28 Matching Annotations
  1. Mar 2026
    1. Unequal prognostic potentials of p53 gain-of-function mutations in human cancers associate with drug-metabolizing activity

      [Paper-level Aggregated] PMCID: PMC3973211

      Evidence Type(s): Functional

      Summary: Mutation: R273H | Summary: The R273H mutation is involved in specific gene enrichment profiles and was tested for its effects on CYP3A4 expression, suggesting alterations in molecular or biochemical function related to serine-hydrolase pathways.

      Evidence Type: Functional Mutation: R248 | Summary: The p53 R248 mutation induces higher expression of the CYP3A4 protein, indicating an alteration in molecular function.

      Evidence Type: Functional Mutation: R282 | Summary: The p53 R282 mutation also induces higher expression of the CYP3A4 protein, demonstrating a change in molecular function.

      Evidence Type: Functional Mutation: R175H | Summary: The p53 R175H mutation was tested for its effects on CYP3A4 expression, indicating a potential alteration in molecular function.

      Evidence Type: Functional Mutation: R282W | Summary: The R282W mutation significantly upregulates CYP3A4 mRNA and protein levels, indicating an alteration in molecular function related to drug metabolism.

      Gene→Variant (gene-first): TP53(7157):R273H TP53(7157):R248 TP53(7157):R282 TP53(7157):R175H TP53(7157):R282W

      Genes: TP53(7157)

      Variants: R273H R248 R282 R175H R282W

    2. Unequal prognostic potentials of p53 gain-of-function mutations in human cancers associate with drug-metabolizing activity

      [Paper-level Aggregated] PMCID: PMC3973211

      Evidence Type(s): Oncogenic

      Summary: Mutation: R248 | Summary: The R248 mutation contributes to tumor development or progression, as evidenced by survival analysis in mice and increased expression of CYP3A4, suggesting its role in tumor behavior and association with mortality mutations.

      Evidence Type: Oncogenic Mutation: R282 | Summary: The R282 mutation contributes to tumor development or progression, indicated by survival analysis in cancer patients and increased expression of CYP3A4, highlighting its oncogenic potential and association with chemoresistance.

      Evidence Type: Oncogenic Mutation: R248W | Summary: The R248W mutation is implicated in tumor development and progression through its association with p53 mortality mutations and chemoresistance, as well as contributing to increased expression of CYP3A4.

      Evidence Type: Oncogenic Mutation: R282W | Summary: The R282W mutation contributes to tumor development by displaying higher expression and resistance to chemotherapeutic drugs, indicating its oncogenic potential and association with mortality mutations.

      Evidence Type: Oncogenic Mutation: R175H | Summary: The R175H mutation is part of p53 gain-of-function mutations that contribute to tumor development and progression, as indicated by its association with chemoresistance.

      Evidence Type: Oncogenic Mutation: R273 | Summary: The R273 mutation is linked to lower levels of CYP3A4 expression compared to mortality-associated mutations, suggesting its involvement in tumor behavior.

      Evidence Type: Oncogenic Mutation: R273H | Summary: The R273H mutation is associated with p53 mortality mutations that contribute to tumor development and progression.

      Gene→Variant (gene-first): TP53(7157):R248 TP53(7157):R282 TP53(7157):R248W TP53(7157):R282W TP53(7157):R175H TP53(7157):R273 TP53(7157):R273H

      Genes: TP53(7157)

      Variants: R248 R282 R248W R282W R175H R273 R273H

    3. Unequal prognostic potentials of p53 gain-of-function mutations in human cancers associate with drug-metabolizing activity

      [Paper-level Aggregated] PMCID: PMC3973211

      Evidence Type(s): Prognostic

      Summary: Mutation: Arg248 | Summary: The Arg248 mutation is associated with shorter patient survival, indicating a correlation with disease outcome independent of therapy. Patients carrying p53 mutations at Arg248 had significantly shorter overall survival time compared to those with nonsense mutations, further supporting its prognostic significance in human cancers.

      Evidence Type: Prognostic Mutation: Arg282 | Summary: The Arg282 mutation is linked to shorter patient survival, highlighting its prognostic relevance in cancer outcomes. Similar to Arg248, mutations at Arg282 were associated with a higher hazard ratio in survival analysis, suggesting a negative impact on overall survival.

