) Position b Location Affected residue Minor allele frequency tSNPs c Best pairwise r2 value and the corresponding tSNP d rs28936412 T/C 2316029 Exon 5 L101P 0 - 320-17GwA G/A 2314550 Intron 5 0.055 tSNP1 875AwT A/T 2307765 Exon 9 E292V 0 - rs13332547 C/T 2307425 Intron 9 0.093 tSNP2, r2 51 rs13332514 C/T 2307337 Exon 10 F353F 0.093 tSNP2 rs323069 G/C 2304052 Intron 10 0.271 tSNP3 rs323073 C/T 2298761 Intron 10 0.283 tSNP3, r2 50.831 rs323074 G/A 2298314 Intron 11 0.201 tSNP5, r2 50.848 rs323033 A/G 2296546 Intron 11 0.259 tSNP4 rs323040 G/A 2290527 Intron 12 0.168 tSNP5 rs170447 A/G 2289372 Intron 14 0.396 tSNP6, r2 50.832 rs2240523 T/C 2288658 Intron 14 0.381 tSNP6, r2 50.849 rs17183533 A/G 2285389 Intron 18 0.420 tSNP7, r2 50.986 rs13332760 G/T 2279621 Exon 20 V839F 0 - rs313909 C/T 2277994 Intron 21 0.373 tSNP6 rs2014467 A/G 2276395 Intron 22 0.424 tSNP7 rs2238464 G/A 2272578 Intron 26 0.420 tSNP8 rs149532 T/C 2271431 Exon 27 S1372S 0.020 - rs150926 G/C 2270170 Intron 28 0.372 tSNP6, r2 50.975 rs150928 C/T 2268651 Intron 29 0.226 tSNP9 rs28936690 T/C 2268353 Exon 30 L1552P 0 - rs28936691 A/C 2268018 Exon 31 Q1591P 0 - a rs numbers are shown for SNPs with entries in dbSNP. SNPs without entries in dbSNP are numbered from start codon as advised in (34). Login to comment 129 ABCA3 p.Glu292Val ABCA3 p.Gln1591Pro ABCA3 p.Leu1552Pro ABCA3 p.Val839Phe None of the five nonsynonymous cSNPs (rs28936412, 875AwT, rs13332760, rs28936690, and rs28936691, corresponding to residues L101P, E292V, V839F, L1552P, and Q1591P, respectively) were detected in any individuals. Login to comment 212 ABCA3 p.Leu101Pro ABCA3 p.Gln1591Pro Of these, two (corresponding to L101P and Q1591P) have been previously identified in term infants with fatal surfactant deficiency or chronic lung disease (13). Login to comment 213 ABCA3 p.Leu1552Pro ABCA3 p.Val839Phe In our study population, however, neither these nor the two other nonsynonymous cSNPs (corresponding to V839F and L1552P) listed in dbSNP were polymorphic, suggesting that they represent mutations rather than common polymorphisms. Login to comment 214 ABCA3 p.Glu292Val Additionally, we screened for the E292V mutation, which has been associated with pediatric ILD (22). Login to comment 215 ABCA3 p.Glu292Val However, E292V was not detected either in term or in preterm infants in our population. Login to comment