[Paper-level Aggregated] PMCID: PMC10015977

Evidence Type(s): Prognostic

Summary: Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with a favorable prognosis in myelodysplastic syndromes (MDS), correlating with significantly better overall survival (OS) outcomes compared to non-K700E mutations and SF3B1 wild-type patients. It is linked to specific clinical features, such as a higher percentage of ring sideroblasts and lower comprehensive cytogenetic scoring system (CCSS) scores, indicating its relevance in predicting disease outcomes. However, some evidence suggests that the K700E mutation may not show significant differences in OS compared to other SF3B1 mutations, indicating variability in its prognostic significance.

Evidence Type: Prognostic Mutation: R625 | Summary: The presence of the R625 mutation, as a recurrent mutation in MDS, may correlate with disease outcomes in patients, independent of therapy.

Gene→Variant (gene-first): SF3B1(23451):K700E SF3B1(23451):R625

Genes: SF3B1(23451)

Variants: K700E R625

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 21

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The presence of the SF3B1 K700E mutation is associated with worse overall survival (OS) outcomes in the MDS cohort, indicating its role as an independent prognostic factor.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 20

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E SF3B1 mutation in low-grade MDS is associated with a trend for longer overall survival compared to non-K700E SF3B1 mutations, indicating a potential prognostic significance.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 19

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with significantly better overall survival (OS) compared to SF3B1 wild-type MDS, indicating its potential prognostic value in disease outcomes.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 18

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1mut MDS is associated with a significantly improved overall survival (OS) compared to non-K700E patients, indicating its prognostic relevance in disease outcome.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 17

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E SF3B1 mutation does not show significant differences in overall survival (OS) compared to other SF3B1 mutations, indicating it may not correlate with disease outcome independent of therapy.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 16

Evidence Type(s): Prognostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with significantly better overall survival (OS) outcomes in MDS patients compared to SF3B1 wild-type patients, indicating its prognostic value. Evidence Type: Oncogenic | Mutation: K700E | Summary: The K700E mutation contributes to tumor development or progression in MDS, as evidenced by its association with improved survival outcomes in patients with this mutation compared to those without.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 12

Evidence Type(s): Prognostic, Diagnostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with lower comprehensive cytogenetic scoring system (CCSS) scores, indicating a potential correlation with disease outcome in patients. Evidence Type: Diagnostic | Mutation: K700E | Summary: The presence of the K700E mutation helps classify patients into different categories based on their cytogenetic aberrations, distinguishing them from non-K700E MDS patients.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 10

Evidence Type(s): Diagnostic, Prognostic, Oncogenic

Summary: Evidence Type: Diagnostic | Mutation: K700E | Summary: The K700E mutation is associated with specific clinico-pathologic features that help classify and define the subtype of MDS in patients. Evidence Type: Prognostic | Mutation: K700E | Summary: The presence of the K700E mutation correlates with certain clinical features, such as a higher percentage of ring sideroblasts and ANC, which may indicate disease outcome independent of therapy. Evidence Type: Oncogenic | Mutation: K700E | Summary: The K700E mutation contributes to the development and progression of MDS, as indicated by its association with specific clinical features and classifications.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: ABSTRACT PassageIndex: 12

Evidence Type(s): Prognostic, Diagnostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with a favorable prognosis in myelodysplastic syndromes, indicating its relevance in predicting disease outcomes. Evidence Type: Diagnostic | Mutation: K700E | Summary: The K700E mutation is used to refine the sub-classification and risk assessment criteria for myelodysplastic syndromes, highlighting its role in defining disease characteristics.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: ABSTRACT PassageIndex: 10

Evidence Type(s): Prognostic, Diagnostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with significantly better overall survival (OS) in patients with myelodysplastic syndromes (MDS) compared to non-K700E mutations, indicating its prognostic value. Evidence Type: Diagnostic | Mutation: K700E | Summary: The presence of the K700E mutation in SF3B1 is important for risk-assessment in myelodysplastic syndromes (MDS), suggesting its role in classifying the disease.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: ABSTRACT PassageIndex: 6

Evidence Type(s): Oncogenic, Prognostic

Summary: Evidence Type: Oncogenic | Mutation: K700E | Summary: The K700E mutation is associated with superior overall survival in patients with MDS, indicating its role in tumor development or progression. Evidence Type: Prognostic | Mutation: K700E | Summary: The presence of the K700E mutation correlates with improved overall survival outcomes in MDS patients compared to those without this mutation. Evidence Type: Oncogenic | Mutation: R625 | Summary: The R625 mutation is part of recurrent non-K700E mutations associated with MDS, suggesting its contribution to tumor development or progression. Evidence Type: Prognostic | Mutation: R625 | Summary: The presence of R625, as a recurrent mutation, may correlate with disease outcomes in MDS patients, independent of therapy.

Gene→Variant (gene-first): 23451:K666 23451:K700 23451:K700E 23451:R625

Genes: 23451

Variants: K666 K700 K700E R625

[Paragraph-level] PMCID: PMC10015977 Section: ABSTRACT PassageIndex: 4

Evidence Type(s): Diagnostic, Prognostic

Summary: Evidence Type: Diagnostic | Mutation: K700E | Summary: The passage discusses the analysis of clinical-pathologic features and outcomes in MDS patients, indicating that K700E is used to explore differences in disease characteristics, which supports its role in diagnostic classification. Evidence Type: Prognostic | Mutation: K700E | Summary: The mention of outcomes in the context of K700E suggests that this variant may correlate with disease outcomes, supporting its prognostic significance in treatment-naive MDS patients.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: ABSTRACT PassageIndex: 2

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with a favorable prognosis in myelodysplastic syndromes (MDS).

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paper-level Aggregated] PMCID: PMC10011885

Evidence Type(s): Prognostic

Summary: Mutation: V600E | Summary: Higher levels of ctDNA for the BRAF V600E mutation at baseline are associated with inferior progression-free survival (PFS) and overall survival (OS). The mutation correlates with disease outcomes, as patients with higher week 2 and week 4 baseline ratios had inferior PFS and OS, indicating its prognostic significance.

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC10011885 Section: RESULTS PassageIndex: 20

Evidence Type(s): Predictive, Prognostic

Summary: Evidence Type: Predictive | Mutation: V600E | Summary: The BRAF V600E mutation is assessed as a predictor of progression-free survival (PFS) and overall survival (OS) based on the week 2 and week 4 baseline ratios of ctDNA levels, indicating its correlation with treatment response. Evidence Type: Prognostic | Mutation: V600E | Summary: The BRAF V600E mutation correlates with disease outcomes, as patients with higher week 2 and week 4 baseline ratios had inferior PFS and OS, suggesting its role in predicting survival independent of therapy.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC10011885 Section: RESULTS PassageIndex: 15

Evidence Type(s): Diagnostic, Prognostic, Predictive

Summary: Evidence Type: Diagnostic | Mutation: V600E | Summary: The BRAF V600E mutation is used to define and classify patients based on the presence of mutant ctDNA in plasma, indicating its role in diagnosing the disease. Evidence Type: Prognostic | Mutation: V600E | Summary: Higher levels of ctDNA for the BRAF V600E mutation at baseline are associated with inferior progression-free survival (PFS) and overall survival (OS), indicating its prognostic significance. Evidence Type: Predictive | Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with clinical benefit, as patients with lower ctDNA levels achieved better outcomes, suggesting its predictive value for treatment response.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paper-level Aggregated] PMCID: PMC9468105

Evidence Type(s): Prognostic

Summary: Mutation: p.V600E | Summary: Kaplan-Meier survival analysis suggests that patients with NF1-associated gliomas, including those with the p.V600E mutation, have inferior outcomes compared to other groups.

Gene→Variant (gene-first): BRAF(673):p.V600E

Genes: BRAF(673)

Variants: p.V600E

[Paragraph-level] PMCID: PMC9468105 Section: RESULTS PassageIndex: 14

Evidence Type(s): Oncogenic, Prognostic

Summary: Evidence Type: Oncogenic | Mutation: p.V600E | Summary: The BRAF p.V600E mutation is associated with pleomorphic xanthoastrocytoma, indicating its role in tumor development or progression. Evidence Type: Prognostic | Mutation: p.V600E | Summary: Kaplan-Meier survival analysis suggests that patients with NF1-associated gliomas, including those with the p.V600E mutation, have inferior outcomes compared to other groups.

Gene→Variant (gene-first): 673:p.V600E

Genes: 673

Variants: p.V600E

[Paper-level Aggregated] PMCID: PMC9441062

Evidence Type(s): Prognostic

Summary: Mutation: L858R | Summary: The L858R mutation is associated with prognosis in NSCLC patients, as indicated by the analysis of progression-free survival (PFS) among patients with this mutation compared to wild-type counterparts.

Gene→Variant (gene-first): EGFR(1956):L858R

Genes: EGFR(1956)

Variants: L858R

[Paragraph-level] PMCID: PMC9441062 Section: RESULTS PassageIndex: 15

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: L858R | Summary: The L858R mutation is associated with prognosis in NSCLC patients, as indicated by the analysis of progression-free survival (PFS) among patients with this mutation compared to wild-type counterparts.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paper-level Aggregated] PMCID: PMC9338780

Evidence Type(s): Prognostic

Summary: Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with improved long-term survival and disease outcome in patients treated with dabrafenib plus trametinib, as indicated by the median duration of response (DOR).

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC9338780 Section: RESULTS PassageIndex: 4

Evidence Type(s): Predictive, Oncogenic, Prognostic

Summary: Evidence Type: Predictive | Mutation: V600E | Summary: The BRAF V600E mutation is associated with a confirmed response to therapy, as evidenced by a high overall response rate (ORR) in patients with this mutation. Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation contributes to tumor development or progression, as it is identified in patients with BRAF V600E-mutant disease. Evidence Type: Prognostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with disease outcome, as indicated by the median duration of response (DOR) in patients with this mutation.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC9338780 Section: ABSTRACT PassageIndex: 8

Evidence Type(s): Predictive, Prognostic, Oncogenic

Summary: Evidence Type: Predictive | Mutation: V600E | Summary: The BRAF V600E mutation is associated with a substantial clinical benefit from the combination of dabrafenib and trametinib, indicating its predictive value for treatment response in patients with ATC. Evidence Type: Prognostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with improved long-term survival in patients treated with dabrafenib plus trametinib, suggesting its prognostic significance in this context. Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation contributes to tumor development and progression in anaplastic thyroid carcinoma (ATC), indicating its oncogenic role in this aggressive cancer type.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paper-level Aggregated] PMCID: PMC8307492

Evidence Type(s): Prognostic

Summary: Mutation: L858R | Summary: The L858R mutation correlates with overall survival outcomes in non-small-cell lung cancer (NSCLC) patients, independent of therapy. It is associated with a median overall survival (OS) of 16.7 months and 18.3 months for patients treated with first-line targeted therapy. Patients with this mutation have a comparable prognosis to those with uncommon actionable variants when adjusted for age, sex, and year of diagnosis, indicating its relevance in disease prognosis.