      Evidence Type: Prognostic Mutation: R248 | Summary: The R248 mutation is associated with shorter patient survival, indicating a correlation with disease outcome independent of therapy.

      Evidence Type: Prognostic Mutation: R282 | Summary: The R282 mutation is associated with shorter patient survival, indicating a correlation with disease outcome independent of therapy.

      Evidence Type: Prognostic Mutation: R248Q/W | Summary: The R248Q/W mutations are associated with increased mortality in colorectal cancer, indicating a correlation with disease outcome independent of therapy.

      Evidence Type: Prognostic Mutation: R249S | Summary: Very few cases of the R249S mutation were available for analysis, limiting the ability to draw conclusions about its impact on survival.

      Evidence Type: Prognostic

      Gene→Variant (gene-first): TP53(7157):Arg248 TP53(7157):Arg282 TP53(7157):R248 TP53(7157):R282 TP53(7157):R248Q/W TP53(7157):R249S

      Genes: TP53(7157)

      Variants: Arg248 Arg282 R248 R282 R248Q/W R249S

    4. Unequal prognostic potentials of p53 gain-of-function mutations in human cancers associate with drug-metabolizing activity

      [Paper-level Aggregated] PMCID: PMC3973211

      Evidence Type(s): Predictive

      Summary: Mutation: R248W | Summary: The R248W mutation is associated with increased viability in response to etoposide treatment, suggesting a correlation with resistance to chemotherapy.

      Evidence Type: Predictive Mutation: R282 | Summary: The R282 mutation is associated with drug metabolism enzymes, suggesting a correlation with response or sensitivity to specific therapies.

      Evidence Type: Predictive Mutation: R282W | Summary: The R282W mutation is linked to higher viability after etoposide treatment, indicating a potential role in chemotherapy resistance.

      Gene→Variant (gene-first): TP53(7157):R248W TP53(7157):R282 TP53(7157):R282W

      Genes: TP53(7157)

      Variants: R248W R282 R282W

    5. Mutation of p53 is the most common genetic change in human cancer, causing complex effects including not only loss of wild-type function but also gain of novel oncogenic functions (GOF). It is increasingly likely that p5

      [Paragraph-level] PMCID: PMC3973211 Section: ABSTRACT PassageIndex: 1

      Evidence Type(s): Prognostic, Functional, Oncogenic

      Summary: Evidence Type: Prognostic | Mutation: Arg248 | Summary: The Arg248 mutation is associated with shorter patient survival, indicating its prognostic significance in human cancers. Evidence Type: Prognostic | Mutation: Arg282 | Summary: The Arg282 mutation is linked to shorter patient survival, highlighting its prognostic relevance in cancer outcomes. Evidence Type: Functional | Mutation: R282W | Summary: The R282W mutation significantly upregulates CYP3A4 mRNA and protein levels, indicating an alteration in molecular function related to drug metabolism. Evidence Type: Oncogenic | Mutation: R282W | Summary: The R282W mutation contributes to tumor development by displaying higher expression and resistance to chemotherapeutic drugs, demonstrating its oncogenic potential.

      Gene→Variant (gene-first): 7157:Arg248 7157:Arg282 7157:R282W

      Genes: 7157

      Variants: Arg248 Arg282 R282W

    6. To clarify the relationship between CYP3A4 expression and resistance to FOLFIRI and cetuximab, we compared the expression levels of CYP3A4 in CRCs displaying different therapeutic responses (GEO data sets GSE13294 and GS

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 12

      Evidence Type(s): Predictive, Oncogenic

      Summary: Evidence Type: Predictive | Mutation: R248W | Summary: The R248W mutation is associated with increased viability in response to etoposide treatment, suggesting a correlation with resistance to chemotherapy. Evidence Type: Predictive | Mutation: R282W | Summary: The R282W mutation is linked to higher viability after etoposide treatment, indicating a potential role in chemotherapy resistance. Evidence Type: Oncogenic | Mutation: R175H | Summary: The R175H mutation is part of p53 GOF mutations that contribute to tumor development and progression, as indicated by its association with chemoresistance. Evidence Type: Oncogenic | Mutation: R248W | Summary: The R248W mutation is implicated in tumor development and progression through its association with p53 mortality mutations and chemoresistance. Evidence Type: Oncogenic | Mutation: R273H | Summary: The R273H mutation is associated with p53 mortality mutations that contribute to tumor development and progression. Evidence Type: Oncogenic | Mutation: R282W | Summary: The R282W mutation is part of p53 mortality mutations that are linked to tumor development and progression, contributing to chemoresistance.

