diff --git a/apps/platform/src/pages/VariantPage/Profile.tsx b/apps/platform/src/pages/VariantPage/Profile.tsx index 7be750c7d..d8707401b 100644 --- a/apps/platform/src/pages/VariantPage/Profile.tsx +++ b/apps/platform/src/pages/VariantPage/Profile.tsx @@ -1,12 +1,71 @@ +import { Suspense, lazy } from "react"; +import { + // PlatformApiProvider, + SectionContainer, + SummaryContainer, + SectionLoader, +} from "ui"; + +import InSilicoPredictorsSummary from "sections/src/variant/InSilicoPredictors/Summary"; +import EVASummary from "sections/src/variant/EVA/Summary"; +import UniProtVariantsSummary from "sections/src/variant/UniProtVariants/Summary"; + import ProfileHeader from "./ProfileHeader"; +const InSilicoPredictorsSection = lazy(() => import("sections/src/variant/InSilicoPredictors/Body")); +const EVASection = lazy(() => import("sections/src/variant/EVA/Body")); +const UniProtVariantsSection = lazy(() => import("sections/src/variant/UniProtVariants/Body")); + +const summaries = [ + InSilicoPredictorsSummary, + EVASummary, + UniProtVariantsSummary +]; + +const VARIANT = "variant"; + +// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +// TO DO (see e.g. profile.jsx for the evidence page): +// - VARIANT_PROFILE_SUMMARY_FRAGMENT +// - EVIDENCE_PROFILE_QUERY +// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + type ProfileProps = { varId: string; }; function Profile({ varId }: ProfileProps) { - return + return ( + // !!!!!!!!!! + // PUT EVERYTHING INSIDE INSTEAD OF FRAGMENT + // !!!!!!!!!! + <> + + + + + + + + + + + }> + + + }> + + + }> + + + {/* NEED ANYTHING IN ???? see evidence page */} + + + + + ); } diff --git a/apps/platform/src/pages/VariantPage/types.ts b/apps/platform/src/pages/VariantPage/types.ts index 24c24585d..3e3de5f40 100644 --- a/apps/platform/src/pages/VariantPage/types.ts +++ b/apps/platform/src/pages/VariantPage/types.ts @@ -1,3 +1,8 @@ + +// ======== +// Metadata +// ======== + export type AlleleFrequencyType = { populationName: string; alleleFrequency: number; @@ -37,5 +42,56 @@ export type MetadataType = { alleleType: string; alleleFrequencies: AlleleFrequencyType[]; vep: VepType; - inSilicoPredictors: InSilicoPredictorsType; -}; \ No newline at end of file +}; + +// ================== +// InSilicoPredictors +// ================== + +export type InSilicoPredictorsType = { + [index: number]: { + method: string, + assesessment?: string, + flag?: string, + score?: number, + } +}; + +// ======= +// ClinVar +// ======= + +export type ClinVarType = { + alleleOrigins: string[], + alleleRequirements: string[], + approvedSymbol: string, + clinicalSignificances: string[], + cohortPhenotypes: string[], + confidence: string, + directionOnTrait: "risk", + "disease.id": string, + "disease.name": string, + diseaseFromSource: string, + diseaseId: string, + diseaseName: string, + literature: string[], + studyId: string, + targetId: string, + variantId: string, +}; + +// =============== +// UniProtVariants +// =============== + +export type UniProtVariants = { + variantId: string, + confidence: string, + diseaseFromSource: string, + literature: string[], + targetFromSourceId: string, + "target.id": string, + "target.approvedSymbol": string, + "disease.id": string, + "disease.name": string, +}; diff --git a/apps/platform/src/sections/variantSections.js b/apps/platform/src/sections/variantSections.js new file mode 100644 index 000000000..6332e4972 --- /dev/null +++ b/apps/platform/src/sections/variantSections.js @@ -0,0 +1,7 @@ +import { lazy } from "react"; + +const variantSections = new Map([ + ["eva", lazy(() => import("sections/src/evidence/EVA/Body"))], +]); + +export default variantSections; diff --git a/packages/sections/src/variant/EVA/Body.tsx b/packages/sections/src/variant/EVA/Body.tsx new file mode 100644 index 000000000..4a222b85e --- /dev/null +++ b/packages/sections/src/variant/EVA/Body.tsx @@ -0,0 +1,2964 @@ +import { + Link, + Tooltip, + SectionItem, + PublicationsDrawer, + DataTable, + ClinvarStars, +} from "ui"; +import { Typography } from "@mui/material"; +import { + clinvarStarMap, + naLabel, + defaultRowsPerPageOptions, +} from "../../constants"; +import { definition } from "."; + +import Description from "./Description"; +import { epmcUrl } from "../../utils/urls"; +import { sentenceCase } from "../../utils/global"; + +// !! NEEDED?? +const onLinkClick = e => { + // handler to stop propagation of clicks on links in table rows + // to avoid selection of a different row + e.stopPropagation(); +}; + +function getColumns(label: string) { + return [ + { + id: "disease.name", + label: "Disease/phenotype", + renderCell: (d) => { // !! DESTRUCTURE AS NORMAL WHEN USE GQL WITHOUT THESE ODD PROPERTY NAMES + const disease_id = d["disease.id"] + const disease_name = d["disease.name"]; + const { diseaseFromSource, cohortPhenotypes } = d; + return ( + + + Reported disease or phenotype: + + + {diseaseFromSource} + + {cohortPhenotypes?.length > 1 ? ( + <> + + All reported phenotypes: + + + {cohortPhenotypes.map(cp => ( +