Gene→Variant (gene-first): EGFR(1956):L858R

Genes: EGFR(1956)

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 17

Evidence Type(s): Prognostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: L858R | Summary: The L858R mutation is associated with overall survival (OS) outcomes, indicating that patients with this mutation have a comparable prognosis to those with uncommon actionable variants when adjusted for age, sex, and year of diagnosis. Evidence Type: Oncogenic | Mutation: L858R | Summary: The L858R mutation is implicated in tumor development and progression, as it is associated with worse outcomes compared to other variants in the context of overall survival analysis.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 16

Evidence Type(s): Predictive, Prognostic

Summary: Evidence Type: Predictive | Mutation: L858R | Summary: The L858R mutation correlates with response to first-line targeted therapy, as indicated by the proportion of patients receiving this therapy. Evidence Type: Prognostic | Mutation: L858R | Summary: The L858R mutation is associated with median overall survival (OS) outcomes, with a median OS of 18.3 months for patients treated with first-line targeted therapy.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 13

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: L858R | Summary: The L858R mutation is associated with a median overall survival (OS) of 16.7 months, indicating its correlation with disease outcome independent of therapy.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic, Diagnostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: L858R | Summary: The L858R mutation is associated with treatment and survival data, indicating a correlation with disease outcome independent of therapy. Evidence Type: Diagnostic | Mutation: L858R | Summary: The L858R mutation is used to classify and confirm the presence of a specific EGFR mutation in patients, aiding in the diagnosis of the disease. Evidence Type: Oncogenic | Mutation: L858R | Summary: The L858R mutation is a somatic variant that contributes to tumor development and progression in patients with EGFR mutations.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: ABSTRACT PassageIndex: 4

Evidence Type(s): Predictive, Prognostic

Summary: Evidence Type: Predictive | Mutation: L858R | Summary: The L858R mutation is associated with response to first-line EGFR inhibitors, with survival outcomes indicating it may not perform as well as exon 19 deletions in terms of overall survival (OS). Evidence Type: Prognostic | Mutation: L858R | Summary: The L858R mutation correlates with overall survival outcomes in non-small-cell lung cancer (NSCLC) patients, independent of therapy, suggesting its relevance in disease prognosis.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paper-level Aggregated] PMCID: PMC8255005

Evidence Type(s): Prognostic

Summary: Mutation: D835 | Summary: The D835 mutation is associated with poor prognosis in acute myeloid leukemia (AML).

Evidence Type: Prognostic Mutation: D835Y | Summary: The D835Y mutation is associated with poor prognosis in acute myeloid leukemia (AML).

Evidence Type: Prognostic

Gene→Variant (gene-first): FLT3(2322):D835 FLT3(2322):D835Y

Genes: FLT3(2322)

Variants: D835 D835Y

[Paragraph-level] PMCID: PMC8255005 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Prognostic, Predictive, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: D835 | Summary: The D835 mutation is associated with poor prognosis in acute myeloid leukemia (AML). Evidence Type: Predictive | Mutation: F691L | Summary: The F691L mutation is described as a "gatekeeper" mutation that is resistant to most available FLT3 inhibitors, indicating its role in treatment resistance. Evidence Type: Oncogenic | Mutation: D835Y | Summary: The D835Y mutation is part of the FLT3-TKD mutations that contribute to tumor development and progression in AML. Evidence Type: Oncogenic | Mutation: F691 | Summary: The F691 mutation is implicated in the resistance to FLT3 inhibitors and contributes to tumor progression in AML.

Gene→Variant (gene-first): 2322:D835 2322:D835Y 2322:F691 2322:F691L

Genes: 2322

Variants: D835 D835Y F691 F691L

[Paper-level Aggregated] PMCID: PMC8078423

Evidence Type(s): Prognostic

Summary: Mutation: BRAFV600E | Summary: The presence of the BRAFV600E mutation correlates with improved overall survival and objective response rate in patients with metastatic colorectal cancer undergoing treatment.

Evidence Type: Prognostic Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with overall survival (OS) outcomes in patients with metastatic colorectal cancer, independent of the therapy received.

Gene→Variant (gene-first): BRAF(673):BRAFV600E BRAF(673):V600E

Genes: BRAF(673)

Variants: BRAFV600E V600E

[Paragraph-level] PMCID: PMC8078423 Section: ABSTRACT PassageIndex: 4

Evidence Type(s): Predictive, Prognostic, Oncogenic

Summary: Evidence Type: Predictive | Mutation: V600E | Summary: The BRAF V600E mutation is associated with treatment response in patients with mCRC, as indicated by the trial comparing different treatment regimens. Evidence Type: Prognostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with overall survival (OS) outcomes in patients with mCRC, independent of the therapy received. Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation is implicated in tumor development and progression in colorectal cancer.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC8078423 Section: ABSTRACT PassageIndex: 2

Evidence Type(s): Predictive, Prognostic

Summary: Evidence Type: Predictive | Mutation: BRAFV600E | Summary: The BRAFV600E mutation is associated with response to targeted therapies such as encorafenib and cetuximab in patients with metastatic colorectal cancer. Evidence Type: Prognostic | Mutation: BRAFV600E | Summary: The presence of the BRAFV600E mutation correlates with improved overall survival and objective response rate in patients with metastatic colorectal cancer undergoing treatment.

Gene→Variant (gene-first): 673:BRAFV600E

Genes: 673

Variants: BRAFV600E

[Paper-level Aggregated] PMCID: PMC7612117

Evidence Type(s): Prognostic

Summary: Mutation: p.L1363P | Summary: The presence of the BRCA1 p.L1363P variant is associated with distinct histopathological features and stable DNA copy number profiles in tumors, which may correlate with disease outcome.

Gene→Variant (gene-first): TP53BP1(7158):p.L1363P

Genes: TP53BP1(7158)

Variants: p.L1363P

[Paragraph-level] PMCID: PMC7612117 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Functional, Predictive, Prognostic

Summary: Evidence Type: Oncogenic | Mutation: p.L1363P | Summary: The BRCA1 p.L1363P variant contributes to tumor development, as it leads to the acceleration of mammary tumors in genetically engineered mice, indicating its role in cancer progression. Evidence Type: Functional | Mutation: p.L1363P | Summary: The BRCA1 p.L1363P variant disrupts the interaction with PALB2 and results in HRR incompetence, demonstrating an alteration in molecular function. Evidence Type: Predictive | Mutation: p.L1363P | Summary: The BRCA1 p.L1363P variant is responsive to cisplatin and PARP inhibition, indicating its potential correlation with treatment response. Evidence Type: Prognostic | Mutation: p.L1363P | Summary: The presence of the BRCA1 p.L1363P variant is associated with distinct histopathological features and stable DNA copy number profiles in tumors, which may correlate with disease outcome.

Gene→Variant (gene-first): 7158:p.L1363P

Genes: 7158

Variants: p.L1363P

[Paper-level Aggregated] PMCID: PMC7545690

Evidence Type(s): Prognostic

Summary: Mutation: rs3786362 | Summary: The SNP rs3786362 in TYMS is correlated with reduced progression-free survival (PFS) and overall survival (OS) in metastatic colorectal cancer (mCRC) patients. The AG genotype is associated with worse outcomes compared to the AA genotype, and carriers of the G allele are prone to shorter survival times. This variant indicates its potential role as a prognostic marker for disease outcome independent of therapy, particularly in specific subgroups of mCRC patients.

Gene→Variant (gene-first): TYMS(7298):rs3786362

Genes: TYMS(7298)

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: ABSTRACT PassageIndex: 3

Evidence Type(s): Prognostic, Functional

Summary: Evidence Type: Prognostic | Mutation: rs3786362 | Summary: The G allele of the rs3786362 variant in the TYMS gene is significantly associated with progression-free survival (PFS) and overall survival (OS), indicating its potential role as a prognostic marker in cancer outcomes. Evidence Type: Functional | Mutation: rs3786362 | Summary: The rs3786362 variant is associated with altered expression levels of the TYMS gene, suggesting a functional impact on molecular or biochemical activity in colorectal cancer (CRC) tissues compared to normal tissues.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 15

Evidence Type(s): Prognostic, Predictive

Summary: Evidence Type: Prognostic | Mutation: rs3786362 | Summary: The variant rs3786362 is associated with reduced progression-free survival (PFS) and overall survival (OS) in specific subgroups of metastatic colorectal cancer (mCRC) patients, indicating its potential role as a prognostic biomarker. Evidence Type: Predictive | Mutation: rs3786362 | Summary: The variant rs3786362 may serve as a predictive biomarker for survival in mCRC patients, particularly in certain subgroups, suggesting a correlation with treatment response or outcomes.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 14

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs3786362 | Summary: The variant rs3786362 is associated with mCRC survival, indicating its potential role in correlating with disease outcome independent of therapy.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs3786362 | Summary: The variant rs3786362 is associated with reduced progression-free survival (PFS) and overall survival (OS) in metastatic colorectal cancer (mCRC) patients, indicating its prognostic significance.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 10

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs3786362 | Summary: The variant TYMS rs3786362 is associated with reduced overall survival (OS) and progression-free survival (PFS), indicating its correlation with disease outcome independent of therapy. Evidence Type: Prognostic | Mutation: rs3786362 | Summary: The AG genotype of rs3786362 in TYMS is correlated with reduced PFS and OS compared to the AA genotype, further supporting its role in predicting disease outcomes. Evidence Type: Prognostic | Mutation: rs3786362 | Summary: Carriers of the G allele of rs3786362 are prone to shorter PFS and OS times, reinforcing its prognostic significance in the context of cancer survival.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs3786362 | Summary: The variant rs3786362 in TYMS is associated with mCRC survival, indicating its potential role in predicting disease outcome independent of therapy.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 8

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs3786362 | Summary: The SNP rs3786362 in TYMS is correlated with reduced progression-free survival (PFS) in metastatic colorectal cancer (mCRC) patients, indicating its potential as a prognostic marker. Evidence Type: Prognostic | Mutation: rs369803 | Summary: The SNP rs369803 in FOLH1 is associated with progression-free survival (PFS) in mCRC patients, suggesting it may serve as a prognostic indicator for disease outcome.

Gene→Variant (gene-first): 10841:rs10432965 2346:rs369803 7298:rs3786362 113235:rs4795436

Genes: 10841 2346 7298 113235

Variants: rs10432965 rs369803 rs3786362 rs4795436

[Paper-level Aggregated] PMCID: PMC7294133

Evidence Type(s): Prognostic

Summary: Mutation: V871I | Summary: Higher expression of EPHB4, associated with the V871I variant, correlates with advanced disease stages and poor overall survival in neuroblastoma patients.

Gene→Variant (gene-first): EPHB4(2050):V871I

Genes: EPHB4(2050)

Variants: V871I

[Paragraph-level] PMCID: PMC7294133 Section: ABSTRACT PassageIndex: 2

Evidence Type(s): Oncogenic, Functional, Prognostic, Predictive

Summary: Evidence Type: Oncogenic | Mutation: V871I | Summary: The V871I variant in the EPHB4 gene contributes to tumor development and progression in neuroblastoma by increasing proliferation, migration, and invasion properties in cancer cell lines. Evidence Type: Functional | Mutation: V871I | Summary: The V871I variant alters molecular function by affecting the phosphorylation of the ERK1-2 pathway and influencing the expression of target genes related to cancer progression. Evidence Type: Prognostic | Mutation: V871I | Summary: Higher expression of EPHB4, associated with the V871I variant, correlates with advanced disease stages and poor overall survival in neuroblastoma patients. Evidence Type: Predictive | Mutation: V871I | Summary: The use of EPHB4 inhibitors, which target the effects of the V871I variant, suggests potential therapeutic strategies for neuroblastoma patients.