      Gene→Variant (gene-first): 7157:R175H 7157:R248W 7157:R273H 7157:R282W

      Genes: 7157

      Variants: R175H R248W R273H R282W

    7. The GSEA analysis revealed that most of the drug metabolism enzymes in association with p53 R248/R282 mutations are responsible for the clearance of chemotherapeutic drugs. Among these, the most relevant one was cytochro

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 10

      Evidence Type(s): Functional, Oncogenic

      Summary: Evidence Type: Functional | Mutation: R248 | Summary: The p53 R248 mutation was shown to induce higher expression of the CYP3A4 protein, indicating an alteration in molecular function. Evidence Type: Functional | Mutation: R282 | Summary: The p53 R282 mutation also induced higher expression of the CYP3A4 protein, demonstrating a change in molecular function. Evidence Type: Oncogenic | Mutation: R248 | Summary: The p53 R248 mutation is associated with increased expression of CYP3A4, suggesting its role in tumor development or progression. Evidence Type: Oncogenic | Mutation: R282 | Summary: The p53 R282 mutation contributes to increased expression of CYP3A4, indicating its involvement in tumor development or progression. Evidence Type: Functional | Mutation: R175H | Summary: The p53 R175H mutation was tested for its effects on CYP3A4 expression, indicating a potential alteration in molecular function. Evidence Type: Functional | Mutation: R273H | Summary: The p53 R273H mutation was also tested for its effects on CYP3A4 expression, suggesting a change in molecular function. Evidence Type: Oncogenic | Mutation: R175 | Summary: The p53 R175 mutation is associated with lower levels of CYP3A4 expression compared to mortality-associated mutations, indicating its role in tumor behavior. Evidence Type: Oncogenic | Mutation: R273 | Summary: The p53 R273 mutation is linked to lower levels of CYP3A4 expression compared to mortality-associated mutations, suggesting its involvement in tumor behavior.

      Gene→Variant (gene-first): 7157:R175 7157:R175H 7157:R248 7157:R248W 7157:R273 7157:R273H 7157:R282 7157:R282W

      Genes: 7157

      Variants: R175 R175H R248 R248W R273 R273H R282 R282W

    8. To probe the characteristic pathways associated with different p53-hotspot mutations, we selected the colorectal cancer (CRC) data set in TCGA as an example. The CRC cases contain more mortality-associated mutations (R24

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 8

      Evidence Type(s): Prognostic, Oncogenic, Functional

      Summary: Evidence Type: Prognostic | Mutation: R248Q/W | Summary: The R248Q/W mutations are associated with increased mortality in colorectal cancer, indicating a correlation with disease outcome independent of therapy. Evidence Type: Oncogenic | Mutation: R248W | Summary: The R248W mutation contributes to tumor development and progression, as it is classified among mortality-associated mutations in colorectal cancer. Evidence Type: Oncogenic | Mutation: R282W | Summary: The R282W mutation is also classified as a mortality-associated mutation, indicating its role in tumor development and progression. Evidence Type: Functional | Mutation: R273H | Summary: The R273H mutation is involved in specific gene enrichment profiles, suggesting alterations in molecular or biochemical function related to serine-hydrolase pathways.

      Gene→Variant (gene-first): 7157:R175H 7157:R248Q/W 7157:R248W 7157:R273H 7157:R282W

      Genes: 7157

      Variants: R175H R248Q/W R248W R273H R282W

    9. R248 and R282 mutations associate with drug metabolism enzymes

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 7

      Evidence Type(s): Predictive

      Summary: Evidence Type: Predictive | Mutation: R282 | Summary: The R282 mutation is associated with drug metabolism enzymes, suggesting a correlation with response or sensitivity to specific therapies.

