Table 4 Tools for assigning the pathogenic likelihood or functional impact of variants.

From: Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases

 

BaylorSeq

BCM

Duke/Columbia

Harvard

Miami

NIH

PacificNW

Stanford

UCLA

Utah

Vanderbilt

WUSTL

Cross-species conservation scores

 GERP++: Genomic Evolutionary Rate Profiling

 

●

●

  

●

●

   

●

 

 PhastCons

    

●

●

●

     

Predicted functionality or pathogenicity

 PolyPhen-2

●

●

●

●

●

●

●

●

●

●

  

 SIFT

●

●

 

●

●

●

●

●

●

●

  

 MutationTaster

   

●

●

●

 

●

    

 MVP: missense variant pathogenicity

       

●

    

 ReMM: regulatory Mendelian mutation

       

●

    

Ensemble pathogenicity predictors

 CADD: Combined Annotation Dependent Depletion

●

●

  

●

●

●

●

  

●

●

 REVEL: Rare Exome Variant Ensemble Learner

 

●

●

●

 

●

●

●

 

●

 

●

 DANN: Deep Neural Net version of CADD

●

   

●

       

 M-CAP: Mendelian Clinically Applicable Pathogenicity

       

●

   

●

 DOMINO: Dominant Disorder Associated Genesa

 

●

          

 Eigen

     

●

      

Predicted splice- or expression-altering effect

 SpliceAI

●

●

 

●

●

 

●

●

●

●

●

●

 GTEx: Genotype-Tissue Expression

 

●

  

●

  

●

 

●

  

 SpliceRegion annotations from VEP

      

●

●

 

●

 

●

 dbscSNV (splicing consensus SNVs)

    

●

   

●

  

●

 Human Splicing Factor

 

●

        

●

 

 MMSplice: Modular modeling of splicing

    

●

●

      

 MaxEntScan

     

●

    

●

 

 TraP: Transcript-inferred Pathogenicity

  

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  1. Variants of uncertain significance (i.e., that are not already known to be associated with disease) can be evaluated for functional or pathogenic impact using predictive models. Tool citations are listed in Extended Data Table 1.
  2. aUnlike other tools, DOMINO provides scores per gene rather than per variant.
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