Gene→Variant (gene-first): 2050:V871I

Genes: 2050

Variants: V871I

[Paper-level Aggregated] PMCID: PMC7099049

Evidence Type(s): Prognostic

Summary: Mutation: rs16879870 | Summary: The variant rs16879870 is significantly associated with HNSCC survival and correlates with disease outcome independent of therapy. It is linked to an increased risk of death in patients with HNSCC, and higher expression of GJB7 in cancer tissues correlates with worse prognosis, indicating its potential role as a prognostic marker.

Evidence Type: Prognostic Mutation: rs2641256 | Summary: The variant rs2641256 shows a significant association with HNSCC patients' survival and contributes to the risk of death, suggesting it may serve as a prognostic indicator with implications for survival independent of therapy.

Evidence Type: Prognostic Mutation: rs2761591 | Summary: The variant rs2761591 is significantly associated with HNSCC survival and linked to an increased risk of overall death, highlighting its potential prognostic value and role in disease outcome independent of therapy.

Evidence Type: Prognostic Mutation: rs854936 | Summary: The variant rs854936 demonstrates a significant correlation with HNSCC patients' survival and is associated with a higher risk of death, indicating its relevance as a prognostic factor. Increased expression of RTN4R in cancer tissues is also associated with worse prognosis in HNSCC patients.

Gene→Variant (gene-first): NA:rs16879870 SCIMP(388325):rs2641256 DCDC1(341019):rs2761591 NA:rs854936

Genes: NA SCIMP(388325) DCDC1(341019)

Variants: rs16879870 rs2641256 rs2761591 rs854936

[Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 13

Evidence Type(s): Functional, Prognostic

Summary: Evidence Type: Functional | Mutation: rs16879870 | Summary: The allele A of rs16879870 is associated with an increased mRNA expression level of gene GJB7, indicating a potential functional impact on gene expression. Evidence Type: Functional | Mutation: rs854936 | Summary: The allele C of rs854936 is associated with an increased mRNA level of gene RTN4R, suggesting a functional role in gene expression. Evidence Type: Prognostic | Mutation: rs16879870 | Summary: Higher expression of GJB7 in cancer tissues correlates with worse prognosis in HNSCC patients, indicating a prognostic significance of this variant. Evidence Type: Prognostic | Mutation: rs854936 | Summary: Increased expression of RTN4R in cancer tissues is associated with worse prognosis in HNSCC patients, highlighting its prognostic relevance.

Gene→Variant (gene-first): NA:rs16879870 NA:rs854936

Genes: NA

Variants: rs16879870 rs854936

[Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs2761591 | Summary: The variant rs2761591 is associated with death in head and neck squamous cell carcinoma (HNSCC), indicating its potential role in disease outcome independent of therapy.

Gene→Variant (gene-first): 341019:rs2761591

Genes: 341019

Variants: rs2761591

[Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic, Predictive

Summary: Evidence Type: Prognostic | Mutation: None | Summary: The passage discusses the use of NRG in predicting survival outcomes in HNSCC, indicating a correlation with disease outcome independent of therapy. Evidence Type: Predictive | Mutation: None | Summary: The mention of the ROC model assessing the ability of NRG in predicting survival suggests a correlation with response to treatment, indicating predictive value.

Gene→Variant (gene-first): 2264:AUC from 0

Genes: 2264

Variants: AUC from 0

[Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 7

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs16879870 | Summary: The variant rs16879870 is associated with an increased risk of death in patients with HNSCC, indicating its prognostic value in survival outcomes. Evidence Type: Prognostic | Mutation: rs2641256 | Summary: The variant rs2641256 contributes to the risk of death in HNSCC patients, suggesting it has prognostic implications for survival. Evidence Type: Prognostic | Mutation: rs2761591 | Summary: The variant rs2761591 is linked to an increased hazard of death in HNSCC, highlighting its role as a prognostic marker. Evidence Type: Prognostic | Mutation: rs854936 | Summary: The variant rs854936 is associated with a higher risk of death in HNSCC patients, indicating its prognostic significance in survival analysis.

Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

Genes: NA 388325 341019

Variants: rs16879870 rs2641256 rs2761591 rs854936

[Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 6

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs16879870 | Summary: The genotypes CA+AA of rs16879870 are associated with a decreased survival time in patients, indicating a correlation with disease outcome independent of therapy. Evidence Type: Prognostic | Mutation: rs2641256 | Summary: The genotype AA of rs2641256 is associated with an increased death risk in HNSCC, suggesting a correlation with disease outcome independent of therapy. Evidence Type: Prognostic | Mutation: rs2761591 | Summary: The genotype GA of rs2761591 is linked to an increased risk of overall death, indicating a correlation with disease outcome independent of therapy. Evidence Type: Prognostic | Mutation: rs854936 | Summary: The genotype AC of rs854936 is associated with an increased risk of overall death, suggesting a correlation with disease outcome independent of therapy.

Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

Genes: NA 388325 341019

Variants: rs16879870 rs2641256 rs2761591 rs854936

[Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 5

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs16879870 | Summary: The variant rs16879870 is significantly correlated with HNSCC patients' survival, indicating its potential role as a prognostic marker. Evidence Type: Prognostic | Mutation: rs2641256 | Summary: The variant rs2641256 shows a significant association with HNSCC patients' survival, suggesting it may serve as a prognostic indicator. Evidence Type: Prognostic | Mutation: rs2761591 | Summary: The variant rs2761591 is correlated with HNSCC patients' survival, highlighting its potential prognostic value. Evidence Type: Prognostic | Mutation: rs854936 | Summary: The variant rs854936 demonstrates a significant correlation with HNSCC patients' survival, indicating its relevance as a prognostic factor.

Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

Genes: NA 388325 341019

Variants: rs16879870 rs2641256 rs2761591 rs854936

[Paragraph-level] PMCID: PMC7099049 Section: ABSTRACT PassageIndex: 4

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: rs16879870 | Summary: The SNP rs16879870 is suggested to correlate with disease outcome in head and neck squamous cell carcinoma (HNSCC). Evidence Type: Prognostic | Mutation: rs2641256 | Summary: The SNP rs2641256 is suggested to correlate with disease outcome in head and neck squamous cell carcinoma (HNSCC). Evidence Type: Prognostic | Mutation: rs2761591 | Summary: The SNP rs2761591 is suggested to correlate with disease outcome in head and neck squamous cell carcinoma (HNSCC). Evidence Type: Prognostic | Mutation: rs854936 | Summary: The SNP rs854936 is suggested to correlate with disease outcome in head and neck squamous cell carcinoma (HNSCC).

Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

Genes: NA 388325 341019

Variants: rs16879870 rs2641256 rs2761591 rs854936

[Paragraph-level] PMCID: PMC7099049 Section: ABSTRACT PassageIndex: 3

Evidence Type(s): Prognostic, Functional

Summary: Evidence Type: Prognostic | Mutation: rs16879870 | Summary: The variant rs16879870 is significantly associated with HNSCC survival, indicating its correlation with disease outcome independent of therapy. Evidence Type: Prognostic | Mutation: rs2641256 | Summary: The variant rs2641256 is significantly associated with HNSCC survival, suggesting it correlates with disease outcome independent of therapy. Evidence Type: Prognostic | Mutation: rs2761591 | Summary: The variant rs2761591 is significantly associated with HNSCC survival, indicating its correlation with disease outcome independent of therapy. Evidence Type: Prognostic | Mutation: rs854936 | Summary: The variant rs854936 is significantly associated with HNSCC survival, suggesting it correlates with disease outcome independent of therapy. Evidence Type: Functional | Mutation: rs16879870 | Summary: The genotype of rs16879870 is significantly associated with the expression of the gene GJB7 in cancer tissues, indicating an alteration in molecular function. Evidence Type: Functional | Mutation: rs854936 | Summary: The genotype of rs854936 is significantly associated with the expression of the gene RTN4R in cancer tissues, indicating an alteration in molecular function.

Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

Genes: NA 388325 341019

Variants: rs16879870 rs2641256 rs2761591 rs854936

[Paper-level Aggregated] PMCID: PMC7074098

Evidence Type(s): Prognostic

Summary: Mutation: I643T | Summary: The I643T mutation is part of a group of BAP1 mutations that were not associated with overall survival in cutaneous melanoma (CM), indicating it does not correlate with disease outcome.

Evidence Type: Prognostic Mutation: E30K | Summary: The E30K mutation is included in the BAP1 mutations that were not associated with overall survival in CM, suggesting it does not correlate with disease outcome.

Evidence Type: Prognostic Mutation: P629S | Summary: The P629S mutation is among the BAP1 mutations that were not associated with overall survival in CM, indicating it does not correlate with disease outcome.

Evidence Type: Prognostic Mutation: R417M | Summary: The R417M mutation is part of the BAP1 mutations that were not associated with overall survival in CM, suggesting it does not correlate with disease outcome.

Evidence Type: Prognostic Mutation: S143N | Summary: The S143N mutation is included in the BAP1 mutations that were not associated with overall survival in CM, indicating it does not correlate with disease outcome.

Evidence Type: Prognostic Mutation: L416F | Summary: The L416F mutation is part of the BAP1 mutations that were not associated with overall survival in CM, suggesting it does not correlate with disease outcome.

Evidence Type: Prognostic Mutation: R59W | Summary: The R59W mutation is included in the BAP1 mutations that were not associated with overall survival in CM, indicating it does not correlate with disease outcome.

Gene→Variant (gene-first): BAP1(8314):I643T BAP1(8314):E30K BAP1(8314):P629S BAP1(8314):R417M PMEL(6490):S143N BAP1(8314):L416F BAP1(8314):R59W

Genes: BAP1(8314) PMEL(6490)

Variants: I643T E30K P629S R417M S143N L416F R59W

[Paragraph-level] PMCID: PMC7074098 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: I643T | Summary: The I643T mutation is part of a group of BAP1 mutations that were not associated with overall survival in cutaneous melanoma (CM), indicating it does not correlate with disease outcome. Evidence Type: Prognostic | Mutation: E30K | Summary: The E30K mutation is included in the BAP1 mutations that were not associated with overall survival in CM, suggesting it does not correlate with disease outcome. Evidence Type: Prognostic | Mutation: P629S | Summary: The P629S mutation is among the BAP1 mutations that were not associated with overall survival in CM, indicating it does not correlate with disease outcome. Evidence Type: Prognostic | Mutation: R417M | Summary: The R417M mutation is part of the BAP1 mutations that were not associated with overall survival in CM, suggesting it does not correlate with disease outcome. Evidence Type: Prognostic | Mutation: S143N | Summary: The S143N mutation is included in the BAP1 mutations that were not associated with overall survival in CM, indicating it does not correlate with disease outcome. Evidence Type: Prognostic | Mutation: L416F | Summary: The L416F mutation is part of the BAP1 mutations that were not associated with overall survival in CM, suggesting it does not correlate with disease outcome. Evidence Type: Prognostic | Mutation: R59W | Summary: The R59W mutation is included in the BAP1 mutations that were not associated with overall survival in CM, indicating it does not correlate with disease outcome.

