ABCA1 p.Cys1359Arg
| Predicted by SNAP2: | A: N (87%), D: D (59%), E: D (63%), F: N (53%), G: N (78%), H: D (75%), I: N (57%), K: D (66%), L: N (72%), M: N (66%), N: N (53%), P: D (63%), Q: D (59%), R: D (63%), S: N (82%), T: N (72%), V: N (61%), W: D (85%), Y: D (66%), |
| Predicted by PROVEAN: | A: N, D: D, E: D, F: N, G: D, H: D, I: N, K: D, L: N, M: N, N: D, P: D, Q: D, R: D, S: D, T: D, V: N, W: D, Y: N, |
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[hide] Genome of The Netherlands population-specific impu... Nat Commun. 2015 Mar 9;6:6065. doi: 10.1038/ncomms7065. van Leeuwen EM, Karssen LC, Deelen J, Isaacs A, Medina-Gomez C, Mbarek H, Kanterakis A, Trompet S, Postmus I, Verweij N, van Enckevort DJ, Huffman JE, White CC, Feitosa MF, Bartz TM, Manichaikul A, Joshi PK, Peloso GM, Deelen P, van Dijk F, Willemsen G, de Geus EJ, Milaneschi Y, Penninx BW, Francioli LC, Menelaou A, Pulit SL, Rivadeneira F, Hofman A, Oostra BA, Franco OH, Mateo Leach I, Beekman M, de Craen AJ, Uh HW, Trochet H, Hocking LJ, Porteous DJ, Sattar N, Packard CJ, Buckley BM, Brody JA, Bis JC, Rot
Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels.
Nat Commun. 2015 Mar 9;6:6065. doi: 10.1038/ncomms7065., [PMID:25751400]
Abstract [show]
Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of The Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value <6.61 x 10(-4)), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted to be deleterious. The frequency of this ABCA6 variant is 3.65-fold increased in the Dutch and its effect (betaLDL-C=0.135, betaTC=0.140) is estimated to be very similar to those observed for single variants in well-known lipid genes, such as LDLR.
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No. Sentence Comment
41 This missense variant changes the amino acid cysteine into arginine at position 1359 (Cys1359Arg) and is predicted to be damaging for the structure and function of the protein by Polyphen2 (ref. 12), MutationTaster13 and LRT14.
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ABCA1 p.Cys1359Arg 25751400:41:86
status: NEW