Add AlphaMissense in Functional prediction

genome-nexus · Aug 21, 2024 · 5442d52 · 5442d52
1 parent 89c36f8
commit 5442d52
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Showing 2 changed files with 25 additions and 28 deletions.
diff --git a/src/component/variantPage/FunctionalPrediction.tsx b/src/component/variantPage/FunctionalPrediction.tsx
@@ -8,7 +8,10 @@ import MutationAssessor from './functionalPrediction/MutationAssesor';
 import Sift from './functionalPrediction/Sift';
 import PolyPhen2 from './functionalPrediction/PolyPhen2';
 import AlphaMissense from './functionalPrediction/AlphaMissense';
-import { SHOW_ALPHAMISSENSE } from '../../config/configDefaults';
+import {
+    SHOW_ALPHAMISSENSE,
+    SHOW_MUTATION_ASSESSOR,
+} from '../../config/configDefaults';
 import Separator from '../Separator';
 import { GENOME_BUILD } from '../../util/SearchUtils';
 
@@ -61,7 +64,6 @@ class FunctionalPrediction extends React.Component<IFunctionalPredictionProps> {
         const amPathogenicityScore =
             genomeNexusData?.annotation_summary?.transcriptConsequenceSummary
                 ?.alphaMissense?.score || undefined;
-
         return {
             amClass,
             amPathogenicityScore,
@@ -74,29 +76,34 @@ class FunctionalPrediction extends React.Component<IFunctionalPredictionProps> {
     }
     public render() {
         const data = this.getData(this.props.variantAnnotation);
-        const shouldShowAlphaMissense = SHOW_ALPHAMISSENSE;
+        // Mutation Assessor only available in grch37
+        const shouldShowMutationAssessor =
+            SHOW_MUTATION_ASSESSOR &&
+            this.props.genomeBuild === GENOME_BUILD.GRCh37;
         return (
             <div>
                 <PolyPhen2
                     polyPhenScore={data.polyPhenScore}
                     polyPhenPrediction={data.polyPhenPrediction}
                 />
                 <Separator />
-                <>
-                    <MutationAssessor
-                        mutationAssessor={data.mutationAssessor}
-                        isCanonicalTranscriptSelected={
-                            this.props.isCanonicalTranscriptSelected
-                        }
-                    />
-                    <Separator />
-                </>
+                {shouldShowMutationAssessor && (
+                    <>
+                        <MutationAssessor
+                            mutationAssessor={data.mutationAssessor}
+                            isCanonicalTranscriptSelected={
+                                this.props.isCanonicalTranscriptSelected
+                            }
+                        />
+                        <Separator />
+                    </>
+                )}
                 <Sift
                     siftScore={data.siftScore}
                     siftPrediction={data.siftPrediction}
                 />
                 <Separator />
-                {shouldShowAlphaMissense && (
+                {SHOW_ALPHAMISSENSE && (
                     <AlphaMissense
                         amClass={data.amClass}
                         amPathogenicityScore={data.amPathogenicityScore}

diff --git a/src/component/variantPage/functionalPrediction/AlphaMissense.tsx b/src/component/variantPage/functionalPrediction/AlphaMissense.tsx
@@ -1,7 +1,6 @@
 import * as React from 'react';
 import { DefaultTooltip } from 'cbioportal-frontend-commons';
 import { makeObservable, observable } from 'mobx';
-import { observer } from 'mobx-react';
 import functionalGroupsStyle from '../functionalGroups.module.scss';
 
 export interface IAlphaMissenseProps {
@@ -45,13 +44,10 @@ const AlphaMissenseInfo: React.FunctionComponent = () => {
     );
 };
 
-@observer
 export default class AlphaMissense extends React.Component<
     IAlphaMissenseProps,
     {}
 > {
-    @observable showDetails = false;
-
     constructor(props: IAlphaMissenseProps) {
         super(props);
         makeObservable(this);
@@ -66,18 +62,12 @@ export default class AlphaMissense extends React.Component<
                 <i className="fas fa-external-link-alt" />
             </>
         );
-        if (
-            this.props.amClass &&
-            this.props.amClass.length > 0 &&
-            this.props.amClass !== 'N/A'
-        ) {
+        if (this.props.amClass) {
             alphaMissenseContent = (
-                <span>
-                    <p>
-                        {this.props.amClass + ' '}(
-                        {this.props.amPathogenicityScore})
-                    </p>{' '}
-                </span>
+                <p>
+                    {this.props.amClass + ' '}({this.props.amPathogenicityScore}
+                    )
+                </p>
             );
         } else {
             alphaMissenseContent = <span> N/A </span>;