Gene→Variant (gene-first): 8314:E30K 8314:I643T 8314:L416F 8314:P629S 8314:R417M 8314:R59W 6490:S143N

Genes: 8314 6490

Variants: E30K I643T L416F P629S R417M R59W S143N

[Paper-level Aggregated] PMCID: PMC7068240

Evidence Type(s): Prognostic

Summary: Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with poorer mortality, shorter median survival time, and poorer outcomes in patients with advanced and stage IV colorectal cancer, indicating its role as a significant prognostic biomarker.

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with poorer outcomes in patients with stage IV colorectal cancer, indicating its prognostic significance.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: RESULTS PassageIndex: 4

Evidence Type(s): Oncogenic, Prognostic

Summary: Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation is associated with non-MSI tumors and contributes to tumor development or progression in colorectal cancer. Evidence Type: Prognostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with the expression of specific miRNAs, indicating its potential as a prognostic biomarker in colorectal cancer.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Prognostic

Summary: Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation is associated with tumor development and progression in colorectal cancer (CRC), as indicated by its presence in CRC specimens and its correlation with miR-31 expression levels. Evidence Type: Prognostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with poorer mortality and shorter median survival time in patients with advanced CRC, suggesting its role as a prognostic biomarker.

Gene→Variant (gene-first): 673:V600E 673:serine/threonine

Genes: 673

Variants: V600E serine/threonine

[Paper-level Aggregated] PMCID: PMC6627713

Evidence Type(s): Prognostic

Summary: Mutation: c.1798G>A (p.Asp600Asn) | Summary: The c.1798G>A variant is associated with a shorter progression-free survival (PFS) in patients, indicating a potential prognostic role.

Evidence Type: Prognostic Mutation: c.199G>A | Summary: The c.199G>A variant in the MAP2K1 gene is correlated with worse disease/progression-free survival in CRC patients.

Evidence Type: Prognostic Mutation: c.169A>G | Summary: The c.169A>G variant in the MAP2K1 gene is correlated with worse disease/progression-free survival in CRC patients.

Gene→Variant (gene-first): NA:c.1798G>A (p.Asp600Asn) MAP2K1(5604):c.199G>A MAP2K1(5604):c.169A>G

Genes: NA MAP2K1(5604)

Variants: c.1798G>A (p.Asp600Asn) c.199G>A c.169A>G

[Paragraph-level] PMCID: PMC6627713 Section: RESULTS PassageIndex: 20

Evidence Type(s): Prognostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: c.199G>A | Summary: The c.199G>A variant in the MAP2K1 gene is correlated with worse disease/progression-free survival in CRC patients. Evidence Type: Prognostic | Mutation: c.169A>G | Summary: The c.169A>G variant in the MAP2K1 gene is correlated with worse disease/progression-free survival in CRC patients. Evidence Type: Oncogenic | Mutation: c.199G>A | Summary: The c.199G>A variant contributes to tumor development or progression as it is associated with acquired resistance to anti-EGFR MoAbs. Evidence Type: Oncogenic | Mutation: c.169A>G | Summary: The c.169A>G variant contributes to tumor development or progression as it is associated with acquired resistance to anti-EGFR MoAbs.

Gene→Variant (gene-first): 5604:c.169A>G 5604:c.199G>A 5604:p.Asp67Asn 5604:p.Lys57Glu

Genes: 5604

Variants: c.169A>G c.199G>A p.Asp67Asn p.Lys57Glu

[Paragraph-level] PMCID: PMC6627713 Section: RESULTS PassageIndex: 14

Evidence Type(s): Prognostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: c.1798G>A (p.Asp600Asn) | Summary: The c.1798G>A variant is associated with a shorter progression-free survival (PFS) in patients, indicating a potential prognostic role. Evidence Type: Oncogenic | Mutation: c.1513C>T (p.Arg505Cys) | Summary: The c.1513C>T variant has been reported in several cancer types and is associated with loss of function of the protein, suggesting both oncogenic potential and functional impact.

Gene→Variant (gene-first): 55294:c.1513C>T 1956:c.1798G>A 55294:p.Arg505Cys 673:p.Asp600Asn

Genes: 55294 1956 673

Variants: c.1513C>T c.1798G>A p.Arg505Cys p.Asp600Asn

[Paper-level Aggregated] PMCID: PMC6549573

Evidence Type(s): Prognostic

Summary: Mutation: G12D | Summary: The KRAS G12D mutation is associated with prolonged survival in models with p53 deficiency, indicating a correlation with disease outcome independent of therapy.

Gene→Variant (gene-first): KRAS(3845):G12D

Genes: KRAS(3845)

Variants: G12D

[Paragraph-level] PMCID: PMC6549573 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: G12D | Summary: The KRAS G12D mutation is associated with prolonged survival in models with p53 deficiency, indicating a correlation with disease outcome independent of therapy. Evidence Type: Oncogenic | Mutation: G12D | Summary: The KRAS G12D mutation contributes to tumor development or progression, as evidenced by its presence in tumor models.

Gene→Variant (gene-first): 3845:G12D

Genes: 3845

Variants: G12D

[Paper-level Aggregated] PMCID: PMC6368247

Evidence Type(s): Prognostic

Summary: Mutation: Y537S | Summary: The presence of the Y537S mutation correlates with progression-free survival outcomes, suggesting its prognostic significance.

Gene→Variant (gene-first): PTEN(5728):Y537S

Genes: PTEN(5728)

Variants: Y537S

[Paragraph-level] PMCID: PMC6368247 Section: RESULTS PassageIndex: 17

Evidence Type(s): Predictive, Oncogenic, Prognostic

Summary: Evidence Type: Predictive | Mutation: Y537S | Summary: The Y537S mutation is associated with resistance to fulvestrant treatment, indicating its predictive value in therapy response. Evidence Type: Oncogenic | Mutation: Y537S | Summary: The Y537S mutation contributes to tumor development or progression, as it is positively selected during treatment. Evidence Type: Prognostic | Mutation: Y537S | Summary: The presence of the Y537S mutation correlates with progression-free survival outcomes, suggesting its prognostic significance.

Gene→Variant (gene-first): 5728:Y537S

Genes: 5728

Variants: Y537S

[Paper-level Aggregated] PMCID: PMC5822176

Evidence Type(s): Prognostic

Summary: Mutation: K27M | Summary: The H3 K27M mutation has been associated with longer survival in some patients with tumors of alternate morphologies, indicating a potential correlation with disease outcome independent of therapy.

Gene→Variant (gene-first): IDH1(3417):K27M

Genes: IDH1(3417)

Variants: K27M

[Paragraph-level] PMCID: PMC5822176 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Prognostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: K27M | Summary: The H3 K27M mutation has been associated with longer survival in some patients with tumors of alternate morphologies, indicating a potential correlation with disease outcome independent of therapy. Evidence Type: Oncogenic | Mutation: K27M | Summary: The H3 K27M mutation contributes to tumor development and progression, as it is implicated in various types of gliomas, including pediatric diffuse intrinsic pontine gliomas and adult midline diffuse gliomas.

Gene→Variant (gene-first): 3417:K27M

Genes: 3417

Variants: K27M

[Paper-level Aggregated] PMCID: PMC5652823

Evidence Type(s): Prognostic

Summary: Mutation: T790M | Summary: The T790M mutation may correlate with disease outcome, as indicated by the progression-free survival (PFS) and overall survival (OS) data, although specific median values have not been reached.

Gene→Variant (gene-first): EGFR(1956):T790M

Genes: EGFR(1956)

Variants: T790M

[Paragraph-level] PMCID: PMC5652823 Section: RESULTS PassageIndex: 25

Evidence Type(s): Predictive, Prognostic

Summary: Evidence Type: Predictive | Mutation: T790M | Summary: The T790M mutation is associated with treatment response to osimertinib, as evidenced by the observed partial remissions and stable disease in patients treated with this therapy. Evidence Type: Prognostic | Mutation: T790M | Summary: The T790M mutation may correlate with disease outcome, as indicated by the progression-free survival (PFS) and overall survival (OS) data, although specific median values have not been reached.

Gene→Variant (gene-first): 1956:T790M

Genes: 1956

Variants: T790M

[Paper-level Aggregated] PMCID: PMC5613053

Evidence Type(s): Prognostic

Summary: Mutation: D835Y | Summary: The D835Y mutation in FLT3 is linked to poor overall survival in patients with AML, indicating its prognostic significance independent of therapy.

Evidence Type: Prognostic Mutation: F691 | Summary: The F691 mutation in FLT3 is associated with poor overall survival in AML, highlighting its prognostic implications.

Gene→Variant (gene-first): FLT3(2322):D835Y FLT3(2322):F691

Genes: FLT3(2322)

Variants: D835Y F691

[Paragraph-level] PMCID: PMC5613053 Section: ABSTRACT PassageIndex: 2

Evidence Type(s): Predictive, Prognostic

Summary: Evidence Type: Predictive | Mutation: D835Y | Summary: The D835Y mutation in FLT3 is associated with response to the FLT3/AXL inhibitor gilteritinib, indicating its predictive value for treatment efficacy in AML. Evidence Type: Predictive | Mutation: F691 | Summary: The F691 mutation in FLT3 is also associated with response to gilteritinib, suggesting its predictive role in treatment outcomes for AML. Evidence Type: Prognostic | Mutation: D835Y | Summary: The D835Y mutation in FLT3 is linked to poor overall survival in patients with AML, indicating its prognostic significance independent of therapy. Evidence Type: Prognostic | Mutation: F691 | Summary: The F691 mutation in FLT3 is associated with poor overall survival in AML, highlighting its prognostic implications.

Gene→Variant (gene-first): 2322:D835Y 2322:F691

Genes: 2322

Variants: D835Y F691

[Paper-level Aggregated] PMCID: PMC5355930

Evidence Type(s): Prognostic

Summary: Mutation: E542K | Summary: The E542K mutation is associated with shorter progression-free survival (PFS) and overall survival compared to wild-type PIK3CA, indicating a potential prognostic role in disease outcome.

Evidence Type: Prognostic Mutation: E545K | Summary: The E545K mutation is associated with shorter progression-free survival (PFS) and overall survival compared to wild-type PIK3CA, indicating a potential prognostic role in disease outcome.

Gene→Variant (gene-first): PIK3CA(5290):E542K PIK3CA(5290):E545K

Genes: PIK3CA(5290)

Variants: E542K E545K

[Paragraph-level] PMCID: PMC5355930 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic, Predictive

Summary: Evidence Type: Prognostic | Mutation: E542K | Summary: The E542K mutation is associated with shorter progression-free survival (PFS) and overall survival compared to wild-type PIK3CA, indicating a potential prognostic role in disease outcome. Evidence Type: Prognostic | Mutation: E545K | Summary: The E545K mutation is associated with shorter progression-free survival (PFS) and overall survival compared to wild-type PIK3CA, indicating a potential prognostic role in disease outcome. Evidence Type: Predictive | Mutation: E542K | Summary: The E542K mutation suggests a role in resistance to hormone therapy, indicating a potential predictive value regarding treatment response. Evidence Type: Predictive | Mutation: E545K | Summary: The E545K mutation suggests a role in resistance to hormone therapy, indicating a potential predictive value regarding treatment response.

Gene→Variant (gene-first): 5290:E542K 5290:E545K

Genes: 5290

Variants: E542K E545K

[Paper-level Aggregated] PMCID: PMC5083195

Evidence Type(s): Prognostic

Summary: Mutation: rs1122269 | Summary: The mRNA expression levels of CDH4, associated with variant rs1122269, correlated with overall survival (OS) in pancreatic cancer patients, indicating a potential prognostic role.