      Gene→Variant (gene-first): 7157:R282

      Genes: 7157

      Variants: R282

    10. We tested the association between R248/R282 mutations and cancer patient survival using an independent data set extracted from published literatures (data in Supplementary Table 1), and found these mutations are indeed a

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 6

      Evidence Type(s): Prognostic, Oncogenic

      Summary: Evidence Type: Prognostic | Mutation: R248 | Summary: The R248 mutation is associated with shorter patient survival, indicating a correlation with disease outcome independent of therapy. Evidence Type: Prognostic | Mutation: R282 | Summary: The R282 mutation is associated with shorter patient survival, indicating a correlation with disease outcome independent of therapy. Evidence Type: Oncogenic | Mutation: R248 | Summary: The R248 mutation contributes to tumor development or progression, as evidenced by the survival analysis in mice carrying the mutation. Evidence Type: Oncogenic | Mutation: R282 | Summary: The R282 mutation contributes to tumor development or progression, as evidenced by the survival analysis in cancer patients.

      Gene→Variant (gene-first): 7157:R175 7157:R248 7157:R273 7157:R282

      Genes: 7157

      Variants: R175 R248 R273 R282

    11. Kaplan-Meier survival analysis revealed that patients carrying p53 mutations on Arg248 and Arg282 residues had significantly shorter overall survival time than those carrying nonsense mutations (Figures 2a and b). Other

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 4

      Evidence Type(s): Prognostic

      Summary: Evidence Type: Prognostic | Mutation: Arg248 | Summary: Patients carrying p53 mutations at Arg248 had significantly shorter overall survival time compared to those with nonsense mutations, indicating a correlation with disease outcome. Evidence Type: Prognostic | Mutation: Arg282 | Summary: Similar to Arg248, mutations at Arg282 were associated with a higher hazard ratio in survival analysis, suggesting a negative impact on overall survival. Evidence Type: Prognostic | Mutation: Y220 | Summary: The mutation at Y220 showed similar survival curves to nonsense mutations, indicating it may not significantly affect disease outcome. Evidence Type: Prognostic | Mutation: G245 | Summary: G245 exhibited comparable survival curves to nonsense mutations, suggesting it does not have a significant impact on overall survival. Evidence Type: Prognostic | Mutation: R175 | Summary: The R175 mutation showed similar survival patterns to nonsense mutations, indicating no significant effect on patient survival. Evidence Type: Prognostic | Mutation: R273 | Summary: R273 displayed comparable survival curves to nonsense mutations, suggesting it does not significantly influence disease outcome. Evidence Type: Prognostic | Mutation: R249S | Summary: Very few cases of the R249S mutation were available for analysis, limiting the ability to draw conclusions about its impact on survival.

      Gene→Variant (gene-first): 7157:Arg248 7157:Arg282 7157:G245 7157:R175 7157:R248 7157:R249S 7157:R273 7157:R282 7157:Y220

      Genes: 7157

      Variants: Arg248 Arg282 G245 R175 R248 R249S R273 R282 Y220

    12. Mutations on Arg282 and Arg248 residues associate with shorter patient survival

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 2

      Evidence Type(s): Prognostic

      Summary: Evidence Type: Prognostic | Mutation: Arg248 | Summary: The mutation at Arg248 is associated with shorter patient survival, indicating a correlation with disease outcome independent of therapy. Evidence Type: Prognostic | Mutation: Arg282 | Summary: The mutation at Arg282 is associated with shorter patient survival, indicating a correlation with disease outcome independent of therapy.

      Gene→Variant (gene-first): 7157:Arg248 7157:Arg282

      Genes: 7157

      Variants: Arg248 Arg282

  2. Feb 2026
    1. Unequal prognostic potentials of p53 gain-of-function mutations in human cancers associate with drug-metabolizing activity

      [Paper-level Aggregated] PMCID: PMC3973211

      Evidence Type(s): Prognostic, Oncogenic, Functional

      Justification: Prognostic: The text indicates that mutations on Arg248 and Arg282 residues are associated with significantly shorter overall survival times in cancer patients, as demonstrated by Kaplan-Meier survival analysis and multivariate Cox regression analysis. Oncogenic: The passage discusses how p53 mutations, particularly R248 and R282, confer novel oncogenic functions and are linked to increased expression of drug metabolism enzymes, suggesting a role in cancer progression and treatment resistance. Functional: The evidence shows that p53 mutations R248W and R282W induce higher expression of the CYP3A4 enzyme, which is involved in drug metabolism, indicating a functional impact of these mutations on cellular processes related to chemotherapy response.