{cp}
+ ))} +
+ + ) : ( + "" + )} + + } + showHelpIcon + > + {/* !! ANY !! as any needed below since onClick sig expects no args !! */} + + {disease_name} + +
+ ) + }, + exportLabel: "Disease/Phenotype", + exportValue: disease_name => disease_name, + filterValue: disease_name => disease_name, + }, + { + id: "studyId", + label: "ClinVar ID", + renderCell: ({ studyId }) => + studyId ? ( + + {studyId} + + ) : ( + naLabel + ), + exportLabel: "ClinVar ID", + }, + { + id: "clinicalSignificances", + label: "Clinical significance", + renderCell: ({ clinicalSignificances }) => { + if (!clinicalSignificances) return naLabel; + if (clinicalSignificances.length === 1) return sentenceCase(clinicalSignificances[0]); + if (clinicalSignificances.length > 1) + return ( +
    + {clinicalSignificances.map(clinicalSignificance => ( +
  • {sentenceCase(clinicalSignificance)}
  • + ))} +
+ ); + return naLabel; + }, + filterValue: ({ clinicalSignificances }) => clinicalSignificances.join(), + }, + { + id: "allelicRequirements", + label: "Allele origin", + renderCell: ({ alleleOrigins, allelicRequirements }) => { + if (!alleleOrigins || alleleOrigins.length === 0) return naLabel; + if (allelicRequirements) + return ( + + + Allelic requirements: + + {allelicRequirements.map(r => ( + + {r} + + ))} + + } + showHelpIcon + > + {alleleOrigins.map(a => sentenceCase(a)).join("; ")} + + ); + return alleleOrigins.map(a => sentenceCase(a)).join("; "); + }, + filterValue: ({ alleleOrigins }) => (alleleOrigins ? alleleOrigins.join() : ""), + }, + { + id: "reviewStatus", + label: "Review status", + renderCell: ({ confidence }) => ( + + + + + + ), + }, + { + id: "literature", + label: "Literature", + renderCell: ({ literature }) => { + const literatureList = + literature?.reduce((acc, id) => { + if (id !== "NA") { + acc.push({ + name: id, + url: epmcUrl(id), + group: "literature", + }); + } + return acc; + }, []) || []; + return ( + + ); + }, + }, + ]; +} + +// !!!! LOAD LOCAL DATA FOR NOW +// const [metadata, setMetadata] = +// useState("waiting"); +const request = mockQuery(); + +type BodyProps = { + id: string, + label: string, + entity: string, +}; + +function Body({ id, label, entity }: BodyProps) { + + const columns = getColumns(label); + const rows = request.data.variant.eva; + + return ( + } + renderBody={() => ( + + )} + /> + ); + +} + +export default Body; + + +// !! HARDCODE DATA FOR NOW !! +function mockQuery() { + return { + loading: false, + error: undefined, + data: JSON.parse(` +{ + "variant": { + "eva": [ + { + "alleleOrigins": [ + "germline", + "maternal", + "paternal" + ], + "allelicRequirements": [ + "Autosomal recessive inheritance" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Diffuse cerebral degeneration in infancy", + "Infantile poliodystrophy", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Neuronal degeneration of childhood with liver disease, progressive", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive sclerosing poliodystrophy" + ], + "confidence": "criteria provided, multiple submitters, no conflicts", + "directionOnTrait": "risk", + "disease.id": "MONDO_0008758", + "disease.name": "mitochondrial DNA depletion syndrome 4a", + "diseaseFromSource": "Progressive sclerosing poliodystrophy", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "literature": [ + "11431686", + "11571332", + "12565911", + "14694057", + "15122711", + "15477547", + "15824347", + "16130100", + "16177225", + "17426723", + "19251978", + "21276947", + "26942291", + "26942292", + "632821" + ], + "studyId": "RCV000014443", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline", + "maternal", + "paternal" + ], + "allelicRequirements": [ + "Autosomal recessive inheritance" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Diffuse cerebral degeneration in infancy", + "Infantile poliodystrophy", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Neuronal degeneration of childhood with liver disease, progressive", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive sclerosing poliodystrophy" + ], + "confidence": "criteria provided, multiple submitters, no conflicts", + "directionOnTrait": "risk", + "disease.id": "Orphanet_726", + "disease.name": "Alpers syndrome", + "diseaseFromSource": "Progressive sclerosing poliodystrophy", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "literature": [ + "11431686", + "11571332", + "12565911", + "14694057", + "15122711", + "15477547", + "15824347", + "16130100", + "16177225", + "17426723", + "19251978", + "21276947", + "26942291", + "26942292", + "632821" + ], + "studyId": "RCV000014443", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline", + "maternal", + "paternal" + ], + "allelicRequirements": [ + "Autosomal recessive inheritance" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Epilepsy, progressive myoclonic, type 5", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, multiple submitters, no conflicts", + "directionOnTrait": "risk", + "disease.id": "MONDO_0011835", + "disease.name": "sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "diseaseFromSource": "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "literature": [ + "11431686", + "11571332", + "12565911", + "14694057", + "15122711", + "15477547", + "15824347", + "16130100", + "16177225", + "17426723", + "19251978", + "21276947", + "26942291", + "26942292", + "632821" + ], + "studyId": "RCV000014441", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline", + "maternal", + "paternal" + ], + "allelicRequirements": [ + "Autosomal recessive inheritance" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Epilepsy, progressive myoclonic, type 5", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, multiple submitters, no conflicts", + "directionOnTrait": "risk", + "disease.id": "Orphanet_70595", + "disease.name": "Sensory ataxic neuropathy - dysarthria - ophthalmoparesis", + "diseaseFromSource": "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "literature": [ + "11431686", + "11571332", + "12565911", + "14694057", + "15122711", + "15477547", + "15824347", + "16130100", + "16177225", + "17426723", + "19251978", + "21276947", + "26942291", + "26942292", + "632821" + ], + "studyId": "RCV000014441", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "allelicRequirements": [ + "Autosomal recessive inheritance" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1" + ], + "confidence": "criteria provided, multiple submitters, no conflicts", + "directionOnTrait": "risk", + "disease.id": "MONDO_0018002", + "disease.name": "adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy", + "diseaseFromSource": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "literature": [ + "11431686", + "11571332", + "12565911", + "14694057", + "15122711", + "15477547", + "15824347", + "16130100", + "16177225", + "17426723", + "19251978", + "21276947", + "26942291", + "26942292", + "632821" + ], + "studyId": "RCV000014440", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "allelicRequirements": [ + "Autosomal recessive inheritance" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1" + ], + "confidence": "criteria provided, multiple submitters, no conflicts", + "directionOnTrait": "risk", + "disease.id": "MONDO_0016810", + "disease.name": "autosomal recessive progressive external ophthalmoplegia", + "diseaseFromSource": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "literature": [ + "11431686", + "11571332", + "12565911", + "14694057", + "15122711", + "15477547", + "15824347", + "16130100", + "16177225", + "17426723", + "19251978", + "21276947", + "26942291", + "26942292", + "632821" + ], + "studyId": "RCV000014440", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "maternal" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1" + ], + "confidence": "criteria provided, multiple submitters, no conflicts", + "directionOnTrait": "risk", + "disease.id": "MONDO_0008003", + "disease.name": "autosomal dominant progressive external ophthalmoplegia", + "diseaseFromSource": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "studyId": "RCV000184011", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MNGIE, POLG-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Neuronal degeneration of childhood with liver disease, progressive", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0018002", + "disease.name": "adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy", + "diseaseFromSource": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "studyId": "RCV001731286", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "MNGIE, POLG-RELATED", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0017575", + "disease.name": "mitochondrial neurogastrointestinal encephalomyopathy", + "diseaseFromSource": "Mitochondrial DNA depletion syndrome 4b", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "studyId": "RCV001198082", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MITOCHONDRIAL NEUROGASTROINTESTINAL ENCEPHALOPATHY SYNDROME, TYMP-RELATED", + "MNGIE, POLG-RELATED", + "MNGIE, TYMP-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA Depletion Syndrome, MNGIE Form", + "Mitochondrial DNA depletion syndrome 1", + "Mitochondrial DNA depletion syndrome 1 (MNGIE type)", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Mitochondrial neurogastrointestinal encephalomyopathy syndrome", + "Neuronal degeneration of childhood with liver disease, progressive", + "POLIP SYNDROME", + "POLYNEUROPATHY, OPHTHALMOPLEGIA, LEUKOENCEPHALOPATHY, AND INTESTINAL