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Add AlphaMissense in Functional prediction
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118
src/component/variantPage/functionalPrediction/AlphaMissense.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,118 @@ | ||
| import * as React from 'react'; | ||
| import { DefaultTooltip } from 'cbioportal-frontend-commons'; | ||
| import { action, makeObservable, observable } from 'mobx'; | ||
| import { observer } from 'mobx-react'; | ||
| import functionalGroupsStyle from '../functionalGroups.module.scss'; | ||
|
|
||
| export interface IAlphaMissenseProps { | ||
| amClass?: string; | ||
| amPathogenicityScore?: number; | ||
| } | ||
|
|
||
| const ALPHAMISSENSE_URL = 'https://www.science.org/doi/10.1126/science.adg7492'; | ||
|
|
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| const AlphaMissenseInfo: React.FunctionComponent = () => { | ||
| return ( | ||
| <div> | ||
| <a | ||
| href={ALPHAMISSENSE_URL} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| AlphaMissense | ||
| </a>{' '} | ||
| is a feature within the VEP plugin used to predict the pathogenicity | ||
| of missense variants. Missense variants refer to changes in a single | ||
| base of the gene that result in a change in the encoded amino acid, | ||
| potentially affecting the function of the protein. AlphaMissense | ||
| utilizes deep learning algorithms to assess the potential impact of | ||
| these variants, aiding researchers in better understanding the | ||
| relationship between the variant, gene function, and disease.{' '} | ||
| <b>Pathogenic:</b> Score > 0.564; significant impact; may cause | ||
| disease. | ||
| <b>Benign:</b> Score < 0.34; minor impact; unlikely to cause | ||
| disease. | ||
| <b>Ambiguous:</b> Score between 0.34 and 0.564; intermediate score; | ||
| insufficient data.-{' '} | ||
| </div> | ||
| ); | ||
| }; | ||
|
|
||
| @observer | ||
| export default class AlphaMissense extends React.Component< | ||
| IAlphaMissenseProps, | ||
| {} | ||
| > { | ||
| @observable showDetails = false; | ||
|
|
||
| constructor(props: IAlphaMissenseProps) { | ||
| super(props); | ||
| makeObservable(this); | ||
| } | ||
|
|
||
| public render() { | ||
| let alphaMissenseContent: JSX.Element; | ||
|
|
||
| const dataSource = ( | ||
| <> | ||
| AlphaMissense | ||
| <i className="fas fa-external-link-alt" /> | ||
| </> | ||
| ); | ||
| if ( | ||
| this.props.amClass && | ||
| this.props.amClass.length > 0 && | ||
| this.props.amClass !== 'N/A' | ||
| ) { | ||
| alphaMissenseContent = ( | ||
| <span> | ||
| <p> | ||
| {this.props.amClass + ' '}( | ||
| {this.props.amPathogenicityScore}) | ||
| </p>{' '} | ||
| </span> | ||
| ); | ||
| } else { | ||
| alphaMissenseContent = <span> N/A </span>; | ||
| } | ||
|
|
||
| return ( | ||
| <div className={functionalGroupsStyle['functional-group']}> | ||
| <div className={functionalGroupsStyle['data-source']}> | ||
| <DefaultTooltip | ||
| placement="top" | ||
| overlay={ | ||
| <div style={{ maxWidth: 450 }}> | ||
| <AlphaMissenseInfo /> | ||
| </div> | ||
| } | ||
| > | ||
| <a | ||
| href={ALPHAMISSENSE_URL} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| {dataSource} | ||
| </a> | ||
| </DefaultTooltip> | ||
| </div> | ||
| <div> | ||
| <span className={functionalGroupsStyle['data-with-link']}> | ||
| <a | ||
| href={ALPHAMISSENSE_URL} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| {alphaMissenseContent} | ||
| </a> | ||
| </span> | ||
| </div> | ||
| </div> | ||
| ); | ||
| } | ||
|
|
||
| @action | ||
| onToggleDetails = () => { | ||
| this.showDetails = !this.showDetails; | ||
| }; | ||
| } |
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