diff --git a/packages/react-variant-view/src/component/functionalPrediction/FunctionalPrediction.tsx b/packages/react-variant-view/src/component/functionalPrediction/FunctionalPrediction.tsx index 63b2de35916..63fe6274dca 100644 --- a/packages/react-variant-view/src/component/functionalPrediction/FunctionalPrediction.tsx +++ b/packages/react-variant-view/src/component/functionalPrediction/FunctionalPrediction.tsx @@ -30,8 +30,7 @@ class FunctionalPrediction extends React.Component { public getData( genomeNexusData: VariantAnnotation | undefined ): IFunctionalImpactData { - const mutationAssessor = - genomeNexusData && genomeNexusData.mutation_assessor; + const mutationAssessor = genomeNexusData?.mutation_assessor; const siftScore = genomeNexusData && genomeNexusData.transcript_consequences && diff --git a/packages/react-variant-view/src/component/functionalPrediction/MutationAssessor.tsx b/packages/react-variant-view/src/component/functionalPrediction/MutationAssessor.tsx index 255153a4d21..9f97b7c656c 100644 --- a/packages/react-variant-view/src/component/functionalPrediction/MutationAssessor.tsx +++ b/packages/react-variant-view/src/component/functionalPrediction/MutationAssessor.tsx @@ -27,20 +27,32 @@ export default class MutationAssessor extends React.Component< IMutationAssessorProps, {} > { - // Change to new url when available + // TODO Change to new url when manuscript is available // New url will need to be added in tooltip, discrption, "Please refer to the score range here." and "Go to Mutation Assessor" // private static MUTATION_ASSESSOR_URL: string = 'http://mutationassessor.org/r3/'; private static mutationAssessorText() { return ( -
+
Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on - a large set of disease associated and polymorphic variants - (ClinVar). + a large set of disease associated and polymorphic variants ( + + ClinVar + + ). +
+ + Mutation Assessor V4 data is now available in the portal! + {' '} + New manuscript is in progress. Click{` `} + + here + + {` `} to see information about V3 data.
); } @@ -146,14 +158,6 @@ export default class MutationAssessor extends React.Component< public render() { let maContent: JSX.Element = ; - const dataSource = ( - <> - Mutation Assessor  - - {!this.props.isCanonicalTranscriptSelected && *} - - ); - if ( this.props.mutationAssessor && this.props.mutationAssessor.functionalImpactPrediction != null && @@ -168,7 +172,15 @@ export default class MutationAssessor extends React.Component< return (
- {this.mutationAssessorTooltip(<>{dataSource})} + {this.mutationAssessorTooltip( + <> + Mutation Assessor  + + {!this.props.isCanonicalTranscriptSelected && ( + * + )} + + )}
{this.mutationAssessorTooltip( diff --git a/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx b/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx index 592387c6b6b..d9749083751 100644 --- a/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx +++ b/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx @@ -19,7 +19,7 @@ export default class MutationAssessor extends React.Component< IMutationAssessorProps, {} > { - // Replace to new url when publication available + // TODO Replace to new url when manuscript is available // static MUTATION_ASSESSOR_URL: string = 'http://mutationassessor.org/r3/'; constructor(props: IMutationAssessorProps) { @@ -87,8 +87,8 @@ export default class MutationAssessor extends React.Component< Source - {/* Add link when pubilcation is available */} - MutationAssessor + {/* TODO Add link when manuscript is available */} + Mutation Assessor diff --git a/src/shared/components/mutationTable/column/FunctionalImpactColumnFormatter.tsx b/src/shared/components/mutationTable/column/FunctionalImpactColumnFormatter.tsx index ddb2254f69d..1dad21853fc 100644 --- a/src/shared/components/mutationTable/column/FunctionalImpactColumnFormatter.tsx +++ b/src/shared/components/mutationTable/column/FunctionalImpactColumnFormatter.tsx @@ -305,14 +305,26 @@ class FunctionalImpactColumnTooltip extends React.Component< public static mutationAssessorText() { return ( -
+
Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on - a large set of disease associated and polymorphic variants - (ClinVar). + a large set of disease associated and polymorphic variants ( + + ClinVar + + ). +
+ + Mutation Assessor V4 data is now available in the portal! + {' '} + New manuscript is in progress. Click{` `} + + here + + {` `} to see information about V3 data.
); }