PSEUDOOBSTRUCTION", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0008003", + "disease.name": "autosomal dominant progressive external ophthalmoplegia", + "diseaseFromSource": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "studyId": "RCV000515354", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MNGIE, POLG-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Neuronal degeneration of childhood with liver disease, progressive", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0018002", + "disease.name": "adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy", + "diseaseFromSource": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "studyId": "RCV001813983", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MNGIE, POLG-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Neuronal degeneration of childhood with liver disease, progressive", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "Orphanet_726", + "disease.name": "Alpers syndrome", + "diseaseFromSource": "Progressive sclerosing poliodystrophy", + "diseaseId": "EFO_0000508", + "diseaseName": "genetic disorder", + "studyId": "RCV001731286", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" 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depletion syndrome 4b", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV000515354", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MITOCHONDRIAL NEUROGASTROINTESTINAL ENCEPHALOPATHY SYNDROME, TYMP-RELATED", + "MNGIE, POLG-RELATED", + "MNGIE, TYMP-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA Depletion Syndrome, MNGIE Form", + "Mitochondrial DNA depletion syndrome 1", + "Mitochondrial DNA depletion syndrome 1 (MNGIE type)", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Mitochondrial neurogastrointestinal encephalomyopathy syndrome", + "Neuronal degeneration of childhood with liver disease, progressive", + "POLIP SYNDROME", + "POLYNEUROPATHY, OPHTHALMOPLEGIA, LEUKOENCEPHALOPATHY, AND INTESTINAL PSEUDOOBSTRUCTION", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0018002", + "disease.name": "adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy", + "diseaseFromSource": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV000515354", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MITOCHONDRIAL NEUROGASTROINTESTINAL ENCEPHALOPATHY SYNDROME, TYMP-RELATED", + "MNGIE, POLG-RELATED", + "MNGIE, TYMP-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA Depletion Syndrome, MNGIE Form", + "Mitochondrial DNA depletion syndrome 1", + "Mitochondrial DNA depletion syndrome 1 (MNGIE type)", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Mitochondrial neurogastrointestinal encephalomyopathy syndrome", + "Neuronal degeneration of childhood with liver disease, progressive", + "POLIP SYNDROME", + "POLYNEUROPATHY, OPHTHALMOPLEGIA, LEUKOENCEPHALOPATHY, AND INTESTINAL PSEUDOOBSTRUCTION", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0008758", + "disease.name": "mitochondrial DNA depletion syndrome 4a", + "diseaseFromSource": "Progressive sclerosing poliodystrophy", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV000515354", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MNGIE, POLG-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Neuronal degeneration of childhood with liver disease, progressive", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0008003", + "disease.name": "autosomal dominant progressive external ophthalmoplegia", + "diseaseFromSource": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV001731286", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MITOCHONDRIAL NEUROGASTROINTESTINAL ENCEPHALOPATHY SYNDROME, TYMP-RELATED", + "MNGIE, POLG-RELATED", + "MNGIE, TYMP-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA Depletion Syndrome, MNGIE Form", + "Mitochondrial DNA depletion syndrome 1", + "Mitochondrial DNA depletion syndrome 1 (MNGIE type)", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Mitochondrial neurogastrointestinal encephalomyopathy syndrome", + "Neuronal degeneration of childhood with liver disease, progressive", + "POLIP SYNDROME", + "POLYNEUROPATHY, OPHTHALMOPLEGIA, LEUKOENCEPHALOPATHY, AND INTESTINAL PSEUDOOBSTRUCTION", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0011283", + "disease.name": "mitochondrial DNA depletion syndrome 1", + "diseaseFromSource": "Mitochondrial DNA depletion syndrome 1", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV000515354", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MNGIE, POLG-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Neuronal degeneration of childhood with liver disease, progressive", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0016810", + "disease.name": "autosomal recessive progressive external