Evidence Type: Prognostic Mutation: rs4925193 | Summary: The mRNA expression levels of CDH4, associated with variant rs4925193, correlated with overall survival (OS) in pancreatic cancer patients, suggesting a potential prognostic significance.

Gene→Variant (gene-first): CDH4(1002):rs1122269 CDH4(1002):rs4925193

Genes: CDH4(1002)

Variants: rs1122269 rs4925193

[Paragraph-level] PMCID: PMC5083195 Section: RESULTS PassageIndex: 12

Evidence Type(s): Functional, Prognostic

Summary: Evidence Type: Functional | Mutation: rs1122269 | Summary: The variant rs1122269 showed negative correlations with the expression of CDH4 in a cis-manner, indicating it may alter molecular function related to gene expression. Evidence Type: Functional | Mutation: rs4925193 | Summary: The variant rs4925193 also demonstrated negative correlations with the expression of CDH4 in a cis-manner, suggesting it may influence molecular function associated with gene expression. Evidence Type: Prognostic | Mutation: rs1122269 | Summary: The mRNA expression levels of CDH4, associated with variant rs1122269, correlated with overall survival (OS) in pancreatic cancer patients, indicating a potential prognostic role. Evidence Type: Prognostic | Mutation: rs4925193 | Summary: The mRNA expression levels of CDH4, associated with variant rs4925193, correlated with overall survival (OS) in pancreatic cancer patients, suggesting a potential prognostic significance.

Gene→Variant (gene-first): 1002:rs1122269 1002:rs4925193 NA:rs9637468

Genes: 1002 NA

Variants: rs1122269 rs4925193 rs9637468

[Paper-level Aggregated] PMCID: PMC4999563

Evidence Type(s): Prognostic

Summary: Mutation: G12C | Summary: The KRAS G12C mutation is associated with inferior progression-free and overall survival in metastatic colorectal cancer (mCRC) patients compared to those with non-mutated tumors. It correlates with a median overall survival (OS) of 16.8 months, indicating a negative prognostic effect.

Evidence Type: Prognostic Mutation: G13D | Summary: The KRAS G13D mutation is associated with inferior progression-free and overall survival in mCRC patients compared to those with non-mutated tumors. It shows a median progression-free survival (PFS) of 8.8 months and a trend towards inferior overall survival (OS), suggesting potential negative prognostic implications.

Evidence Type: Prognostic Mutation: G12D | Summary: The KRAS G12D variant shows a median PFS of 10.5 months and a median overall survival (OS) of 25.2 months, suggesting its impact on disease outcome, but did not show a significant impact on overall survival, indicating it may not have a strong prognostic role.

Evidence Type: Prognostic Mutation: G12V | Summary: The KRAS G12V variant did not demonstrate a significant impact on overall survival (OS) and had a negative prognostic effect on progression-free survival (PFS) in the multivariate analysis, suggesting limited prognostic value.

Gene→Variant (gene-first): KRAS(3845):G12C KRAS(3845):G13D KRAS(3845):G12D KRAS(3845):G12V

Genes: KRAS(3845)

Variants: G12C G13D G12D G12V

[Paragraph-level] PMCID: PMC4999563 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: G12C | Summary: The KRAS exon 2 G12C variant correlates with inferior overall survival (OS) compared to non-mutated tumors, indicating a negative prognostic effect. Evidence Type: Prognostic | Mutation: G13D | Summary: The KRAS exon 2 G13D variant shows a trend towards inferior overall survival (OS) compared to non-mutated tumors, suggesting a potential negative prognostic effect. Evidence Type: Prognostic | Mutation: G12V | Summary: The KRAS exon 2 G12V mutation variant had a negative prognostic effect on progression-free survival (PFS) in the multivariate analysis.

Gene→Variant (gene-first): 3845:G12C 3845:G12D 3845:G12V 3845:G13D

Genes: 3845

Variants: G12C G12D G12V G13D

[Paragraph-level] PMCID: PMC4999563 Section: RESULTS PassageIndex: 10

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: G13D | Summary: The G13D mutation is associated with a median progression-free survival (PFS) of 8.8 months, indicating its correlation with disease outcome. Evidence Type: Prognostic | Mutation: G12D | Summary: The G12D variant shows a median PFS of 10.5 months and a median overall survival (OS) of 25.2 months, suggesting its impact on disease outcome. Evidence Type: Prognostic | Mutation: G12C | Summary: The G12C mutation is linked to a median overall survival (OS) of 16.8 months, indicating its association with disease outcome.

Gene→Variant (gene-first): 3845:A146T 3845:G12C 3845:G12D 3845:G13D 3845:Q61H

Genes: 3845

Variants: A146T G12C G12D G13D Q61H

[Paragraph-level] PMCID: PMC4999563 Section: ABSTRACT PassageIndex: 9

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: G12C | Summary: The KRAS G12C mutation is associated with poor survival outcomes in mCRC patients compared to those with non-mutated tumors. Evidence Type: Prognostic | Mutation: G13D | Summary: The KRAS G13D mutation is associated with poor survival outcomes in mCRC patients compared to those with non-mutated tumors.

Gene→Variant (gene-first): 3845:G12C 3845:G13D

Genes: 3845

Variants: G12C G13D

[Paragraph-level] PMCID: PMC4999563 Section: ABSTRACT PassageIndex: 7

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: G12C | Summary: The KRAS G12C variant is associated with inferior overall survival (OS) compared to unmutated tumors, indicating a prognostic role. Evidence Type: Prognostic | Mutation: G13D | Summary: The KRAS G13D variant shows a similar trend for inferior overall survival (OS), suggesting it may also have prognostic implications. Evidence Type: Prognostic | Mutation: G12D | Summary: The KRAS G12D variant did not show a significant impact on overall survival (OS), indicating it may not have a strong prognostic role. Evidence Type: Prognostic | Mutation: G12V | Summary: The KRAS G12V variant also did not demonstrate a significant impact on overall survival (OS), suggesting limited prognostic value.

Gene→Variant (gene-first): 3845:G12C 3845:G12D 3845:G12V 3845:G13D

Genes: 3845

Variants: G12C G12D G12V G13D

[Paragraph-level] PMCID: PMC4999563 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: G12C | Summary: The KRAS G12C mutation is associated with inferior progression-free and overall survival in metastatic colorectal cancer patients compared to those with non-mutated tumors. Evidence Type: Prognostic | Mutation: G13D | Summary: The KRAS G13D mutation is associated with inferior progression-free and overall survival in metastatic colorectal cancer patients compared to those with non-mutated tumors.

Gene→Variant (gene-first): 3845:G12C 3845:G13D

Genes: 3845

Variants: G12C G13D

[Paper-level Aggregated] PMCID: PMC4899144

Evidence Type(s): Prognostic

Summary: Mutation: Y641F | Summary: The presence of the Ezh2Y641F mutation correlates with a median survival of one year in tumor-bearing mice, indicating its association with disease outcome.

Gene→Variant (gene-first): EZH2(2146):Y641F

Genes: EZH2(2146)

Variants: Y641F

[Paragraph-level] PMCID: PMC4899144 Section: RESULTS PassageIndex: 4

Evidence Type(s): Oncogenic, Prognostic

Summary: Evidence Type: Oncogenic | Mutation: Y641F | Summary: The Ezh2Y641F mutation contributes to tumor development, as it induces highly penetrant B-cell lymphoma in mice, demonstrating its role in malignancy. Evidence Type: Prognostic | Mutation: Y641F | Summary: The presence of the Ezh2Y641F mutation correlates with a median survival of one year in tumor-bearing mice, indicating its association with disease outcome.

Gene→Variant (gene-first): 2146:Y641F

Genes: 2146

Variants: Y641F

[Paper-level Aggregated] PMCID: PMC4741605

Evidence Type(s): Prognostic

Summary: Mutation: D835Y | Summary: The increase in the D835Y mutated clone at relapse suggests that this mutation may correlate with disease outcome independent of therapy, highlighting its prognostic significance.

Gene→Variant (gene-first): FLT3(2322):D835Y

Genes: FLT3(2322)

Variants: D835Y

[Paragraph-level] PMCID: PMC4741605 Section: RESULTS PassageIndex: 20

Evidence Type(s): Predictive, Prognostic, Oncogenic

Summary: Evidence Type: Predictive | Mutation: D835Y | Summary: The D835Y mutation is associated with the patient's response to chemotherapy treatment, indicating its relevance in predicting treatment outcomes. Evidence Type: Prognostic | Mutation: D835Y | Summary: The increase in the D835Y mutated clone at relapse suggests that this mutation may correlate with disease outcome independent of therapy, highlighting its prognostic significance. Evidence Type: Oncogenic | Mutation: D835Y | Summary: The D835Y mutation contributes to tumor development or progression, as indicated by its increase in frequency at relapse.

Gene→Variant (gene-first): 2322:D835Y

Genes: 2322

Variants: D835Y

[Paper-level Aggregated] PMCID: PMC4654747

Evidence Type(s): Prognostic

Summary: Mutation: K27M | Summary: Patients with tumors harboring the K27M mutation in H3.3 exhibited significantly earlier relapse and more metastatic recurrences, indicating a poor prognosis. The presence of the K27M mutation correlates with disease outcome, as indicated by clinico-radiological follow-up of DIPG patients showing a significant association with metastatic relapse. Additionally, the K27M mutation is associated with a less aggressive behavior in DIPG, indicating its correlation with disease outcome independent of therapy. Furthermore, the K27M mutation in histone H3.1 is associated with a better overall survival length compared to H3.3-K27M, indicating its prognostic significance in disease outcome.

Gene→Variant (gene-first): H3-3B(3021):K27M

Genes: H3-3B(3021)

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 14

Evidence Type(s): Prognostic, Predictive, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M mutation in histone H3.1 is associated with a better overall survival length compared to H3.3-K27M, indicating its prognostic significance in disease outcome. Evidence Type: Predictive | Mutation: K27M | Summary: Patients with the H3.1-K27M mutation show a better clinical response to radiotherapy, suggesting that this mutation may predict treatment response. Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M mutation in histone H3 is implicated in tumor development and progression, contributing to the oncogenic characteristics of the tumors.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 13

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M mutation is associated with a less aggressive behavior in diffuse intrinsic pontine glioma (DIPG), indicating its correlation with disease outcome independent of therapy.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 11

Evidence Type(s): Diagnostic, Prognostic, Functional

Summary: Evidence Type: Diagnostic | Mutation: K27M | Summary: The K27M mutation is associated with the proneural-glioblastoma multiforme subtype, indicating its role in classifying and defining this specific disease subtype. Evidence Type: Prognostic | Mutation: K27M | Summary: The presence of the K27M mutation correlates with disease outcome, as indicated by the clinico-radiological follow-up of DIPG patients showing a significant association with metastatic relapse. Evidence Type: Functional | Mutation: K27M | Summary: The K27M mutation is linked to alterations in molecular functions, specifically affecting adhesion properties and deregulating genes related to migration and invasion in tumors.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Prognostic

Summary: Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M mutation in H3.3 (H3F3A) contributes to tumor development and progression in diffuse intrinsic pontine glioma (DIPG), driving distinct oncogenic programs. Evidence Type: Oncogenic | Mutation: K27I | Summary: The K27I mutation in H3F3A is associated with tumor development in DIPG, contributing to the loss of trimethylation and driving oncogenic behavior. Evidence Type: Prognostic | Mutation: K27M | Summary: Patients with tumors harboring the K27M mutation in H3.3 exhibited significantly earlier relapse and more metastatic recurrences, indicating a poor prognosis.

