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Journal Article
GeVIR is a continuous gene-level metric that uses variant distribution patterns to prioritize disease candidate genes
2020
Overview
With large-scale population sequencing projects gathering pace, there is a need for strategies that advance disease gene prioritization
1
,
2
. Metrics that provide information about a gene and its ability to tolerate protein-altering variation can aid in clinical interpretation of human genomes and can advance disease gene discovery
1
–
4
. Previous reported methods analyzed the total variant load in a gene
1
–
4
, but did not analyze the distribution pattern of variants within a gene. Using data from 138,632 exome and genome sequences
2
, we developed gene variation intolerance rank (GeVIR), a continuous gene-level metric for 19,361 genes that is able to prioritize both dominant and recessive Mendelian disease genes
5
, that outperforms missense constraint metrics
3
and that is comparable—but complementary—to loss-of-function (LOF) constraint metrics
2
. GeVIR is also able to prioritize short genes, for which LOF constraint cannot be estimated with confidence
2
. The majority of the most intolerant genes identified here have no defined phenotype and are candidates for severe dominant disorders.
GeVIR is a continuous gene-level metric that uses variant distribution patterns to prioritize both dominant and recessive Mendelian disease genes. GeVIR outperforms missense constraint metrics and complements loss-of-function constraint metrics.
Publisher
Nature Publishing Group US,Nature Publishing Group