ophthalmoplegia", + "diseaseFromSource": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV001731286", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MNGIE, POLG-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Neuronal degeneration of childhood with liver disease, progressive", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0008758", + "disease.name": "mitochondrial DNA depletion syndrome 4a", + "diseaseFromSource": "Progressive sclerosing poliodystrophy", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV001731286", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MNGIE, POLG-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Neuronal degeneration of childhood with liver disease, progressive", + "PROGRESSIVE EXTERNAL OPHTHALMOPLEGIA, AUTOSOMAL DOMINANT 1", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0017575", + "disease.name": "mitochondrial neurogastrointestinal encephalomyopathy", + "diseaseFromSource": "Mitochondrial DNA depletion syndrome 4b", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV001731286", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MNGIE, POLG-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Neuronal degeneration of childhood with liver disease, progressive", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0011835", + "disease.name": "sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "diseaseFromSource": "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV001813983", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + }, + { + "alleleOrigins": [ + "germline" + ], + "approvedSymbol": "POLG", + "clinicalSignificances": [ + "pathogenic" + ], + "cohortPhenotypes": [ + "Alpers Syndrome", + "Alpers diffuse degeneration of cerebral gray matter with hepatic cirrhosis", + "Alpers disease", + "Alpers progressive infantile poliodystrophy", + "Alpers-Huttenlocher Syndrome", + "Cerebellar ataxia infantile with progressive external ophthalmoplegia", + "Diffuse cerebral degeneration in infancy", + "Epilepsy, progressive myoclonic, type 5", + "Infantile poliodystrophy", + "MNGIE, POLG-RELATED", + "Mitochondrial DNA Depletion Syndrome 4A", + "Mitochondrial DNA depletion syndrome 4A (Alpers type)", + "Mitochondrial DNA depletion syndrome 4B, MNGIE type", + "Mitochondrial DNA depletion syndrome 4b", + "Mitochondrial Neurogastrointestinal Encephalopathy Disease, POLG-Related", + "Neuronal degeneration of childhood with liver disease, progressive", + "Poliodystrophia cerebri progressiva", + "Progressive cerebral poliodystrophy", + "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1", + "Progressive external ophthalmoplegia, autosomal recessive 1", + "Progressive sclerosing poliodystrophy", + "SENSORY ATAXIC NEUROPATHY WITH MITOCHONDRIAL DNA DELETIONS, AUTOSOMAL RECESSIVE", + "Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis", + "Sensory ataxic neuropathy-dysarthria-ophthalmoparesis syndrome" + ], + "confidence": "criteria provided, single submitter", + "directionOnTrait": "risk", + "disease.id": "MONDO_0008758", + "disease.name": "mitochondrial DNA depletion syndrome 4a", + "diseaseFromSource": "Progressive sclerosing poliodystrophy", + "diseaseId": "MONDO_0044970", + "diseaseName": "mitochondrial disease", + "studyId": "RCV001813983", + "targetId": "ENSG00000140521", + "variantId": "15_89327201_C_T" + } + ] + } +}`), + }; +} \ No newline at end of file diff --git a/packages/sections/src/variant/EVA/Description.tsx b/packages/sections/src/variant/EVA/Description.tsx new file mode 100644 index 000000000..be03b02b6 --- /dev/null +++ b/packages/sections/src/variant/EVA/Description.tsx @@ -0,0 +1,18 @@ +import { Link } from "ui"; + +type DescriptionProps = { + variantId: string; +}; + +function Description({ variantId }: DescriptionProps) { + return ( + <> + Genetic variation from clinical submissions associating {variantId} to a disease/phenotype. Source:{" "} + + EVA + + + ); +} + +export default Description; diff --git a/packages/sections/src/variant/EVA/Summary.tsx b/packages/sections/src/variant/EVA/Summary.tsx new file mode 100644 index 000000000..437471d25 --- /dev/null +++ b/packages/sections/src/variant/EVA/Summary.tsx @@ -0,0 +1,42 @@ +import { SummaryItem, usePlatformApi } from "ui"; + +import { definition } from "."; +import { dataTypesMap } from "../../dataTypes"; +// import EVA_SUMMARY from "./EVASummaryQuery.gql"; + +function Summary() { + + // !! THIS IS UGLY BUT AVOIDS ADDING TYPES IN dataType FILE FOR NOW + type dataTypesMapType = { + [index: string]: number; + }; + const dataTypesMapTyped = dataTypesMap as dataTypesMapType; + + // !! USE PLACEHOLDER REQUEST FOR NOW !! + // const request = usePlatformApi(EVA_SUMMARY); + const request = { + loading: false, + error: undefined, + data: true, // data is not actually used by summary - only cares if there is data + }; + + return ( + {}} // !! renderSummary PROP NOT USED ANYMORE ANYWAY? + // renderSummary={({ evaSummary }) => { + // const { count } = evaSummary; + // return `${count} ${count === 1 ? "entry" : "entries"}`; + // }} + subText={dataTypesMapTyped.genetic_association} + /> + ); +} + +// !!!!!!!!!!! +// Summary.fragments = { +// evaSummary: EVA_SUMMARY, +// }; + +export default Summary; \ No newline at end of file diff --git a/packages/sections/src/variant/EVA/index.ts b/packages/sections/src/variant/EVA/index.ts new file mode 100644 index 000000000..2e223cb27 --- /dev/null +++ b/packages/sections/src/variant/EVA/index.ts @@ -0,0 +1,16 @@ + +// !!!!!!!!!! +// ADD POSSIBILITY FOR PRIVATE SECTIONS IN PARTNER PAGE +// !!!!!!!!!! +// import { isPrivateVariantSection } from "../../utils/partnerPreviewUtils"; + +// !! NEED TO TYPE WHATEVER PASSED INTO HASDATA - SEE SUMMARY +const id = "eva"; +export const definition = { + id, + name: "ClinVar", + shortName: "CV", + hasData: () => true, // !! CHANGE WHEN USE GQL !! + // hasData: ({ eva }) => eva.count > 0, + isPrivate: false, // isPrivateVariantSection(id), +}; diff --git a/packages/sections/src/variant/InSilicoPredictors/Body.tsx b/packages/sections/src/variant/InSilicoPredictors/Body.tsx new file mode 100644 index 000000000..a618f622a --- /dev/null +++ b/packages/sections/src/variant/InSilicoPredictors/Body.tsx @@ -0,0 +1,135 @@ +// import { useQuery } from "@apollo/client"; +import { Typography } from "@mui/material"; +import { Link, SectionItem, Tooltip, PublicationsDrawer, DataTable } from "ui"; +import { definition } from "../InSilicoPredictors"; +import Description from "../InSilicoPredictors/Description"; +import { epmcUrl } from "../../utils/urls"; +import { identifiersOrgLink } from "../../utils/global"; +import { defaultRowsPerPageOptions, naLabel, sectionsBaseSizeQuery, +} from "../../constants"; +// import UNIPROT_VARIANTS_QUERY from "./UniprotVariantsQuery.gql"; + +function getColumns(label: string) { + return [ + { + id: "method", + label: "Method", + }, + { + id: "assessment", + label: "Prediction", + renderCell: ({ assessment, flag }) => ( + flag + ? ( + + + Flag: {flag} + + + } + showHelpIcon + > + {assessment ?? naLabel} + + ) : ( + assessment ?? naLabel + ) + ) + }, + { + id: "score", + label: "Score", + }, + ]; +} + +type BodyProps = { + id: string, + label: string, + entity: string, +}; + + +export function Body({ id, label, entity }) { + + // const variables = { + // ensemblId: ensgId, + // efoId, + // size: sectionsBaseSizeQuery, + // }; + + const columns = getColumns(label); + + // const request = useQuery(UNIPROT_VARIANTS_QUERY, { + // variables, + // }); + const request = mockQuery(); + + return ( + } + renderBody={() => { + // const rows = request.data.variant.inSilicoPredictors; + const rows = + [...request.data.variant.inSilicoPredictors].sort((row1, row2) => { + return row1.method.localeCompare(row2.method); + }); + return ( + + ); + }} + /> + ); +} + +export default Body; + +function mockQuery() { + return { + loading: false, + error: undefined, + data: JSON.parse(` +{ + "variant": { + "inSilicoPredictors": [ + { + "method": "alphaMissense", + "score": 0.077, + "assessment": "likely_benign" + }, + { + "method": "phred scaled CADD", + "score": 7.293 + }, + { + "method": "sift max", + "score": 0.2, + "assessment": "MODERATE" + }, + { + "method": "polyphen max", + "score": 0.069, + "assessment": "tolerated" + }, + { + "method": "loftee", + "assessment": "high-confidence LoF variant", + "flag": "PHYLOCSF_WEAK" + } + ] + } +}`), + }; +} diff --git a/packages/sections/src/variant/InSilicoPredictors/Description.tsx b/packages/sections/src/variant/InSilicoPredictors/Description.tsx new file mode 100644 index 000000000..7125d6ea3 --- /dev/null +++ b/packages/sections/src/variant/InSilicoPredictors/Description.tsx @@ -0,0 +1,18 @@ +import { Link } from "ui"; + +type DescriptionProps = { + variantId: string; +}; + +function Description({ variantId }: DescriptionProps) { + return ( + <> + Predicted functional effect of {variantId}. {" "}Source:{" "} + + VEP + + + ); +} + +export default Description; \ No newline at end of file diff --git a/packages/sections/src/variant/InSilicoPredictors/Summary.tsx b/packages/sections/src/variant/InSilicoPredictors/Summary.tsx new file mode 100644 index 000000000..fd8d58567 --- /dev/null +++ b/packages/sections/src/variant/InSilicoPredictors/Summary.tsx @@ -0,0 +1,42 @@ +import { SummaryItem, usePlatformApi } from "ui"; + +import { definition } from "."; +import { dataTypesMap } from "../../dataTypes"; +// import UNIPROT_VARIANTS_SUMMARY from "./UniprotVariantsSummaryQuery.gql"; + +function Summary() { + + // !! THIS IS UGLY BUT AVOIDS ADDING TYPES IN dataType FILE FOR NOW + type dataTypesMapType = { + [index: string]: number; + }; + const dataTypesMapTyped = dataTypesMap as dataTypesMapType; + + // !! USE PLACEHOLDER REQUEST FOR NOW !! + // const request = usePlatformApi(UNIPROT_VARIANTS_SUMMARY); + const request = { + loading: false, + error: undefined, + data: true, // data is not actually used by summary - only cares if there is data + }; + + return ( + {}} // !! renderSummary PROP NOT USED ANYMORE ANYWAY? + // renderSummary={({ uniprotVariantsSummary }) => { + // const { count } = uniprotVariantsSummary; + // return `${count} ${count === 1 ? "entry" : "entries"}`; + // }} + subText={dataTypesMapTyped.genetic_association} // !! LEAVE AS GENETIC ASSOCITION FOR NOW + /> + ); +} + +// !!!!!!!!!!!!! +// Summary.fragments = { +// UniprotVariantsSummary: UNIPROT_VARIANTS_SUMMARY, +// }; + +export default Summary; diff --git a/packages/sections/src/variant/InSilicoPredictors/index.ts b/packages/sections/src/variant/InSilicoPredictors/index.ts new file mode 100644 index 000000000..2b681c2fd --- /dev/null +++ b/packages/sections/src/variant/InSilicoPredictors/index.ts @@ -0,0 +1,11 @@ +// import { isPrivateEvidenceSection } from "../../utils/partnerPreviewUtils"; + +const id = "in_silico_predictors"; +export const definition = { + id, + name: "In silico predictors", + shortName: "VP", + // UPDATE HERE ONCE HAVE PROPER DATA + hasData: data => true, // data.uniprotVariantsSummary.count > 0, + isPrivate: false, // isPrivateEvidenceSection(id), +}; diff --git a/packages/sections/src/variant/UniProtVariants/Body.tsx b/packages/sections/src/variant/UniProtVariants/Body.tsx new file mode 100644 index 000000000..103e99baf --- /dev/null +++ b/packages/sections/src/variant/UniProtVariants/Body.tsx @@ -0,0 +1,289 @@ +// import { useQuery } from "@apollo/client"; +import { Typography } from "@mui/material"; +import { Link, SectionItem, Tooltip, PublicationsDrawer, DataTable } from "ui"; +import { definition } from "../../variant/UniProtVariants"; +import Description from "../../variant/UniProtVariants/Description"; +import { epmcUrl } from "../../utils/urls"; +import { identifiersOrgLink } from "../../utils/global"; +import { defaultRowsPerPageOptions, sectionsBaseSizeQuery, +} from "../../constants"; +// import UNIPROT_VARIANTS_QUERY from "./UniprotVariantsQuery.gql"; + +function getColumns(label: string) { + return [ + { + id: "targetFromSourceId", + label: "Reported protein", + renderCell: ({ targetFromSourceId }) => ( + + {targetFromSourceId} + + ), + }, + { + id: "disease.name", + label: "Disease/phenotype", + renderCell: ({ + "disease.id": disease_id, + "disease.name": disease_name, + diseaseFromSource + }) => ( + + + Reported disease or phenotype: + + + {diseaseFromSource} + + + } + showHelpIcon + > + {disease_name} + + ), + }, + { + id: "confidence", + label: "Confidence", + }, + { + label: "Literature", + renderCell: ({ literature }) => { + const literatureList = + literature?.reduce((acc, id) => { + if (id !== "NA") { + acc.push({ + name: id, + url: epmcUrl(id), + group: "literature", + }); + } + return acc; + }, []) || []; + + return ( + + ); + }, + }, + ]; +} + +type BodyProps = { + id: string, + label: string, + entity: string, +}; + + +export function Body({ id, label, entity }) { + + // ID IS JUST THE VARIANT ID STRING FOR NOW + // const { ensgId, efoId } = id; + + // const variables = { + // ensemblId: ensgId, + // efoId, + // size: sectionsBaseSizeQuery, + // }; + + const columns = getColumns(label); + + // const request = useQuery(UNIPROT_VARIANTS_QUERY, { + // variables, + // }); + const request = mockQuery(); + + return ( + } + renderBody={({ disease }) => { + // const { rows } = disease.uniprotVariantsSummary; + const rows = request.data.variant.uniProtVariants; + return ( + + ); + }} + /> + ); +} + +export default Body; + +function mockQuery() { + return { + loading: false, + error: undefined, + data: JSON.parse(` +{ + "variant": { + "uniProtVariants": [ + { + "variantId": "15_89327201_C_T", + "confidence": "high", + "diseaseFromSource": "Mitochondrial DNA depletion syndrome 4A", + "literature": [ + "16639411", + "15917273", + "15477547", + "14635118", + "15824347", + "11431686", + "15122711", + "26942291", + "12565911", + "18828154", + "14694057", + "15689359", + "12707443" + ], + "targetFromSourceId": "P54098", + "target.id": "ENSG00000140521", + "target.approvedSymbol": "POLG", + "disease.id": "Orphanet_726", + "disease.name": "Alpers syndrome" + }, + { + "variantId": "15_89327201_C_T", + "confidence": "high", + "diseaseFromSource": "Mitochondrial DNA depletion syndrome 4A", + "literature": [ + "16639411", + "15917273", + "15477547", + "14635118", + "15824347", + "11431686", + "15122711", + "26942291", + "12565911", + "18828154", + "14694057", + "15689359", + "12707443" + ], + "targetFromSourceId": "P54098", + "target.id": "ENSG00000140521", + "target.approvedSymbol": "POLG", + "disease.id": "MONDO_0008758", + "disease.name": "mitochondrial DNA depletion syndrome 4a" + }, + { + "variantId": "15_89327201_C_T", + "confidence": "high", + "diseaseFromSource": "Sensory