ABCMdb

PMID: 20880529

Candini C, Schimmel AW, Peter J, Bochem AE, Holleboom AG, Vergeer M, Dullaart RP, Dallinga-Thie GM, Hovingh GK, Khoo KL, Fasano T, Bocchi L, Calandra S, Kuivenhoven JA, Motazacker MM
Identification and characterization of novel loss of function mutations in ATP-binding cassette transporter A1 in patients with low plasma high-density lipoprotein cholesterol.
Atherosclerosis. 2010 Dec;213(2):492-8. Epub 2010 Aug 26., [PubMed]

Sentences

No. Mutations Sentence Comment

61 ABCA1 p.Leu1056Pro ABCA1 p.Thr1512Met ABCA1 p.Cys1941Arg ABCA1 p.Asp575Gly ABCA1 p.Glu1253Lys ABCA1 p.Ser100Cys ABCA1 p.Phe593Leu ABCA1 p.Val1858Ala Eight novel missense variations [c.299C > G (p.S100C), c.1724A > G (p.D575G), c.1779C > G (p.F593L), c.3167T > C (p.L1056P), c.3757G > A (p.E1253K), c.4535C > T (p.T1512M), c.5573T > C (p.V1858A), c.5821T > C (p.C1941R)] were introduced into this chimeric construct by site-directed mutagenesis using Stratagene QuikChange XL site-directed mutagenesis kit according to manufacturer`s instructions (La Jolla, CA, USA). Login to comment 76 ABCA1 p.Cys1477Arg ABCA1 p.Asn1800His ABCA1 p.Asn1800His ABCA1 p.Asn1800His ABCA1 p.Arg282* ABCA1 p.Ser1181Phe ABCA1 p.Gln1038* ABCA1 p.Leu1056Pro ABCA1 p.Thr1512Met ABCA1 p.Glu1172Asp ABCA1 p.Asp575Gly ABCA1 p.Glu1253Lys ABCA1 p.Ser100Cys ABCA1 p.Phe593Leu ABCA1 p.Val1858Ala ABCA1 p.Trp424* Patients (gender, age) Amino acida (nucleotidea ) change TC TG LDL-c HDL-c Clinical manifestations of TD CVD Other relevant clinical data Homozygotes Patient 1 (female, 42) p.L1056P (c.3167T > C) 2.4 0.9 1.99 <0.10 Absent CAD Thrombocytopenia Patient 2 (male, 40) p.Wl747X (c.5240G > A) 1.76 1.93 0.52 0.1-0.3 Neuropathy, splenomegaly, thrombocytopenia Mild stenosis (20-30%) of coronary arteries None Patient 3 (male, 55) p.F593L (c.1779C > G) 4.4 1.4 3.6 <0.10 Absent CAD None p.E1253K (c.3757G > A) Compound heterozygotes Patient 4 (female, 63) p.Q1038X (c.3112C > T) 6.68 2.72 5.4 <0.10 Absent None None p.N1800H (c.5398A > C) [32] Patient 5 (female, 28) p.T1512M (c.4535C > T) 4.42 1.83 3.46 0.1 Absent None None p.N1800H (c.5398A > C) [32] p.C978fsX988 (c.2934delT) Patient 6 (female, 17) p.D575G (c.1724A > G) 4.96 2.84 4.35 <0.10 Absent None DM1 p.C1941R(c.5821T > C) Heterozygotes Patient 7 (male, 42) p.S100C (c.299C > G) 8.5 8.7 4.3 0.3 N.A. None None Patient 8 (male, 58) p.E1172D (c.3516G > C) [33] 6.4 2.7 4.1 0.9 N.A. None None Patient 9 (male, 35) p.S1181F (c.3542C > T) [17] 2.9 0.31 1.88 0.88 N.A. None None Patient 10 (male, 48) p.C1477R (c.4429T > C) [13] 2.01 1.4 0.92 0.46 N.A. CAD None Patient 11 (male, 68) p.V1858A (c.5573T > C) 4.9 3.78 2.41 0.75 N.A. CAD None Patient 12 (female, 36) p.N1800H (c.5398A > C) [32] 4.6 1.2 4 <0.10 N.A. None DM2, obesity Patient 13 (male, 67) p.R282X (c.844C > T) [34] 3.2 1.21 2.14 0.51 N.A. None DM2 Patient 14 (female, 42) p.W424X (c.1272G > A) 2.07 1.04 1.39 0.21 N.A. None None Patient 15 (female, 52) N.A. - (IVS11 - 1G > A) 5.51 3.51 3.28 0.56 N.A. None Hypothyroidism, hypertension Patient 16 (female, 54) N.A. - (IVS48 + 2T > C) 3.29 1.92 1.94 0.49 N.A. None DM2, hypertension a Nomenclature based on guidelines of Human Genome Variation Society. Login to comment 89 ABCA1 p.Cys1477Arg ABCA1 p.Asn1800His ABCA1 p.Arg282* ABCA1 p.Ser1181Phe ABCA1 p.Gln1038* ABCA1 p.Leu1056Pro ABCA1 p.Thr1512Met ABCA1 p.Glu1172Asp ABCA1 p.Cys1941Arg ABCA1 p.Asp575Gly ABCA1 p.Glu1253Lys ABCA1 p.Ser100Cys ABCA1 p.Phe593Leu ABCA1 p.Val1858Ala ABCA1 p.Trp424* In ABCA1, we identified 14 novel and 5 known genetic variations in 16 subjects including one frameshift (p.C978fsX988), 2 splice-site (IVS11-1G > C and IVS48 + 2T > C), 4 nonsense (p.R282X, p.W424X, p.Q1038X, p.Wl747X) and 12 missense variations (p.S100C, p.D575G, p.F593L, p.L1056P, p.E1172D, p.S1181F, p.E1253K, p.C1477R, p.T1512M, p.N1800H, p.V1858A, p.C1941R). Login to comment 94 ABCA1 p.Leu1056Pro ABCA1 p.Thr1512Met ABCA1 p.Cys1941Arg ABCA1 p.Asp575Gly ABCA1 p.Glu1253Lys ABCA1 p.Ser100Cys ABCA1 p.Phe593Leu ABCA1 p.Val1858Ala From eight novel missense variations identified in our