ABCB4 p.Gly622Glu
| Predicted by SNAP2: | A: D (66%), C: D (66%), D: D (71%), E: D (75%), F: D (75%), H: D (63%), I: D (75%), K: D (85%), L: D (75%), M: D (59%), N: D (59%), P: D (80%), Q: D (66%), R: D (80%), S: D (66%), T: D (66%), V: D (71%), W: D (80%), Y: D (80%), |
| Predicted by PROVEAN: | A: D, C: D, D: D, E: D, F: D, H: D, I: D, K: D, L: D, M: D, N: D, P: D, Q: D, R: D, S: D, T: D, V: D, W: D, Y: D, |
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[hide] Large-scale whole-genome sequencing of the Iceland... Nat Genet. 2015 May;47(5):435-44. doi: 10.1038/ng.3247. Epub 2015 Mar 25. Gudbjartsson DF, Helgason H, Gudjonsson SA, Zink F, Oddson A, Gylfason A, Besenbacher S, Magnusson G, Halldorsson BV, Hjartarson E, Sigurdsson GT, Stacey SN, Frigge ML, Holm H, Saemundsdottir J, Helgadottir HT, Johannsdottir H, Sigfusson G, Thorgeirsson G, Sverrisson JT, Gretarsdottir S, Walters GB, Rafnar T, Thjodleifsson B, Bjornsson ES, Olafsson S, Thorarinsdottir H, Steingrimsdottir T, Gudmundsdottir TS, Theodors A, Jonasson JG, Sigurdsson A, Bjornsdottir G, Jonsson JJ, Thorarensen O, Ludvigsson P, Gudb
Large-scale whole-genome sequencing of the Icelandic population.
Nat Genet. 2015 May;47(5):435-44. doi: 10.1038/ng.3247. Epub 2015 Mar 25., [PMID:25807286]
Abstract [show]
Here we describe the insights gained from sequencing the whole genomes of 2,636 Icelanders to a median depth of 20x. We found 20 million SNPs and 1.5 million insertions-deletions (indels). We describe the density and frequency spectra of sequence variants in relation to their functional annotation, gene position, pathway and conservation score. We demonstrate an excess of homozygosity and rare protein-coding variants in Iceland. We imputed these variants into 104,220 individuals down to a minor allele frequency of 0.1% and found a recessive frameshift mutation in MYL4 that causes early-onset atrial fibrillation, several mutations in ABCB4 that increase risk of liver diseases and an intronic variant in GNAS associating with increased thyroid-stimulating hormone levels when maternally inherited. These data provide a study design that can be used to determine how variation in the sequence of the human genome gives rise to human diversity.
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No. Sentence Comment
224 ABCB4 and liver diseases and function Our GWAS of gallstone disease (n = 8,258) led us to a missense SNP, encoding p.Gly622Glu, and a frameshift insertion, encoding p.Leu445Glyfs*22, in ABCB4 (Supplementary Table 12).
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ABCB4 p.Gly622Glu 25807286:224:117
status: NEW225 ABCB4 and liver diseases and function Our GWAS of gallstone disease (n = 8,258) led us to a missense SNP, encoding p.Gly622Glu, and a frameshift insertion, encoding p.Leu445Glyfs*22, in ABCB4 (Supplementary Table 12).
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ABCB4 p.Gly622Glu 25807286:225:117
status: NEW[hide] A letter on ABCB4 from Iceland: On the highway to ... Clin Res Hepatol Gastroenterol. 2015 Dec;39(6):655-8. doi: 10.1016/j.clinre.2015.08.004. Epub 2015 Sep 26. Lammert F, Hochrath K
A letter on ABCB4 from Iceland: On the highway to liver disease.
Clin Res Hepatol Gastroenterol. 2015 Dec;39(6):655-8. doi: 10.1016/j.clinre.2015.08.004. Epub 2015 Sep 26., [PMID:26410236]
Abstract [show]
Large-scale whole-genome sequencing of the Icelandic population identified an association between several mutations of ABCB4 encoding the hepatobiliary phosphatiylcholine floppase with liver diseases and function in the general population. Whereas rare mutations of this transporter were known to cause progressive familial intrahepatic cholestasis, the genome-wide association studies in Iceland find the common ABCB4 variant c.711A>T to be a general risk factor for elevated aminotransferases and higher impact variants to be potential determinants of early-onset gallstone disease, cholestasis of pregnancy, liver cirrhosis, and hepatobiliary cancer.
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27 The two ABCB4 mutations that were significantly associated with gallstones at the genome-wide level are the missense SNP p.Gly622Glu and the frameshift insertion p.Leu445GlyfsX22, which conferred odds ratios (OR) for gallstones of 2.74 and 3.10, respectively [3].
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ABCB4 p.Gly622Glu 26410236:27:123
status: NEW37 In total, Gudbjartsson et al. [3] identified four ABCB4 variants (p.Gly622Glu, p.Leu445GlyfsX22, p.Asn510Ser, c.711A > T) to be associated with these liver-specific traits (Table 1).
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ABCB4 p.Gly622Glu 26410236:37:68
status: NEW44 n p.G622E p.L445GfsX22 p.N510S c.711A > T MAF 0.22% 0.21% 0.16% 20.54% P /OR P /OR P /OR P /OR ALT 143.693 3.0 &#d7; 10-18 0.46 2.2 &#d7; 10-11 0.35 0.004 0.18 5.7 &#d7; 10-10 -0.04 AST 144.255 2.0 &#d7; 10-10 0.28 6.8 &#d7; 10-8 0.24 0.02 0.12 0.0006 -0.02 AP 125.496 0.0004 0.17 ॹ-GT 138.195 6.5 &#d7; 10-19 0.30 0.001 0.17 1.5 &#d7; 10-5 -0.03 Gallstones 8258 7.2 &#d7; 10-10 2.74 2.6 &#d7; 10-12 3.10 0.004 1.84 0.0002 0.91 Gallstones < 40 years 2023 1.8 &#d7; 10-9 4.97 4.0 &#d7; 10-10 5.43 0.001 0.84 ICP 688 5.0 &#d7; 10-6 7.29 3.2 &#d7; 10-5 6.35 0.002 5.10 HCC/CCA 565 0.04 3.07 0.002 4.75 Cirrhosis 263 0.007 5.52 Data from Supplementary Table 13 in [3].
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ABCB4 p.Gly622Glu 26410236:44:4
status: NEW