ataxic neuropathy dysarthria and ophthalmoparesis", + "literature": [ + "16639411", + "15917273", + "15477547", + "14635118", + "15824347", + "11431686", + "15122711", + "26942291", + "12565911", + "18828154", + "14694057", + "15689359", + "12707443" + ], + "targetFromSourceId": "P54098", + "target.id": "ENSG00000140521", + "target.approvedSymbol": "POLG", + "disease.id": "MONDO_0011835", + "disease.name": "sensory ataxic neuropathy, dysarthria, and ophthalmoparesis" + }, + { + "variantId": "15_89327201_C_T", + "confidence": "high", + "diseaseFromSource": "Spinocerebellar ataxia with epilepsy", + "literature": [ + "16639411", + "15917273", + "15477547", + "14635118", + "15824347", + "11431686", + "15122711", + "26942291", + "12565911", + "18828154", + "14694057", + "15689359", + "12707443" + ], + "targetFromSourceId": "P54098", + "target.id": "ENSG00000140521", + "target.approvedSymbol": "POLG", + "disease.id": "Orphanet_70595", + "disease.name": "Sensory ataxic neuropathy - dysarthria - ophthalmoparesis" + }, + { + "variantId": "15_89327201_C_T", + "confidence": "high", + "diseaseFromSource": "Sensory ataxic neuropathy dysarthria and ophthalmoparesis", + "literature": [ + "16639411", + "15917273", + "15477547", + "14635118", + "15824347", + "11431686", + "15122711", + "26942291", + "12565911", + "18828154", + "14694057", + "15689359", + "12707443" + ], + "targetFromSourceId": "P54098", + "target.id": "ENSG00000140521", + "target.approvedSymbol": "POLG", + "disease.id": "Orphanet_70595", + "disease.name": "Sensory ataxic neuropathy - dysarthria - ophthalmoparesis" + }, + { + "variantId": "15_89327201_C_T", + "confidence": "high", + "diseaseFromSource": "Spinocerebellar ataxia with epilepsy", + "literature": [ + "16639411", + "15917273", + "15477547", + "14635118", + "15824347", + "11431686", + "15122711", + "26942291", + "12565911", + "18828154", + "14694057", + "15689359", + "12707443" + ], + "targetFromSourceId": "P54098", + "target.id": "ENSG00000140521", + "target.approvedSymbol": "POLG", + "disease.id": "MONDO_0011835", + "disease.name": "sensory ataxic neuropathy, dysarthria, and ophthalmoparesis" + } + ] + } +}`), + }; +} diff --git a/packages/sections/src/variant/UniProtVariants/Description.tsx b/packages/sections/src/variant/UniProtVariants/Description.tsx new file mode 100644 index 000000000..5f5ecf471 --- /dev/null +++ b/packages/sections/src/variant/UniProtVariants/Description.tsx @@ -0,0 +1,18 @@ +import { Link } from "ui"; + +type DescriptionProps = { + variantId: string; +}; + +function Description({ variantId }: DescriptionProps) { + return ( + <> + Literature-based curation associating {variantId}{" "} to a disease/phenotype. Source:{" "} + + UniProt + + + ); +} + +export default Description; \ No newline at end of file diff --git a/packages/sections/src/variant/UniProtVariants/Summary.tsx b/packages/sections/src/variant/UniProtVariants/Summary.tsx new file mode 100644 index 000000000..ba8a8ed22 --- /dev/null +++ b/packages/sections/src/variant/UniProtVariants/Summary.tsx @@ -0,0 +1,42 @@ +import { SummaryItem, usePlatformApi } from "ui"; + +import { definition } from "."; +import { dataTypesMap } from "../../dataTypes"; +// import UNIPROT_VARIANTS_SUMMARY from "./UniprotVariantsSummaryQuery.gql"; + +function Summary() { + + // !! THIS IS UGLY BUT AVOIDS ADDING TYPES IN dataType FILE FOR NOW + type dataTypesMapType = { + [index: string]: number; + }; + const dataTypesMapTyped = dataTypesMap as dataTypesMapType; + + // !! USE PLACEHOLDER REQUEST FOR NOW !! + // const request = usePlatformApi(UNIPROT_VARIANTS_SUMMARY); + const request = { + loading: false, + error: undefined, + data: true, // data is not actually used by summary - only cares if there is data + }; + + return ( + {}} // !! renderSummary PROP NOT USED ANYMORE ANYWAY? + // renderSummary={({ uniprotVariantsSummary }) => { + // const { count } = uniprotVariantsSummary; + // return `${count} ${count === 1 ? "entry" : "entries"}`; + // }} + subText={dataTypesMapTyped.genetic_association} + /> + ); +} + +// !!!!!!!!!!!!! +// Summary.fragments = { +// UniprotVariantsSummary: UNIPROT_VARIANTS_SUMMARY, +// }; + +export default Summary; diff --git a/packages/sections/src/variant/UniProtVariants/index.ts b/packages/sections/src/variant/UniProtVariants/index.ts new file mode 100644 index 000000000..a653651b0 --- /dev/null +++ b/packages/sections/src/variant/UniProtVariants/index.ts @@ -0,0 +1,11 @@ +// import { isPrivateEvidenceSection } from "../../utils/partnerPreviewUtils"; + +const id = "uniprot_variants"; +export const definition = { + id, + name: "UniProt variants", + shortName: "UV", + // !! UPDATE HERE ONCE HAVE PROPER DATA + hasData: data => true, // data.uniprotVariantsSummary.count > 0, + isPrivate: false, // isPrivateEvidenceSection(id), +};