Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus

Anubha Mahajan, Xueling Sim, Hui Jin Ng, Alisa Manning, Manuel A. Rivas, Heather M. Highland, Adam E. Locke, Niels Grarup, Hae Kyung Im, Pablo Cingolani, Jason Flannick, Pierre Fontanillas, Christian Fuchsberger, Kyle J. Gaulton, Tanya M. Teslovich, N. William Rayner, Neil R. Robertson, Nicola L. Beer, Jana K. Rundle, Jette Bork-JensenClaes Ladenvall, Christine Blancher, David Buck, Gemma Buck, Noël P. Burtt, Stacey Gabriel, Anette P. Gjesing, Christopher J. Groves, Mette Hollensted, Jeroen R. Huyghe, Anne U. Jackson, Goo Jun, Johanne Marie Justesen, Massimo Mangino, Jacquelyn Murphy, Matt Neville, Robert Onofrio, Kerrin S. Small, Heather M. Stringham, Ann-Christine Syvänen, Joseph Trakalo, Goncalo Abecasis, Graeme I. Bell, John Blangero, Nancy J. Cox, Ravindranath Duggirala, Craig L. Hanis, Alex S. F. Doney, Andrew D. Morris, Colin N. A. Palmer, On Behalf of the T2D-GENES consortium and GoT2D consortium

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    Abstract

    Genome wide association studies (GWAS) for fasting glucose (FG) and insulin (FI) have identified common variant signals which explain 4.8% and 1.2% of trait variance, respectively. It is hypothesized that low-frequency and rare variants could contribute substantially to unexplained genetic variance. To test this, we analyzed exome-array data from up to 33,231 non-diabetic individuals of European ancestry. We found exome-wide significant (P<5×10-7) evidence for two loci not previously highlighted by common variant GWAS: GLP1R (p.Ala316Thr, minor allele frequency (MAF)=1.5%) influencing FG levels, and URB2 (p.Glu594Val, MAF = 0.1%) influencing FI levels. Coding variant associations can highlight potential effector genes at (non-coding) GWAS signals. At the G6PC2/ABCB11 locus, we identified multiple coding variants in G6PC2 (p.Val219Leu, p.His177Tyr, and p.Tyr207Ser) influencing FG levels, conditionally independent of each other and the non-coding GWAS signal. In vitro assays demonstrate that these associated coding alleles result in reduced protein abundance via proteasomal degradation, establishing G6PC2 as an effector gene at this locus. Reconciliation of single-variant associations and functional effects was only possible when haplotype phase was considered. In contrast to earlier reports suggesting that, paradoxically, glucose-raising alleles at this locus are protective against type 2 diabetes (T2D), the p.Val219Leu G6PC2 variant displayed a modest but directionally consistent association with T2D risk. Coding variant associations for glycemic traits in GWAS signals highlight PCSK1, RREB1, and ZHX3 as likely effector transcripts. These coding variant association signals do not have a major impact on the trait variance explained, but they do provide valuable biological insights.

    Original languageEnglish
    Article numbere1004876
    Number of pages25
    JournalPLoS Genetics
    Volume11
    Issue number1
    DOIs
    Publication statusPublished - 27 Jan 2015

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    Mahajan, A., Sim, X., Ng, H. J., Manning, A., Rivas, M. A., Highland, H. M., Locke, A. E., Grarup, N., Im, H. K., Cingolani, P., Flannick, J., Fontanillas, P., Fuchsberger, C., Gaulton, K. J., Teslovich, T. M., Rayner, N. W., Robertson, N. R., Beer, N. L., Rundle, J. K., ... On Behalf of the T2D-GENES consortium and GoT2D consortium (2015). Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus. PLoS Genetics, 11(1), [e1004876]. https://doi.org/10.1371/journal.pgen.1004876