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222 changes: 222 additions & 0 deletions
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screenshot-test/data/api-private-search-variants-bio-APC.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,222 @@ | ||
| [ | ||
| { | ||
| "mutationEffectDescription": "The APC R640G mutation is located in the Armadillo repeat region of the APC protein. This mutation has been found as a germline mutation in familial adenomatous polyposis (FAP), a cancer predisposition syndrome. In vitro studies have demonstrated that this mutation is likely inactivating as measured by defective splicing of the APC protein compared to wildtype (PMID: 19111562).", | ||
| "variant": { | ||
| "gene": { | ||
| "entrezGeneId": 324, | ||
| "hugoSymbol": "APC", | ||
| "oncogene": false, | ||
| "grch37Isoform": "ENST00000257430", | ||
| "grch37RefSeq": "NM_000038.5", | ||
| "grch38Isoform": "ENST00000257430", | ||
| "grch38RefSeq": "NM_000038.5", | ||
| "geneAliases": [ | ||
| "PPP1R46", | ||
| "DP2.5" | ||
| ], | ||
| "genesets": [], | ||
| "tsg": true | ||
| }, | ||
| "consequence": { | ||
| "term": "missense_variant", | ||
| "isGenerallyTruncating": false, | ||
| "description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved" | ||
| }, | ||
| "alteration": "R640G", | ||
| "name": "R640G", | ||
| "refResidues": "R", | ||
| "proteinStart": 640, | ||
| "proteinEnd": 640, | ||
| "variantResidues": "G", | ||
| "referenceGenomes": [ | ||
| "GRCh37", | ||
| "GRCh38" | ||
| ] | ||
| }, | ||
| "mutationEffect": "Loss-of-function", | ||
| "mutationEffectPmids": [ | ||
| "19111562" | ||
| ], | ||
| "mutationEffectAbstracts": [], | ||
| "oncogenic": "Oncogenic", | ||
| "oncogenicPmids": [], | ||
| "oncogenicAbstracts": [] | ||
| }, | ||
| { | ||
| "mutationEffectDescription": "APC deletions have been detected in patients with familial adenomatous polyposis (PMID: 15643602, 25317407). These alterations predominantly encompass the entire APC locus leading to haploinsuffuciciency (PMID: 11867715). Based on the function of APC as a tumor suppressor, loss of APC through deletion mutations is likely to result in aberrant WNT-pathway activation and is associated with hyperplasia and eventual tumor progression (PMID: 8259511).", | ||
| "variant": { | ||
| "gene": { | ||
| "entrezGeneId": 324, | ||
| "hugoSymbol": "APC", | ||
| "oncogene": false, | ||
| "grch37Isoform": "ENST00000257430", | ||
| "grch37RefSeq": "NM_000038.5", | ||
| "grch38Isoform": "ENST00000257430", | ||
| "grch38RefSeq": "NM_000038.5", | ||
| "geneAliases": [ | ||
| "PPP1R46", | ||
| "DP2.5" | ||
| ], | ||
| "genesets": [], | ||
| "tsg": true | ||
| }, | ||
| "consequence": { | ||
| "term": "NA", | ||
| "isGenerallyTruncating": false, | ||
| "description": "NA" | ||
| }, | ||
| "alteration": "Deletion", | ||
| "name": "Deletion", | ||
| "refResidues": null, | ||
| "proteinStart": -1, | ||
| "proteinEnd": 100000, | ||
| "variantResidues": null, | ||
| "referenceGenomes": [ | ||
| "GRCh37", | ||
| "GRCh38" | ||
| ] | ||
| }, | ||
| "mutationEffect": "Likely Loss-of-function", | ||
| "mutationEffectPmids": [ | ||
| "8259511", | ||
| "15643602", | ||
| "25317407", | ||
| "11867715" | ||
| ], | ||
| "mutationEffectAbstracts": [], | ||
| "oncogenic": "Likely Oncogenic", | ||
| "oncogenicPmids": [], | ||
| "oncogenicAbstracts": [] | ||
| }, | ||
| { | ||
| "mutationEffectDescription": "Truncating APC mutations result in loss of full-length APC protein leading to impaired or abnormal APC function. APC deregulation is associated with accumulation of β-catenin, an oncogenic transcription factor, which in turn leads to aberrant target gene expression and tumorigenesis (PMID: 11062151). APC truncating mutations are typically early events occurring on a single allele (germline or somatic); however, the tumor often acquires a second hit on the second allele, reducing the overall amount of functional APC in the cell (PMID: 11257105). Furthermore, expression of truncating mutations of APC has been shown to result in chromosomal instability in a dominant manner, postulated to play an important role in the accumulation of additional oncogenic alterations (PMID: 15561772).", | ||
| "variant": { | ||
| "gene": { | ||
| "entrezGeneId": 324, | ||
| "hugoSymbol": "APC", | ||
| "oncogene": false, | ||
| "grch37Isoform": "ENST00000257430", | ||
