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Association of a Low-Frequency Variant in HNF1A With Type 2 Diabetes in a Latino Population
Open accessAbstract
IMPORTANCE: Latino populations have one of the highest prevalences of type 2 diabetes worldwide. OBJECTIVES: To investigate the association between rare protein-coding genetic variants and prevalence of type 2 diabetes in a large Latino population and to explore potential molecular and physiological mechanisms for the observed relationships. DESIGN, SETTING, AND PARTICIPANTS: Whole-exome sequencing was performed on DNA samples from 3756 Mexican and US Latino individuals (1794 with type 2 diabetes and 1962 without diabetes) recruited from 1993 to 2013. One variant was further tested for allele frequency and association with type 2 diabetes in large multiethnic data sets of 14,276 participants and characterized in experimental assays. MAIN OUTCOME AND MEASURES: Prevalence of type 2 diabetes. Secondary outcomes included age of onset, body mass index, and effect on protein function. RESULTS: A single rare missense variant (c.1522G>A [p.E508K]) was associated with type 2 diabetes prevalence (odds ratio [OR], 5.48; 95% CI, 2.83-10.61; P = 4.4 × 10(-7)) in hepatocyte nuclear factor 1-α (HNF1A), the gene responsible for maturity onset diabetes of the young type 3 (MODY3). This variant was observed in 0.36% of participants without type 2 diabetes and 2.1% of participants with it. In multiethnic replication data sets, the p.E508K variant was seen only in Latino patients (n = 1443 with type 2 diabetes and 1673 without it) and was associated with type 2 diabetes (OR, 4.16; 95% CI, 1.75-9.92; P = .0013). In experimental assays, HNF-1A protein encoding the p.E508K mutant demonstrated reduced transactivation activity of its target promoter compared with a wild-type protein. In our data, carriers and noncarriers of the p.E508K mutation with type 2 diabetes had no significant differences in compared clinical characteristics, including age at onset. The mean (SD) age for carriers was 45.3 years (11.2) vs 47.5 years (11.5) for noncarriers (P = .49) and the mean (SD) BMI for carriers was 28.2 (5.5) vs 29.3 (5.3) for noncarriers (P = .19). CONCLUSIONS AND RELEVANCE: Using whole-exome sequencing, we identified a single low-frequency variant in the MODY3-causing gene HNF1A that is associated with type 2 diabetes in Latino populations and may affect protein function. This finding may have implications for screening and therapeutic modification in this population, but additional studies are required.
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“Another example is the p.E508K missense mutation in HNF1A, with carrier frequency of 0.1% of the general population and 0.7% of Latinos,8 which confers up to 5-fold increased risk for type 2 diabetes.9”
From Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations (2018) · cites this paper as [9]
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Metadata
- Authors
- Estrada, K., Aukrust, I., Bjørkhaug, L., Burtt, N. P., Mercader, J. M., García-Ortiz, H., Huerta-Chagoya, A., Moreno-Macías, H., Walford, G., Flannick, J., Williams, A. L., Gómez-Vázquez, M. J., Fernandez-Lopez, J. C., Martínez-Hernández, A., Centeno-Cruz, F., Mendoza-Caamal, E., Revilla-Monsalve, C., Islas-Andrade, S., Córdova, E. J., Soberón, X., González-Villalpando, M. E., Henderson, E., Wilkens, L. R., Le Marchand, L., Arellano-Campos, O., Ordóñez-Sánchez, M. L., Rodríguez-Torres, M., Rodríguez-Guillén, R., Riba, L., Najmi, L. A., Jacobs, S. B. R., Fennell, T., Gabriel, S., Fontanillas, P., Hanis, C. L., Lehman, D. M., Jenkinson, C. P., Abboud, H. E., Bell, G. I., Cortes, M. L., Boehnke, M., González-Villalpando, C., Orozco, L., Haiman, C. A., Tusié-Luna, T., Aguilar-Salinas, C. A., Altshuler, D., Njølstad, P. R., Florez, J. C., & MacArthur, D. G.
