Gene Scoring

About the Gene Scoring Module

Our gene scoring system takes into account all available evidence supporting a gene's relevance to ASD risk and places each gene into a category reflecting the overall strength of that evidence.

SFARI Gene is a comprehensive database that includes any gene associated with autism risk, regardless of the nature of the evidence supporting its link to ASD. Given this approach and the potentially large number of false-positives it invites, we recognize the importance of establishing a ranking system that gives users an estimate of the strength of the evidence in favor of each gene. In collaboration with our curators at MindSpec and a team of expert autism geneticists, we've established a set of criteria that allows us to rank genes into one of four categories, enabling users to easily identify the genes whose association with autism risk is most likely to hold up over time.

number of reports

score categories

  • More Genes
  • Less Genes
  • Syndromic


The syndromic category includes mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis. If there is independent evidence implicating a gene in idiopathic ASD, it will be listed as “#S” (e.g., 2S, 3S). If there is no such independent evidence, the gene will be listed simply as “S”.

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Category 1(High Confidence)

Each of these genes has been clearly implicated in ASD—typically by the presence of at least three de novo likely-gene-disrupting mutations being reported in the literature—and such mutations identified in the sequencing of the SPARK cohort are typically returned to the participants. Some of these gene meet the most rigorous threshold of genome-wide significance; all at least meet a threshold false discovery rate of < 0.1

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Category 2(Strong Candidate)

  • Genes with two reported de novo likely-gene-disrupting mutations.
  • A gene uniquely implicated by a genome-wide association study, either reaching genome-wide significance or, if not, consistently replicated and accompanied by evidence that the risk variant has a functional effect.
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Category 3(Suggestive Evidence)

  • Genes with a single reported de novo likely-gene-disrupting mutation.
  • Evidence from a significant but unreplicated association study, or a series of rare inherited mutations for which there is not a rigorous statistical comparison with controls.
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