Gene→Variant (gene-first): 3021:K27I 3021:K27M 126961:lysine-to-isoleucine

Genes: 3021 126961

Variants: K27I K27M lysine-to-isoleucine

[Paper-level Aggregated] PMCID: PMC4378307

Evidence Type(s): Prognostic

Summary: Mutation: G12D | Summary: The G12D mutation in KRAS is associated with a poor prognosis in progression-free survival (PFS), serving as an independent negative prognostic factor.

Evidence Type: Prognostic Mutation: G12S | Summary: The G12S subtype of KRAS mutation is associated with poor prognosis in overall survival (OS).

Gene→Variant (gene-first): KRAS(3845):G12D KRAS(3845):G12S

Genes: KRAS(3845)

Variants: G12D G12S

[Paragraph-level] PMCID: PMC4378307 Section: RESULTS PassageIndex: 7

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: G12D | Summary: The G12D subtype of KRAS mutation is associated with poor prognosis in progression-free survival (PFS). Evidence Type: Prognostic | Mutation: G12S | Summary: The G12S subtype of KRAS mutation is associated with poor prognosis in overall survival (OS).

Gene→Variant (gene-first): 3845:G12D 3845:G12S

Genes: 3845

Variants: G12D G12S

[Paragraph-level] PMCID: PMC4378307 Section: ABSTRACT PassageIndex: 3

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: G12D | Summary: The G12D mutation in KRAS is associated with a poor prognosis in progression-free survival (PFS), indicating it serves as an independent negative prognostic factor.

Gene→Variant (gene-first): 3845:G12D

Genes: 3845

Variants: G12D

[Paper-level Aggregated] PMCID: PMC4159563

Evidence Type(s): Prognostic

Summary: Mutation: K27M | Summary: The K27M-H3 mutation correlates with disease behavior and outcomes in pediatric brainstem gliomas, indicating it may not predict outcomes accurately according to the current WHO grading scheme. It is associated with worse overall survival in patients with leptomeningeal spread, averaging 0.63 years compared to 1.84 years for wild-type cases. Additionally, the K27M mutation in histone H3 is linked to worse overall survival in DIPG patients compared to those without histone mutations, highlighting its prognostic significance.

Gene→Variant (gene-first): ACVR1(90):K27M

Genes: ACVR1(90)

Variants: K27M

[Paragraph-level] PMCID: PMC4159563 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic, Diagnostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M mutation in histone H3 is associated with worse overall survival in DIPG patients compared to those without histone mutations, indicating its prognostic significance. Evidence Type: Diagnostic | Mutation: K27M | Summary: The presence of the K27M mutation in histone H3 is used to classify and define the subtype of tumors in DIPG patients, serving as a diagnostic marker. Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M mutation in histone H3 contributes to tumor development and progression in DIPG, indicating its oncogenic potential.

Gene→Variant (gene-first): 90:K27M

Genes: 90

Variants: K27M

[Paragraph-level] PMCID: PMC4159563 Section: RESULTS PassageIndex: 7

Evidence Type(s): Prognostic, Oncogenic, Functional

Summary: Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M mutation is associated with worse overall survival in patients with leptomeningeal spread, averaging 0.63 years compared to 1.84 years for wild-type cases. Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M mutation contributes to tumor development, as indicated by its presence in cases of GBM and its association with leptomeningeal dissemination. Evidence Type: Functional | Mutation: p.Glu545Gly | Summary: The p.Glu545Gly alteration in PIK3CA is a mutation that may alter the molecular function of the protein, contributing to tumorigenesis. Evidence Type: Functional | Mutation: p.Gly328Val | Summary: The p.Gly328Val substitution in ACVR1 is a mutation that may affect the molecular function of the protein, potentially playing a role in tumor development.

Gene→Variant (gene-first): 90:K27M 5290:p.Glu545Gly 90:p.Gly328Val

Genes: 90 5290

Variants: K27M p.Glu545Gly p.Gly328Val

[Paragraph-level] PMCID: PMC4159563 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Diagnostic, Prognostic

Summary: Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M-H3 mutation is associated with high-grade astrocytomas and contributes to tumor development in diffuse intrinsic pontine glioma (DIPG). Evidence Type: Diagnostic | Mutation: K27M | Summary: The presence of the K27M-H3 mutation is used to classify and define the histological subtype of astrocytomas in DIPG cases. Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M-H3 mutation correlates with disease behavior and outcome in pediatric brainstem gliomas, indicating that it may not predict outcomes accurately according to the current WHO grading scheme.

Gene→Variant (gene-first): 90:K27M

Genes: 90

Variants: K27M

[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

[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

[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

[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

[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

[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

[Paper-level Aggregated] PMCID: PMC3422615

Evidence Type(s): Prognostic

Summary: Mutation: K27M | Summary: The K27M-H3.3 mutation is universally associated with short survival in DIPG and correlates with significantly worse overall survival in DIPG patients compared to wild-type tumors, indicating its prognostic significance in disease outcome.

Gene→Variant (gene-first): H3-3B(3021):K27M

Genes: H3-3B(3021)

Variants: K27M

[Paragraph-level] PMCID: PMC3422615 Section: RESULTS PassageIndex: 12

Evidence Type(s): Prognostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M-H3.3 mutation correlates with significantly worse overall survival in DIPG patients compared to wild-type tumors, indicating its role as a prognostic factor for disease outcome. Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M-H3.3 mutation contributes to tumor development or progression in DIPG, as evidenced by its association with poor survival outcomes in affected patients.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC3422615 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Prognostic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M-H3.3 mutation is prevalent in pediatric glioblastomas and contributes to tumor development, defining clinically and biologically distinct subgroups. Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M-H3.3 mutation is universally associated with short survival in DIPG, indicating its prognostic significance in disease outcome. Evidence Type: Diagnostic | Mutation: K27M | Summary: The K27M-H3.3 mutation is used to define clinically and biologically distinct subgroups in pediatric glioblastomas, supporting its role in diagnostic testing.

Gene→Variant (gene-first): 3021:G34V 3021:G34V/R 3021:K27M

Genes: 3021

Variants: G34V G34V/R K27M

[Paper-level Aggregated] PMCID: PMC2970593

Evidence Type(s): Prognostic

Summary: Mutation: L858R | Summary: Patients with the L858R mutation had a median follow-up time of 22 months, with some developing progressive disease and death, suggesting a correlation with disease outcome.

Gene→Variant (gene-first): EGFR(1956):L858R

Genes: EGFR(1956)

Variants: L858R

[Paragraph-level] PMCID: PMC2970593 Section: ABSTRACT PassageIndex: 6

Evidence Type(s): Functional, Predictive, Prognostic

Summary: Evidence Type: Functional | Mutation: L858R | Summary: The L858R mutation is described as a functional mutation that is activating in nature. Evidence Type: Predictive | Mutation: L858R | Summary: The L858R mutation is responsive to erlotinib, indicating a correlation with treatment response. Evidence Type: Prognostic | Mutation: L858R | Summary: Patients with the L858R mutation had a median follow-up time of 22 months, with some developing progressive disease and death, suggesting a correlation with disease outcome.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paper-level Aggregated] PMCID: PMC2736831

Evidence Type(s): Prognostic

Summary: Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlated with significantly shorter overall survival (OS) and a trend towards shorter progression-free survival (PFS), suggesting its prognostic implications for disease outcome.

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC2736831 Section: RESULTS PassageIndex: 10

Evidence Type(s): Predictive, Prognostic, Oncogenic

Summary: Evidence Type: Predictive | Mutation: V600E | Summary: The BRAF V600E mutation was associated with a lack of response to treatment compared to BRAF wild-type patients, indicating its predictive value regarding treatment resistance. Evidence Type: Prognostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlated with significantly shorter overall survival (OS) and a trend towards shorter progression-free survival (PFS), suggesting its prognostic implications for disease outcome. Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation is implicated in tumor development or progression, as indicated by its presence in the study population and its association with poor clinical outcomes.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paper-level Aggregated] PMCID: PMC2360265

Evidence Type(s): Prognostic

Summary: Mutation: L858R | Summary: The L858R mutation is associated with time to tumor progression (TTP), indicating its potential role in influencing disease outcome independent of therapy. However, the difference in TTP compared to other mutations did not reach statistical significance. Additionally, when analyzed in relation to overall survival (OS), no statistically significant difference in OS was found when compared to patients with the DEL19 mutation.

Gene→Variant (gene-first): EGFR(1956):L858R

Genes: EGFR(1956)

Variants: L858R

[Paragraph-level] PMCID: PMC2360265 Section: RESULTS PassageIndex: 16

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: L858R | Summary: The L858R mutation was analyzed in relation to overall survival (OS), but no statistically significant difference in OS was found when compared to patients with the DEL19 mutation.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC2360265 Section: RESULTS PassageIndex: 14

Evidence Type(s): Prognostic

Summary: Evidence Type: Prognostic | Mutation: L858R | Summary: The L858R mutation is associated with time to tumor progression (TTP), indicating its potential role in influencing disease outcome independent of therapy. However, the difference in TTP compared to other mutations did not reach statistical significance.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 14

Evidence Type(s): Diagnostic, Prognostic, Oncogenic

Justification: Diagnostic: The passage discusses the association of H3.1-K27M tumors with clinical characteristics and outcomes, indicating its role in defining and classifying the disease. Prognostic: The variant K27M is correlated with overall survival outcomes, with H3.1 mutations showing a better prognosis compared to H3.3 mutations, independent of therapy. Oncogenic: The mention of H3.1-K27M tumors suggests that this somatic variant contributes to tumor development or progression, as it is associated with clinical characteristics and outcomes in cancer patients.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 13

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The K27M mutation is associated with disease behavior, indicating a correlation with disease outcome, specifically suggesting a less aggressive behavior in DIPG. Diagnostic: The mention of the K27M mutation being associated with DIPG suggests its role in defining or classifying this specific disease subtype.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC6549573 Section: RESULTS PassageIndex: 11

Evidence Type(s): Oncogenic, Prognostic

Justification: Oncogenic: The passage discusses the KRAS G12D variant in the context of tumor regression and survival in specific mouse models, indicating its role in tumor development or progression. Prognostic: The mention of prolonged survival in the context of the KRAS G12D variant suggests a correlation with disease outcome, independent of therapy.

Gene→Variant (gene-first): 3845:G12D

Genes: 3845

Variants: G12D

[Paragraph-level] PMCID: PMC4899144 Section: RESULTS PassageIndex: 4

Evidence Type(s): Oncogenic, Prognostic

Justification: Oncogenic: The passage describes how the Ezh2Y641F variant contributes to the development of B-cell lymphoma in mice, indicating its role in tumor progression. Prognostic: The median survival of one year for mice with the Ezh2Y641F variant suggests a correlation with disease outcome, specifically survival, independent of therapy.