| "grch37RefSeq": "NM_000038.5", | ||
| "grch38Isoform": "ENST00000257430", | ||
| "grch38RefSeq": "NM_000038.5", | ||
| "geneAliases": [ | ||
| "PPP1R46", | ||
| "DP2.5" | ||
| ], | ||
| "genesets": [], | ||
| "tsg": true | ||
| }, | ||
| "consequence": { | ||
| "term": "feature_truncation", | ||
| "isGenerallyTruncating": true, | ||
| "description": "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence" | ||
| }, | ||
| "alteration": "Truncating Mutations", | ||
| "name": "Truncating Mutations", | ||
| "refResidues": null, | ||
| "proteinStart": -1, | ||
| "proteinEnd": 100000, | ||
| "variantResidues": null, | ||
| "referenceGenomes": [ | ||
| "GRCh37", | ||
| "GRCh38" | ||
| ] | ||
| }, | ||
| "mutationEffect": "Likely Loss-of-function", | ||
| "mutationEffectPmids": [ | ||
| "11062151", | ||
| "15561772", | ||
| "11257105" | ||
| ], | ||
| "mutationEffectAbstracts": [], | ||
| "oncogenic": "Likely Oncogenic", | ||
| "oncogenicPmids": [], | ||
| "oncogenicAbstracts": [] | ||
| }, | ||
| { | ||
| "mutationEffectDescription": "The APC I1307K mutation is located near a β-catenin binding domain in the APC protein. This mutation has been found as a germline mutation in familial adenomatous polyposis (FAP), a cancer predisposition syndrome, and sporadic colorectal cancer. While this mutation has not been functionally characterized, structural modeling shows that this mutation is likely inactivating because the I1307K mutation is predicted to impact β-catenin binding (PMID: 9724771).", | ||
| "variant": { | ||
| "gene": { | ||
| "entrezGeneId": 324, | ||
| "hugoSymbol": "APC", | ||
| "oncogene": false, | ||
| "grch37Isoform": "ENST00000257430", | ||
| "grch37RefSeq": "NM_000038.5", | ||
| "grch38Isoform": "ENST00000257430", | ||
| "grch38RefSeq": "NM_000038.5", | ||
| "geneAliases": [ | ||
| "PPP1R46", | ||
| "DP2.5" | ||
| ], | ||
| "genesets": [], | ||
| "tsg": true | ||
| }, | ||
| "consequence": { | ||
| "term": "missense_variant", | ||
| "isGenerallyTruncating": false, | ||
| "description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved" | ||
| }, | ||
| "alteration": "I1307K", | ||
| "name": "I1307K", | ||
| "refResidues": "I", | ||
| "proteinStart": 1307, | ||
| "proteinEnd": 1307, | ||
| "variantResidues": "K", | ||
| "referenceGenomes": [ | ||
| "GRCh37", | ||
| "GRCh38" | ||
| ] | ||
| }, | ||
| "mutationEffect": "Inconclusive", | ||
| "mutationEffectPmids": [ | ||
| "9724771" | ||
| ], | ||
| "mutationEffectAbstracts": [], | ||
| "oncogenic": "Inconclusive", | ||
| "oncogenicPmids": [], | ||
| "oncogenicAbstracts": [] | ||
| }, | ||
| { | ||
| "mutationEffectDescription": "The APC N1026S mutation is located near a β-catenin binding domain in the APC protein. This mutation has been found as a germline mutation in familial adenomatous polyposis (FAP), a cancer predisposition syndrome, and sporadic colorectal cancer. In vitro studies have demonstrated that this mutation is likely inactivating as measured by decreased β-catenin binding compared to wildtype (PMID: 18166348).", | ||
| "variant": { | ||
| "gene": { | ||
| "entrezGeneId": 324, | ||
| "hugoSymbol": "APC", | ||
| "oncogene": false, | ||
| "grch37Isoform": "ENST00000257430", | ||
| "grch37RefSeq": "NM_000038.5", | ||
| "grch38Isoform": "ENST00000257430", | ||
| "grch38RefSeq": "NM_000038.5", | ||
| "geneAliases": [ | ||
| "PPP1R46", | ||
| "DP2.5" | ||
| ], | ||
| "genesets": [], | ||
| "tsg": true | ||
| }, | ||
| "consequence": { | ||
| "term": "missense_variant", | ||
| "isGenerallyTruncating": false, | ||
| "description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved" | ||
| }, | ||
| "alteration": "N1026S", | ||
| "name": "N1026S", | ||
| "refResidues": "N", | ||
| "proteinStart": 1026, | ||
| "proteinEnd": 1026, | ||
| "variantResidues": "S", | ||
| "referenceGenomes": [ | ||
| "GRCh37", | ||
| "GRCh38" | ||
| ] | ||
| }, | ||
| "mutationEffect": "Loss-of-function", | ||
| "mutationEffectPmids": [ | ||
| "18166348" | ||
| ], | ||
| "mutationEffectAbstracts": [], | ||
| "oncogenic": "Likely Oncogenic", | ||
| "oncogenicPmids": [], | ||
| "oncogenicAbstracts": [] | ||
| } | ||
| ] |
53 changes: 53 additions & 0 deletions
53
screenshot-test/data/api-private-utils-variantAnnotation-APC-HGVSG.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| { | ||
| "query": { | ||
| "id": null, | ||
| "referenceGenome": "GRCh37", | ||