      Gene→Variant (gene-first): TP53(7157):Arg248 TP53(7157):Arg282 TP53(7157):G245 TP53(7157):R175 TP53(7157):R248 TP53(7157):R249S TP53(7157):R273 TP53(7157):R282 TP53(7157):Y220 TP53(7157):R282W TP53(7157):R175H TP53(7157):R248W TP53(7157):R273H TP53(7157):R248Q/W

      Genes: TP53(7157)

      Variants: Arg248 Arg282 G245 R175 R248 R249S R273 R282 Y220 R282W R175H R248W R273H R248Q/W

    2. Mutation of p53 is the most common genetic change in human cancer, causing complex effects including not only loss of wild-type function but also gain of novel oncogenic functions (GOF). It is increasingly likely that p5

      [Paragraph-level] PMCID: PMC3973211 Section: ABSTRACT PassageIndex: 1

      Evidence Type(s): Prognostic, Predictive, Oncogenic

      Justification: Prognostic: The passage indicates that mutations at Arg248 and Arg282 positions are associated with shorter patient survival, suggesting a correlation with disease outcome independent of therapy. Predictive: The passage discusses the association of p53 mutations with resistance to several CYP3A4-metabolized chemotherapeutic drugs, indicating a correlation with treatment response. Oncogenic: The mention of p53 mutations contributing to gain of novel oncogenic functions and their association with cancer cell lines suggests that these somatic variants play a role in tumor development or progression.

      Gene→Variant (gene-first): 7157:Arg248 7157:Arg282 7157:R282W

      Genes: 7157

      Variants: Arg248 Arg282 R282W

    3. To clarify the relationship between CYP3A4 expression and resistance to FOLFIRI and cetuximab, we compared the expression levels of CYP3A4 in CRCs displaying different therapeutic responses (GEO data sets GSE13294 and GS

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 12

      Evidence Type(s): Predictive, Oncogenic

      Justification: Predictive: The passage discusses the relationship between p53 mutations (including R175H, R248W, R273H, R282W) and resistance to chemotherapy, specifically noting that cells with these mutations showed higher viability and increased IC50 for various drugs, indicating a correlation with drug resistance. Oncogenic: The passage implies that the p53 mutations contribute to tumor behavior by affecting cell response to chemotherapy, suggesting their role in tumor development or progression.

      Gene→Variant (gene-first): 7157:R175H 7157:R248W 7157:R273H 7157:R282W

      Genes: 7157

      Variants: R175H R248W R273H R282W

    4. The GSEA analysis revealed that most of the drug metabolism enzymes in association with p53 R248/R282 mutations are responsible for the clearance of chemotherapeutic drugs. Among these, the most relevant one was cytochro

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 10

      Evidence Type(s): Predictive, Functional

      Justification: Predictive: The passage discusses the association between p53 mutations (R248, R282) and the expression of CYP3A4, a drug metabolism enzyme, indicating a correlation with drug clearance and potential response to chemotherapeutic drugs. Functional: The passage describes how p53 mutations (R248, R282) alter the expression levels of the CYP3A4 enzyme, demonstrating a change in molecular function related to drug metabolism.

      Gene→Variant (gene-first): 7157:R175 7157:R175H 7157:R248 7157:R248W 7157:R273 7157:R273H 7157:R282 7157:R282W

      Genes: 7157

      Variants: R175 R175H R248 R248W R273 R273H R282 R282W

    5. To probe the characteristic pathways associated with different p53-hotspot mutations, we selected the colorectal cancer (CRC) data set in TCGA as an example. The CRC cases contain more mortality-associated mutations (R24

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 8

      Evidence Type(s): Prognostic, Functional

      Justification: Prognostic: The passage mentions that R248Q/W and R282W are associated with mortality, indicating a correlation with disease outcome. Functional: The passage discusses the enrichment of specific gene sets linked to cellular respiration and drug metabolism enzymes for certain mutations, suggesting alterations in molecular function.