Gene→Variant (gene-first): 2146:Y641F

Genes: 2146

Variants: Y641F

[Paragraph-level] PMCID: PMC7074098 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic

Justification: Prognostic: The passage discusses the correlation of BAP1 mutations and copy number variations with overall survival in cutaneous melanoma (CM), indicating that certain alterations are associated with better survival outcomes.

Gene→Variant (gene-first): 8314:E30K 8314:I643T 8314:L416F 8314:P629S 8314:R417M 8314:R59W 6490:S143N

Genes: 8314 6490

Variants: E30K I643T L416F P629S R417M R59W S143N

[Paragraph-level] PMCID: PMC3422615 Section: RESULTS PassageIndex: 12

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses the correlation between the K27M-H3.3 mutation and overall survival in DIPG patients, indicating that patients with this mutation have significantly worse survival outcomes compared to those with wild-type tumors. Diagnostic: The K27M-H3.3 mutation is associated with the classification of DIPG patients, as it is mentioned that 69% of the patients carried this mutation, which is relevant for defining their disease status.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC3422615 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Diagnostic, Prognostic, Oncogenic

Justification: Diagnostic: K27M-H3.3 mutation defines clinically and biologically distinct subgroups in DIPG, indicating its use in classifying the disease. Prognostic: K27M-H3.3 is universally associated with short survival in DIPG, while patients wild-type for H3.3 show improved survival, indicating its correlation with disease outcome. Oncogenic: The K27M-H3.3 mutation contributes to tumor development or progression in pediatric glioblastomas, as indicated by its prevalence in DIPG and association with specific copy number changes.

Gene→Variant (gene-first): 3021:G34V 3021:G34V/R 3021:K27M

Genes: 3021

Variants: G34V G34V/R K27M

[Paragraph-level] PMCID: PMC10082285 Section: ABSTRACT PassageIndex: 5

Evidence Type(s): Predictive, Diagnostic, Prognostic, Oncogenic

Justification: Predictive: The passage discusses the assignment of patients with EGFR-mutated NSCLC to receive osimertinib, indicating a correlation between the L858R variant and response to this specific therapy. Diagnostic: The mention of patients with EGFR-mutated NSCLC, specifically referencing the L858R variant, suggests its role in defining or classifying the disease subtype. Prognostic: The passage refers to disease-free survival (DFS) and overall survival as endpoints, indicating that the L858R variant may correlate with disease outcomes independent of therapy. Oncogenic: The context of the L858R variant being part of EGFR mutations in NSCLC implies its contribution to tumor development or progression, characteristic of oncogenic variants.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC7294133 Section: ABSTRACT PassageIndex: 2

Evidence Type(s): Oncogenic, Predictive, Prognostic

Justification: Oncogenic: The variant V871I in the EPHB4 gene is described as contributing to increased proliferation, migration, and invasion properties in neuroblastoma cell lines, indicating its role in tumor development and progression. Predictive: The passage discusses the use of EPHB4 inhibitors that can rescue the phenotype driven by the variant V871I, suggesting a correlation with response to specific therapies. Prognostic: The passage mentions that higher EPHB4 expression is correlated with stage 4 neuroblastoma and poor overall survival, indicating a relationship between the variant and disease outcome.

Gene→Variant (gene-first): 2050:V871I

Genes: 2050

Variants: V871I

[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

[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

[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

[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

[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

[Paragraph-level] PMCID: PMC7068240 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic, Oncogenic

Justification: Prognostic: The passage indicates that the presence of the BRAF V600E mutation correlates with poorer outcomes in patients with stage IV CRC, suggesting its role in prognosis independent of therapy. Oncogenic: The BRAF V600E mutation is associated with tumor development or progression, as indicated by its correlation with poorer prognosis in the context of cancer.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: RESULTS PassageIndex: 4

Evidence Type(s): Diagnostic, Prognostic

Justification: Diagnostic: The passage discusses the association of the BRAF V600E mutation with non-MSI tumors, indicating its role in classifying or defining a specific subtype of colorectal cancer. Prognostic: The passage mentions that miR-31 is being focused on as a candidate prognostic biomarker, suggesting a correlation with disease outcome in the context of tumors harboring the BRAF V600E mutation.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses the association of high miR-31 expression with poorer mortality and shorter median survival time in patients with advanced colorectal cancer, indicating a prognostic relationship. Diagnostic: The study evaluates the potential of miRNAs as biomarkers for colorectal cancer, suggesting that the presence of the BRAF V600E mutation can be used to classify tumors based on miR-31 expression levels.

Gene→Variant (gene-first): 673:V600E 673:serine/threonine

Genes: 673

Variants: V600E serine/threonine

[Paragraph-level] PMCID: PMC5083195 Section: RESULTS PassageIndex: 12

Evidence Type(s): Functional, Prognostic

Justification: Functional: The passage discusses the influence of SNPs (rs9637468 and rs4925193) on the expression of genes in a cis-manner, indicating that these variants alter molecular function related to gene expression. Prognostic: The mRNA expression levels of CDH4 were associated with overall survival (OS) of pancreatic cancer patients, suggesting that the variants may correlate with disease outcome independent of therapy.

Gene→Variant (gene-first): 1002:rs1122269 1002:rs4925193 NA:rs9637468

Genes: 1002 NA

Variants: rs1122269 rs4925193 rs9637468

[Paragraph-level] PMCID: PMC5083195 Section: RESULTS PassageIndex: 10

Evidence Type(s): Predictive, Prognostic

Justification: Predictive: The passage discusses the association of the SNPs rs9637468 and rs4925193 with overall survival (OS) in the context of gemcitabine treatment, indicating their potential as genetic biomarkers for predicting response to therapy. Prognostic: The passage mentions that the SNPs are associated with overall survival (OS) outcomes, suggesting that they may correlate with disease outcome independent of therapy.

Gene→Variant (gene-first): 1002:rs4925193 NA:rs9637468

Genes: 1002 NA

Variants: rs4925193 rs9637468

[Paragraph-level] PMCID: PMC6368247 Section: RESULTS PassageIndex: 17

Evidence Type(s): Predictive, Prognostic, Oncogenic

Justification: Predictive: The passage discusses the positive selection of the ESR1 Y537S mutation through treatment and its association with resistance to fulvestrant, indicating a correlation with treatment response. Prognostic: The exploratory analysis of progression-free survival comparing patients with a Y537S mutation at day 1 to those who acquired it by the end of treatment suggests a correlation with disease outcome, independent of therapy. Oncogenic: The evidence presented indicates that the ESR1 Y537S mutation contributes to tumor development or progression, particularly in the context of promoting resistance to treatment.

Gene→Variant (gene-first): 5728:Y537S

Genes: 5728

Variants: Y537S

[Paragraph-level] PMCID: PMC4378307 Section: RESULTS PassageIndex: 7

Evidence Type(s): Prognostic

Justification: Prognostic: The passage indicates that the G12D and G12S subtypes of KRAS mutations are associated with poor prognosis in progression-free survival (PFS) and overall survival (OS), respectively, which correlates with disease outcomes independent of therapy.

Gene→Variant (gene-first): 3845:G12D 3845:G12S

Genes: 3845

Variants: G12D G12S

[Paragraph-level] PMCID: PMC4378307 Section: ABSTRACT PassageIndex: 3

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage indicates that KRAS mutation, specifically G12D, is associated with a poor prognosis in progression-free survival (PFS), demonstrating its role as an independent negative prognostic factor. Diagnostic: The mention of KRAS mutations, including G12D, being associated with specific outcomes in patients suggests that these mutations can be used to classify or define disease subtypes.

Gene→Variant (gene-first): 3845:G12D

Genes: 3845

Variants: G12D

[Paragraph-level] PMCID: PMC4159563 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic, Diagnostic, Oncogenic

Justification: Prognostic: The passage indicates that patients with the K27M mutation in histone H3 have worse overall survival compared to patients with no histone mutations, suggesting a correlation between the variant and disease outcome. Diagnostic: The K27M mutation is associated with specific tumor histologies and is used to classify patients into different groups based on their histone mutation status, indicating its role in defining disease subtypes. Oncogenic: The K27M mutation in histone H3 is described as contributing to tumor development, as it is found in a significant proportion of tumors and correlates with specific tumor characteristics.

Gene→Variant (gene-first): 90:K27M

Genes: 90

Variants: K27M

[Paragraph-level] PMCID: PMC4159563 Section: RESULTS PassageIndex: 7

Evidence Type(s): Prognostic, Oncogenic

Justification: Prognostic: The passage discusses overall survival rates for patients with and without leptomeningeal spread, indicating that the presence of the K27M mutation correlates with worse survival outcomes. Oncogenic: The K27M variant is mentioned in the context of tumor spread and is associated with specific tumor types (GBM), suggesting its role in tumor development or progression.

Gene→Variant (gene-first): 90:K27M 5290:p.Glu545Gly 90:p.Gly328Val

Genes: 90 5290

Variants: K27M p.Glu545Gly p.Gly328Val

[Paragraph-level] PMCID: PMC5652823 Section: RESULTS PassageIndex: 25

Evidence Type(s): Predictive, Prognostic

Justification: Predictive: The passage discusses the response of patients with a T790M mutation to osimertinib treatment, indicating a correlation between the variant and treatment response. Prognostic: The passage mentions progression-free survival (PFS) and overall survival (OS) in relation to the T790M mutation, suggesting a correlation with disease outcome independent of therapy.

Gene→Variant (gene-first): 1956:T790M

Genes: 1956

Variants: T790M

[Paragraph-level] PMCID: PMC2360265 Section: RESULTS PassageIndex: 16

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses median overall survival (OS) in relation to the L858R mutation, indicating that there is no statistically significant difference in OS between patients with the L858R mutation and those with other mutations, which relates to disease outcome. Diagnostic: The mention of the L858R mutation in the context of comparing survival outcomes suggests its role in classifying or defining patient subgroups based on mutational status.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC2360265 Section: RESULTS PassageIndex: 14

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses time to tumor progression (TTP) in relation to different mutation groups, including L858R, indicating a correlation with disease outcome independent of therapy. Diagnostic: The mention of "classical mutations group" and comparisons with "wild-type" suggests that the L858R variant is used to classify or define a subtype of the disease.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC2360265 Section: RESULTS PassageIndex: 16

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses median overall survival (OS) in relation to the L858R mutation, indicating that there is no statistically significant difference in OS between patients with the L858R mutation and those with other mutations, which relates to disease outcome. Diagnostic: The mention of the L858R mutation in the context of comparing survival outcomes suggests its role in classifying or defining patient subgroups based on mutational status.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC2360265 Section: RESULTS PassageIndex: 14

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses time to tumor progression (TTP) in relation to different mutation groups, including L858R, indicating a correlation with disease outcome independent of therapy. Diagnostic: The mention of "classical mutations group" and comparisons with "wild-type" suggests that the L858R variant is used to classify or define a subtype of the disease.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC7545690 Section: ABSTRACT PassageIndex: 3

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage indicates that the rs3786362 G allele is significantly associated with progression-free survival (PFS) and overall survival (OS), which are outcomes related to disease prognosis. Diagnostic: The association of the rs3786362 G allele with tumor characteristics suggests it may be used to classify or define disease subtypes, particularly in colorectal cancer (CRC).

