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Nucleic Acids Res. 2017 Jan 4;45(D1):D804-D811. doi: 10.1093/nar/gkw865. Epub 2016 Oct 5.

denovo-db: a compendium of human de novo variants.

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Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Medical Scientist Training Program, Department of Pathology, University ofWashington, Seattle, WA 98105, USA.
Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98105, USA.


Whole-exome and whole-genome sequencing have facilitated the large-scale discovery of de novo variants in human disease. To date, most de novo discovery through next-generation sequencing focused on congenital heart disease and neurodevelopmental disorders (NDDs). Currently, de novo variants are one of the most significant risk factors for NDDs with a substantial overlap of genes involved in more than one NDD. To facilitate better usage of published data, provide standardization of annotation, and improve accessibility, we created denovo-db (, a database for human de novo variants. As of July 2016, denovo-db contained 40 different studies and 32,991 de novo variants from 23,098 trios. Database features include basic variant information (chromosome location, change, type); detailed annotation at the transcript and protein levels; severity scores; frequency; validation status; and, most importantly, the phenotype of the individual with the variant. We included a feature on our browsable website to download any query result, including a downloadable file of the full database with additional variant details. denovo-db provides necessary information for researchers to compare their data to other individuals with the same phenotype and also to controls allowing for a better understanding of the biology of de novo variants and their contribution to disease.

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