| "hugoSymbol": "APC", | ||
| "entrezGeneId": 324, | ||
| "alteration": "G279Ffs*10", | ||
| "alterationType": null, | ||
| "svType": null, | ||
| "tumorType": null, | ||
| "consequence": "splice_region_variant", | ||
| "proteinStart": 279, | ||
| "proteinEnd": 10, | ||
| "hgvs": "5:g.112151184A>G" | ||
| }, | ||
| "geneExist": true, | ||
| "variantExist": false, | ||
| "alleleExist": false, | ||
| "oncogenic": "Likely Oncogenic", | ||
| "mutationEffect": { | ||
| "knownEffect": "Likely Loss-of-function", | ||
| "description": "Truncating APC mutations result in loss of full-length APC protein leading to impaired or abnormal APC function. APC deregulation is associated with accumulation of β-catenin, an oncogenic transcription factor, which in turn leads to aberrant target gene expression and tumorigenesis (PMID: 11062151). APC truncating mutations are typically early events occurring on a single allele (germline or somatic); however, the tumor often acquires a second hit on the second allele, reducing the overall amount of functional APC in the cell (PMID: 11257105). Furthermore, expression of truncating mutations of APC has been shown to result in chromosomal instability in a dominant manner, postulated to play an important role in the accumulation of additional oncogenic alterations (PMID: 15561772).", | ||
| "citations": { | ||
| "pmids": [ | ||
| "11062151", | ||
| "15561772", | ||
| "11257105" | ||
| ], | ||
| "abstracts": [] | ||
| } | ||
| }, | ||
| "highestSensitiveLevel": null, | ||
| "highestResistanceLevel": null, | ||
| "highestDiagnosticImplicationLevel": null, | ||
| "highestPrognosticImplicationLevel": null, | ||
| "highestFdaLevel": null, | ||
| "otherSignificantSensitiveLevels": [], | ||
| "otherSignificantResistanceLevels": [], | ||
| "hotspot": false, | ||
| "geneSummary": "APC, a tumor suppressor involved in WNT signaling, is recurrently altered in colorectal cancer.", | ||
| "variantSummary": "The APC G279Ffs*10 mutation is likely oncogenic.", | ||
| "tumorTypeSummary": "", | ||
| "prognosticSummary": "", | ||
| "diagnosticSummary": "", | ||
| "diagnosticImplications": [], | ||
| "prognosticImplications": [], | ||
| "treatments": [], | ||
| "dataVersion": "v4.5", | ||
| "lastUpdate": "10/23/2017", | ||
| "background": "APC is a negative regulator of the pro-oncogenic WNT/ β-catenin signaling pathway (PMID: 8259518, 8259519). The main tumor suppressive role of APC is to modulate intracellular levels of β-catenin (PMID: 11978510). APC is an essential member of the destruction complex, which targets cytosolic β-catenin for ubiquitination and degradation (PMID: 10984057). When the activity of APC is lost, there is an aberrant increase in WNT-pathway activation, often leading to hyperplasia and eventually tumor progression (PMID: 8259511). A threshold of APC expression is required to suppress tumor formation, and this level is finely balanced (PMID: 11743581). Germline mutations in the APC gene cause familial adenomatous polyposis (FAP) (PMID: 1651174, 1651562), a disease in which 95% of people progress to develop colorectal cancer (PMID: 1528264). In addition, heritable mutations in APC are responsible for the development of a number of related diseases, including Turcot Syndrome, Gardner Syndrome and Flat Adenoma Syndrome (FAS) (PMID: 8593545). APC mutations, much like those seen in FAS, have been observed in 50-80% of sporadic colorectal cancers (PMID: 17143297). Somatic mutations in APC function as tumor-initiating events and are also observed in a number of other human cancers including breast, stomach, and prostate (PMID: 27302369, 29316426). The majority of APC mutations are loss-of-function and occur in a region important for β-catenin binding (PMID: 10784639, 1338904). Inhibitors of the WNT pathway are currently in clinical development (PMID: 24981364).", | ||
| "tumorTypes": [], | ||
| "vus": false | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| [ | ||
| { | ||
| "entrezGeneId": 324, | ||
| "hugoSymbol": "APC", | ||
| "oncogene": false, | ||
| "grch37Isoform": "ENST00000257430", | ||
| "grch37RefSeq": "NM_000038.5", | ||
| "grch38Isoform": "ENST00000257430", | ||
| "grch38RefSeq": "NM_000038.5", | ||
| "geneAliases": [ | ||
| "PPP1R46", | ||
| "DP2.5" | ||
| ], | ||
| "genesets": [], | ||
| "tsg": true | ||
| } | ||
| ] |
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