      Gene→Variant (gene-first): 7157:R175H 7157:R248Q/W 7157:R248W 7157:R273H 7157:R282W

      Genes: 7157

      Variants: R175H R248Q/W R248W R273H R282W

    6. R248 and R282 mutations associate with drug metabolism enzymes

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 7

      Evidence Type(s): Diagnostic, Predictive

      Justification: Diagnostic: The passage indicates that the R282 mutation is associated with drug metabolism enzymes, suggesting its role in defining or classifying a specific biological context related to drug metabolism. Predictive: The mention of the R282 mutation in relation to drug metabolism enzymes implies a potential correlation with response or sensitivity to therapies that involve these enzymes.

      Gene→Variant (gene-first): 7157:R282

      Genes: 7157

      Variants: R282

    7. We tested the association between R248/R282 mutations and cancer patient survival using an independent data set extracted from published literatures (data in Supplementary Table 1), and found these mutations are indeed a

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 6

      Evidence Type(s): Prognostic, Oncogenic

      Justification: Prognostic: The passage discusses the association of R248 and R282 mutations with shorter patient survival, indicating a correlation with disease outcome independent of therapy. Oncogenic: The mention of mice carrying the humanized mutation on R248 exhibiting significantly shorter survival time suggests that this somatic variant contributes to tumor development or progression.

      Gene→Variant (gene-first): 7157:R175 7157:R248 7157:R273 7157:R282

      Genes: 7157

      Variants: R175 R248 R273 R282

    8. Kaplan-Meier survival analysis revealed that patients carrying p53 mutations on Arg248 and Arg282 residues had significantly shorter overall survival time than those carrying nonsense mutations (Figures 2a and b). Other

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 4

      Evidence Type(s): Prognostic, Oncogenic

      Justification: Prognostic: The passage discusses how mutations at Arg248 and Arg282 correlate with significantly shorter overall survival times, indicating a relationship between these variants and disease outcome independent of therapy. Oncogenic: The mention of p53 mutations, including those at Arg248 and Arg282, suggests a role in tumor development or progression, as these mutations are associated with survival outcomes in cancer patients.

      Gene→Variant (gene-first): 7157:Arg248 7157:Arg282 7157:G245 7157:R175 7157:R248 7157:R249S 7157:R273 7157:R282 7157:Y220

      Genes: 7157

      Variants: Arg248 Arg282 G245 R175 R248 R249S R273 R282 Y220

    9. Mutations on Arg282 and Arg248 residues associate with shorter patient survival

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 2

      Evidence Type(s): Prognostic

      Justification: Prognostic: The passage indicates that mutations at Arg282 and Arg248 are associated with shorter patient survival, which correlates with disease outcome independent of therapy.

      Gene→Variant (gene-first): 7157:Arg248 7157:Arg282

      Genes: 7157

      Variants: Arg248 Arg282

    10. To clarify the relationship between CYP3A4 expression and resistance to FOLFIRI and cetuximab, we compared the expression levels of CYP3A4 in CRCs displaying different therapeutic responses (GEO data sets GSE13294 and GS

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 12

      Evidence Type(s): Predictive, Oncogenic

      Justification: Predictive: The passage discusses the relationship between p53 mutations (including R175H, R248W, R273H, R282W) and resistance to chemotherapy, specifically noting that cells with these mutations showed higher viability and increased IC50 for various drugs, indicating a correlation with drug resistance. Oncogenic: The passage implies that the p53 mutations contribute to tumor behavior by affecting cell response to chemotherapy, suggesting their role in tumor development or progression.