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 15

Evidence Type(s): Prognostic, Predictive

Justification: Prognostic: The passage discusses how the rs3786362 variant correlates with progression-free survival (PFS) and overall survival (OS) in metastatic colorectal cancer (mCRC) patients, indicating its association with disease outcomes independent of therapy. Predictive: The passage suggests that TYMS rs3786362 could be a predictive biomarker for survival in mCRC patients, indicating a potential correlation with treatment response in specific subgroups.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 14

Evidence Type(s): Prognostic

Justification: Prognostic: The passage indicates that rs3786362 is involved in stratification analysis related to mCRC survival, suggesting a correlation with disease outcome.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses the correlation of the rs3786362 variant with progression-free survival (PFS) and overall survival (OS) in mCRC patients, indicating its association with disease outcome independent of therapy. Diagnostic: The variant rs3786362 is used to classify patients based on their genotypes (AG/GG vs. AA), which suggests its role in defining or associating with a disease subtype in mCRC.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 10

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses the association of the variant rs3786362 with reduced overall survival (OS) and progression-free survival (PFS), indicating its correlation with disease outcomes independent of therapy. Diagnostic: The variant rs3786362 is associated with different genotypes (AG and AA) that correlate with reduced PFS and OS, suggesting its role in classifying disease outcomes based on genotype.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic

Justification: Prognostic: The passage discusses the correlation between the variant rs3786362 and mCRC survival, indicating its association with disease outcome independent of therapy.

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC7545690 Section: RESULTS PassageIndex: 8

Evidence Type(s): Prognostic, Predictive

Justification: Prognostic: The passage discusses the correlation of SNPs, specifically rs3786362 and rs369803, with progression-free survival (PFS) in metastatic colorectal cancer (mCRC) patients, indicating their association with disease outcome. Predictive: The passage mentions the correlation of SNPs with disease control rate (DCR), suggesting that these variants may influence treatment response in mCRC patients.

Gene→Variant (gene-first): 10841:rs10432965 2346:rs369803 7298:rs3786362 113235:rs4795436

Genes: 10841 2346 7298 113235

Variants: rs10432965 rs369803 rs3786362 rs4795436

[Paragraph-level] PMCID: PMC7545690 Section: ABSTRACT PassageIndex: 3

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage indicates that the rs3786362 G allele is significantly associated with progression-free survival (PFS) and overall survival (OS), which are outcomes related to disease prognosis. Diagnostic: The association of the rs3786362 G allele with tumor characteristics suggests it may be used to classify or define disease subtypes, particularly in colorectal cancer (CRC).

Gene→Variant (gene-first): 7298:rs3786362

Genes: 7298

Variants: rs3786362

[Paragraph-level] PMCID: PMC4999563 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic, Oncogenic

Justification: Prognostic: The passage discusses the correlation of KRAS exon 2 variants, specifically G12C and G13D, with overall survival (OS) and progression-free survival (PFS), indicating their impact on disease outcome independent of therapy. Oncogenic: The mention of KRAS exon 2 variants suggests their role in tumor development or progression, as they are associated with inferior survival outcomes in patients with mutated tumors compared to non-mutated tumors.

Gene→Variant (gene-first): 3845:G12C 3845:G12D 3845:G12V 3845:G13D

Genes: 3845

Variants: G12C G12D G12V G13D

[Paragraph-level] PMCID: PMC4999563 Section: RESULTS PassageIndex: 10

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses the median progression-free survival (PFS) and overall survival (OS) associated with specific KRAS mutations, indicating a correlation with disease outcomes independent of therapy. Diagnostic: The mention of KRAS exon 2 mutant tumor subtypes suggests that these variants are used to classify or define a specific disease subtype.

Gene→Variant (gene-first): 3845:A146T 3845:G12C 3845:G12D 3845:G13D 3845:Q61H

Genes: 3845

Variants: A146T G12C G12D G13D Q61H

[Paragraph-level] PMCID: PMC4999563 Section: ABSTRACT PassageIndex: 9

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage indicates that KRAS G12C and G13D mutations are associated with inferior progression-free survival (PFS) and overall survival (OS) in mCRC patients, suggesting a correlation with disease outcome independent of therapy. Diagnostic: The mention of KRAS mutations being associated with heterogeneous outcomes compared to unmutated tumors implies that these variants can be used to classify or define a disease subtype in mCRC.

Gene→Variant (gene-first): 3845:G12C 3845:G13D

Genes: 3845

Variants: G12C G13D

[Paragraph-level] PMCID: PMC4999563 Section: ABSTRACT PassageIndex: 7

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses the correlation of KRAS mutations, including specific variants like G12C and G13D, with inferior overall survival (OS) and progression-free survival (PFS), indicating their impact on disease outcome independent of therapy. Diagnostic: The passage mentions that mutations in KRAS were diagnosed in tumors, indicating that these mutations are used to classify or define the disease.

Gene→Variant (gene-first): 3845:G12C 3845:G12D 3845:G12V 3845:G13D

Genes: 3845

Variants: G12C G12D G12V G13D

[Paragraph-level] PMCID: PMC4999563 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses how KRAS G12C and G13D mutations correlate with inferior progression-free and overall survival in metastatic colorectal cancer patients, indicating their prognostic significance. Diagnostic: The mention of KRAS mutations being associated with tumor characteristics suggests their role in classifying or defining the disease subtype in colorectal cancer.

Gene→Variant (gene-first): 3845:G12C 3845:G13D

Genes: 3845

Variants: G12C G13D

[Paragraph-level] PMCID: PMC4999563 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic, Oncogenic

Justification: Prognostic: The passage discusses the correlation of KRAS exon 2 variants, specifically G12C and G13D, with overall survival (OS) and progression-free survival (PFS), indicating their impact on disease outcome independent of therapy. Oncogenic: The mention of KRAS exon 2 variants suggests their role in tumor development or progression, as they are associated with inferior survival outcomes in patients with mutated tumors compared to non-mutated tumors.

Gene→Variant (gene-first): 3845:G12C 3845:G12D 3845:G12V 3845:G13D

Genes: 3845

Variants: G12C G12D G12V G13D

[Paragraph-level] PMCID: PMC4999563 Section: RESULTS PassageIndex: 10

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses the median progression-free survival (PFS) and overall survival (OS) associated with specific KRAS mutations, indicating a correlation with disease outcomes independent of therapy. Diagnostic: The mention of KRAS exon 2 mutant tumor subtypes suggests that these variants are used to classify or define a specific disease subtype.

Gene→Variant (gene-first): 3845:A146T 3845:G12C 3845:G12D 3845:G13D 3845:Q61H

Genes: 3845

Variants: A146T G12C G12D G13D Q61H

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 17

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses overall survival (OS) outcomes associated with the L858R variant, indicating that it correlates with disease outcome independent of therapy. Diagnostic: The mention of the type of EGFR mutation, including L858R, being associated with overall survival suggests its role in classifying or defining disease outcomes.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 16

Evidence Type(s): Predictive, Prognostic

Justification: Predictive: The passage discusses the proportion of patients receiving first-line targeted therapy based on the presence of the L858R mutation, indicating a correlation with treatment response. Prognostic: The median overall survival (OS) for patients with the L858R mutation is reported, demonstrating its correlation with disease outcome independent of therapy.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 13

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses overall survival (OS) in patients with the L858R variant, indicating a correlation between this variant and disease outcome, independent of therapy. Diagnostic: The mention of distinct survival patterns observed in different EGFR mutation subclasses, including L858R, suggests that this variant is used to classify or define a subtype of disease.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 17

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses overall survival (OS) outcomes associated with the L858R variant, indicating that it correlates with disease outcome independent of therapy. Diagnostic: The mention of the type of EGFR mutation, including L858R, being associated with overall survival suggests its role in classifying or defining disease outcomes.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 16

Evidence Type(s): Predictive, Prognostic

Justification: Predictive: The passage discusses the proportion of patients receiving first-line targeted therapy based on the presence of the L858R mutation, indicating a correlation with treatment response. Prognostic: The median overall survival (OS) for patients with the L858R mutation is reported, demonstrating its correlation with disease outcome independent of therapy.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 13

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses overall survival (OS) in patients with the L858R variant, indicating a correlation between this variant and disease outcome, independent of therapy. Diagnostic: The mention of distinct survival patterns observed in different EGFR mutation subclasses, including L858R, suggests that this variant is used to classify or define a subtype of disease.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC6627713 Section: RESULTS PassageIndex: 20

Evidence Type(s): Diagnostic, Prognostic, Predictive, Oncogenic

Justification: Diagnostic: The passage discusses the frequencies of MAP2K1 variants in CRC patients and their association with specific tumor characteristics, indicating their role in defining or classifying the disease. Prognostic: The variants are correlated with worse disease/progression-free survival, suggesting they have prognostic implications independent of therapy. Predictive: The passage mentions that MAP2K1 mutations are associated with de novo and acquired resistance to anti-EGFR MoAbs, indicating a predictive relationship with therapy response. Oncogenic: The variants are described as contributing to a gain of function of the MEK1 protein, which is indicative of their role in tumor development or progression.

Gene→Variant (gene-first): 5604:c.169A>G 5604:c.199G>A 5604:p.Asp67Asn 5604:p.Lys57Glu

Genes: 5604

Variants: c.169A>G c.199G>A p.Asp67Asn p.Lys57Glu

[Paragraph-level] PMCID: PMC6627713 Section: RESULTS PassageIndex: 14

Evidence Type(s): Prognostic, Oncogenic

Justification: Prognostic: The passage indicates that two missense mutations are associated with patients having a shorter progression-free survival (PFS), suggesting a correlation with disease outcome. Oncogenic: The FBXW7 p.Arg505Cys mutation is reported to lead to loss of function of the protein and has been associated with several cancer types, indicating its contribution to tumor development or progression.

Gene→Variant (gene-first): 55294:c.1513C>T 1956:c.1798G>A 55294:p.Arg505Cys 673:p.Asp600Asn

Genes: 55294 1956 673

Variants: c.1513C>T c.1798G>A p.Arg505Cys p.Asp600Asn

[Paragraph-level] PMCID: PMC6627713 Section: RESULTS PassageIndex: 13

Evidence Type(s): Oncogenic, Prognostic

Justification: Oncogenic: The variants in NF1 are described as contributing to tumor development by leading to a loss of function and increased activation of the RAS signaling pathway, indicating their role in oncogenesis. Prognostic: The passage provides progression-free survival (PFS) times for the patients with the variants, suggesting a correlation between the variants and disease outcome.

Gene→Variant (gene-first): 4763:c.5101A>T 4763:c.638_639insA 4763:p.Asn214Lys fs*2 4763:p.Lys1701Ter

Genes: 4763

Variants: c.5101A>T c.638_639insA p.Asn214Lys fs*2 p.Lys1701Ter

[Paragraph-level] PMCID: PMC9468105 Section: RESULTS PassageIndex: 14

Evidence Type(s): Diagnostic, Prognostic

Justification: Diagnostic: The passage discusses the association of the BRAF p.V600E mutation with pleomorphic xanthoastrocytoma, indicating its role in defining or classifying this specific tumor type. Prognostic: The Kaplan-Meier survival analysis mentioned in the passage indicates that patients with NF1-associated gliomas have inferior outcomes, suggesting a correlation between the presence of certain mutations and disease prognosis.

Gene→Variant (gene-first): 673:p.V600E

Genes: 673

Variants: p.V600E