cohort, one is localized in the first transmembrane domain (p.S100C), two in the first large extracellular loop (p.D575G and p.F593L), two in the first Nuclear Binding Domain (p.L1056P and p.E1253K), one in the second large extracellular loop (p.T1512M), one in the extracellular region, close to the plasma membrane (p.V1858A) and one is localized in the C-terminal domain (p.C1941R). Login to comment 98 ABCA1 p.Leu1056Pro ABCA1 p.Thr1512Met ABCA1 p.Cys1941Arg ABCA1 p.Asp575Gly ABCA1 p.Glu1253Lys ABCA1 p.Ser100Cys ABCA1 p.Phe593Leu ABCA1 p.Val1858Ala Four out of eight mutations were predicted to be probably damaging (p.S100C, p.D575G, p.T1512M, p.C1941R), two as possibly damaging (p.F593L and p.L1056P) and two were described as benign (p.E1253K and p.V1858A) by PolyPhen. Login to comment 99 ABCA1 p.Val1858Ala Using SIFT, seven novel variations were predicted to affect protein function, while one (p.V1858A) was predicted to be tolerated. Login to comment 110 ABCA1 p.Leu1056Pro ABCA1 p.Thr1512Met ABCA1 p.Cys1941Arg ABCA1 p.Asp575Gly ABCA1 p.Glu1253Lys ABCA1 p.Ser100Cys ABCA1 p.Phe593Leu Fig. 2 shows that the ABCA1-p.S100C, p.D575G, p.F593L, p.L1056P, p.E1253K, p.T1512M, p.C1941R mutant proteins all had a significantly reduced capacity to efflux cholesterol to apo A-I compared to wild-type ABCA1 which is in line with the low HDL cholesterol levels of the individuals in whom the mutations were identified. Login to comment 111 ABCA1 p.Val1858Ala The ABCA1-p.V1858A, however, had a normal potential to efflux cholesterol to apo A-I which is in line with the prediction that the mutation is benign (both PolyPhen and SIFT) suggesting that the low HDL cholesterol in this individual is likely the result of other, yet unknown molecular defect. Login to comment 114 ABCA1 p.Val1858Ala While WT-ABCA1 and ABCA1-V1858A variant show normal localization on plasma membrane, ABCA1- L1056 protein shows a complete intracellular retention. Login to comment 136 ABCA1 p.Leu1056Pro The most striking discrepancy was found for the new ABCA1-p.L1056P variant which was only defined as possibly damaging while our data show that this variant is amongst those with the most profound loss of ABCA1-mediated efflux and confocal microscopy revealed complete intracellular retention (Supplementary Fig. 1). Login to comment 138 ABCA1 p.Val1858Ala In contrast to PolyPhen, SIFT predictions for the assessment of the novel variations studied here were more compatible to the outcome of our in vitro experiments, i.e. all variants with significant reduction in cholesterol efflux to apo A-I in our in vitro assay were proposed to be deleterious while ABCA1-p.V1858A was predicted to be tolerated. Login to comment 143 ABCA1 p.Leu1056Pro ABCA1 p.Glu1253Lys The missense mutations ABCA1-p.L1056P and ABCA1-p.E1253K, identified in patients with near HDL deficiency, are located in the intracellular region, inside the nuclear binding domain 1, close to the Walker A motif and after the Walker B motif respectively (Fig. 1). Login to comment 146 ABCA1 p.Leu1056Pro ABCA1 p.Glu1253Lys Thus, lack of proper localization to the plasma membrane for ABCA1-p.L1056P and partial intracellular retention for ABCA1-p.E1253K (Supplementary Fig. 1) results in low cholesterol efflux potential of both ABCA1 mutants and confirms the vital role of this ABCA1 domain (Fig. 2). Login to comment 148 ABCA1 p.Thr1512Met ABCA1 p.Asp575Gly ABCA1 p.Phe593Leu The ABCA1-p.F593L and ABCA1-p.D575G mutations are located in the first large extracellular loop, while ABCA1-p.T1512M is located in the second extracellular loop. Login to comment 152 ABCA1 p.Ser100Cys The cholesterol efflux assay performed for ABCA1-p.S100C revealed a significant reduction in efflux potential to apo A-I. Login to comment 154 ABCA1 p.Cys1941Arg The ABCA1-p.C1941R mutation showed a marked reduction in cholesterol efflux. Login to comment 157 ABCA1 p.Val1858Ala The ABCA1-p.V1858A variant was the only missense variation that was found to have no significant effect on cholesterol efflux and cellular localization. Login to comment