      Gene→Variant (gene-first): 7157:R175H 7157:R248W 7157:R273H 7157:R282W

      Genes: 7157

      Variants: R175H R248W R273H R282W

    11. The GSEA analysis revealed that most of the drug metabolism enzymes in association with p53 R248/R282 mutations are responsible for the clearance of chemotherapeutic drugs. Among these, the most relevant one was cytochro

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 10

      Evidence Type(s): Predictive, Functional

      Justification: Predictive: The passage discusses the association between p53 mutations (R248, R282) and the expression of CYP3A4, a drug metabolism enzyme, indicating a correlation with drug clearance and potential response to chemotherapeutic drugs. Functional: The passage describes how p53 mutations (R248, R282) alter the expression levels of the CYP3A4 enzyme, demonstrating a change in molecular function related to drug metabolism.

      Gene→Variant (gene-first): 7157:R175 7157:R175H 7157:R248 7157:R248W 7157:R273 7157:R273H 7157:R282 7157:R282W

      Genes: 7157

      Variants: R175 R175H R248 R248W R273 R273H R282 R282W

    12. To probe the characteristic pathways associated with different p53-hotspot mutations, we selected the colorectal cancer (CRC) data set in TCGA as an example. The CRC cases contain more mortality-associated mutations (R24

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 8

      Evidence Type(s): Prognostic, Functional

      Justification: Prognostic: The passage mentions that R248Q/W and R282W are associated with mortality, indicating a correlation with disease outcome. Functional: The passage discusses the enrichment of specific gene sets linked to cellular respiration and drug metabolism enzymes for certain mutations, suggesting alterations in molecular function.

      Gene→Variant (gene-first): 7157:R175H 7157:R248Q/W 7157:R248W 7157:R273H 7157:R282W

      Genes: 7157

      Variants: R175H R248Q/W R248W R273H R282W

    13. R248 and R282 mutations associate with drug metabolism enzymes

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 7

      Evidence Type(s): Diagnostic, Predictive

      Justification: Diagnostic: The passage indicates that the R282 mutation is associated with drug metabolism enzymes, suggesting its role in defining or classifying a specific biological context related to drug metabolism. Predictive: The mention of the R282 mutation in relation to drug metabolism enzymes implies a potential correlation with response or sensitivity to therapies that involve these enzymes.

      Gene→Variant (gene-first): 7157:R282

      Genes: 7157

      Variants: R282

    14. We tested the association between R248/R282 mutations and cancer patient survival using an independent data set extracted from published literatures (data in Supplementary Table 1), and found these mutations are indeed a

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 6

      Evidence Type(s): Prognostic, Oncogenic

      Justification: Prognostic: The passage discusses the association of R248 and R282 mutations with shorter patient survival, indicating a correlation with disease outcome independent of therapy. Oncogenic: The mention of mice carrying the humanized mutation on R248 exhibiting significantly shorter survival time suggests that this somatic variant contributes to tumor development or progression.

      Gene→Variant (gene-first): 7157:R175 7157:R248 7157:R273 7157:R282

      Genes: 7157

      Variants: R175 R248 R273 R282

    15. Kaplan-Meier survival analysis revealed that patients carrying p53 mutations on Arg248 and Arg282 residues had significantly shorter overall survival time than those carrying nonsense mutations (Figures 2a and b). Other

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 4

      Evidence Type(s): Prognostic, Oncogenic

      Justification: Prognostic: The passage discusses how mutations at Arg248 and Arg282 correlate with significantly shorter overall survival times, indicating a relationship between these variants and disease outcome independent of therapy. Oncogenic: The mention of p53 mutations, including those at Arg248 and Arg282, suggests a role in tumor development or progression, as these mutations are associated with survival outcomes in cancer patients.

      Gene→Variant (gene-first): 7157:Arg248 7157:Arg282 7157:G245 7157:R175 7157:R248 7157:R249S 7157:R273 7157:R282 7157:Y220

      Genes: 7157

      Variants: Arg248 Arg282 G245 R175 R248 R249S R273 R282 Y220

    16. Mutations on Arg282 and Arg248 residues associate with shorter patient survival

      [Paragraph-level] PMCID: PMC3973211 Section: RESULTS PassageIndex: 2

      Evidence Type(s): Prognostic

      Justification: Prognostic: The passage indicates that mutations at Arg282 and Arg248 are associated with shorter patient survival, which correlates with disease outcome independent of therapy.

      Gene→Variant (gene-first): 7157:Arg248 7157:Arg282

      Genes: 7157

      Variants: Arg248 Arg282