- Affiliations
- Broad Institute (US)
- University of Bergen (NO)
- Haukeland University Hospital (NO)
- Instituto Nacional de Medicina Genómica, Tlalpan, Mexico City, Mexico
- Instituto de Investigaciones Biomédicas, UNAM Unidad de Biología Molecular y Medicina Genómica, UNAM/INCMNSZ, Coyoacán, Mexico City, Mexico
- Universidad Autónoma Metropolitana (MX)
- Harvard University (US)
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (MX)
- National Institute of Genomic Medicine (MX)
- Unidad de Investigación Médica en Enfermedades Metabólicas, CMN SXXI, Instituto Mexicano del Seguro Social, Mexico City
- Instituto Nacional de Salud Pública (MX)
- University of Southern California (US)
- University of Hawaii Cancer Center (US)
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Sección XVI, Tlalpan, Mexico City, Mexico
- The University of Texas Health Science Center at Houston (US)
- The University of Texas at San Antonio Health Science Center (US)
- University of Chicago (US)
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- University of Michigan (US)
- Centro de Estudios en Diabetes, Unidad de Investigacion en Diabetes y Riesgo Cardiovascular, Centro de Investigacion en Salud Poblacional, Instituto Nacional de Salud Publica, Mexico City, Mexico
- Instituto de Investigaciones Biomédicas, UNAM Unidad de Biología Molecular y Medicina Genómica, UNAM/INCMNSZ, Coyoacán, Mexico City, Mexico17Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Sección XVI, Tlalpan, Mexico City, Mexico
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts3Department of Medicine, Harvard Medical School, Boston, Massachusetts7Center for Human Genetic Research and Diabetes Research Center (Diabetes Unit),
- ORCID
- Estrada, Karol
- Aukrust, Ingvild
- Bjørkhaug, Lise
- Burtt, Noël P.
- Mercader, Josep M.
- Moreno-Macías, Hortensia
- Flannick, Jason
- Williams, Amy L.
- Martínez-Hernández, Angélica
- Centeno-Cruz, Federico
- Córdova, Emilio J.
- Soberón, Xavier
- Henderson, E.
- Wilkens, Lynne R.
- Jacobs, Suzanne B.R.
- Gabriel, Stacey
- Fontanillas, Pierre
- Hanis, Craig L.
- Lehman, Donna M.
- Jenkinson, Christopher P.
- Boehnke, Michael
- Orozco, Lorena
- Haiman, Christopher A.
- Aguilar-Salinas, Carlos A.
- Altshuler, David
- Njølstad, Pål R.
- MacArthur, Daniel G.
- Venue
- JAMA
- Publisher
- American Medical Association (AMA)
- Published
- 2014-06-11
- Volume
- 311
- Issue
- 22
- Pages
- 2305
- ISSN
- 0002-9955 (ISSN-L)
- 0098-7484
- PMC
- PMC4425850
- OpenAlex
- W2055830789
- Cited by
- 259
- References
- 57
- Citations by year
- 2026: 7 · 2025: 12 · 2024: 22 · 2023: 24 · 2022: 24 · 2021: 21 · 2020: 15 · 2019: 22 · 2018: 30 · 2017: 22 · 2016: 31 · 2015: 23 · 2014: 6
- FWCI
- 17.95
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- JAMA (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- NORA - Norwegian Open Research Archives (submittedVersion, other-oa)
- Funders
- Consejo Nacional de Ciencia y Tecnología
- Helse Vest
- National Institutes of Health
- National Heart, Lung, and Blood Institute (R01HL024799, P01HL045522, R01HL24799)
- National Cancer Institute (R35CA053890, CA164973, R01CA144034, R01CA080205, U01CA063464, R37CA054281, R35-CA53890, R01CA054281, R01 CA 80205, R01CA063464, UM1CA164973, CA054281, CA063464, R01CA055069, U01CA164973)
- National Institute of Diabetes and Digestive and Kidney Diseases (U01DK085526, R01 DK057295, U01DK057295, U01DK085501, U01DK062370, R01DK042273, R01DK047482, R01DK053889, R01DK098032, R01DK033665, P30DK020572)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Diabetes and associated disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- type 2 diabetes, HNF1A, rare missense variants, Latino population, Mexican Americans, MODY3, genetic susceptibility, transactivation activity, age of onset, body mass index, exome sequencing, genetic association, diabetes prevalence, protein-coding variants, age at onset of diabetes
- MeSH terms
- Adult, Aged, Diabetes Mellitus, Type 2, Female, Genotype, Hispanic or Latino, Humans, Male, Mexico, Middle Aged, United States, Sequence Analysis, DNA, Age of Onset, Mutation, Missense, Hepatocyte Nuclear Factor 1-alpha
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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