Prognostic, Oncogenic, Functional evidence:

Prognostic: The abstract states that "USP19 downregulation was associated with ccRCC progression and poor prognostic outcomes in TCGA cohort," indicating that the variant correlates with disease outcome independent of therapy.

Oncogenic: The findings suggest that "USP19 overexpression inhibited ccRCC proliferation and migration," while "USP19 knockdown promoted ccRCC proliferation and migration," demonstrating that USP19 contributes to tumor development or progression in clear cell renal cell carcinoma.

Functional: The study describes that "USP19 exerted its inhibitory effect on ccRCC proliferation and migration by suppressing the activation of ERK," indicating that the variant alters molecular function related to cancer cell behavior.

Predictive, Prognostic evidence:

Prognostic: The study indicates that TP53 mutations were a negative prognostic factor for disease-free survival (DFS) in untreated patients, suggesting that these mutations correlate with worse outcomes independent of therapy.

Predictive: The results show that TP53 mutations were a positive predictive factor for the efficacy of gemcitabine treatment, indicating that the presence of these mutations correlates with a better response to this specific therapy.

Functional evidence:

Functional: The study indicates that Actinomycin D downregulated Sox2, suggesting that the variant alters the molecular function of Sox2, which is relevant to the stem cell population in GBM tumors. This alteration in expression demonstrates a biochemical effect of the treatment on the variant's activity.

Prognostic, Functional evidence:

Prognostic: The study indicates that higher expression of ELFN1-AS1 is associated with shorter patient survival in esophageal cancer (ESCA), suggesting a correlation with disease outcome independent of therapy.

Functional: The research demonstrates that down-regulation of ELFN1-AS1 restrains cell proliferation, migration, and invasion in ESCA, indicating that this lncRNA alters molecular functions related to cancer progression.

Predictive evidence:

Predictive: The study investigates the association between ABCC11 expression and resistance to alectinib, indicating that increased ABCC11 expression correlates with decreased sensitivity to the drug, which is a clear example of predictive evidence regarding treatment response.

Predictive, Oncogenic evidence:

Oncogenic: The study establishes a causal link between USP10 and hyperactivated YAP/TAZ in hepatocellular carcinoma, indicating that the aberrant activation of YAP/TAZ contributes to tumor progression. This suggests that the variant's role is related to tumor development or progression in the context of hepatocellular carcinoma.

Predictive: The findings provide a rationale for potential therapeutic interventions in patients with hepatocellular carcinoma harboring a high level of YAP/TAZ, indicating that the variant may correlate with treatment response or sensitivity to specific therapies targeting YAP/TAZ.

Prognostic, Oncogenic evidence:

Prognostic: The study found that high GAL1 expression was significantly associated with poor recurrence-free survival (RFS) and low cancer-specific survival (CSS), indicating that GAL1 expression correlates with disease outcome independent of therapy. The multivariate analysis further supports that GAL1-high is an independent predictive factor for RFS and CSS, reinforcing its prognostic significance in upper tract urothelial carcinoma (UTUC).

Oncogenic: The research indicates that GAL1 promotes invasion and metastasis in urothelial carcinoma by activating specific signaling pathways, suggesting that GAL1 contributes to tumor development and progression. The in vitro studies demonstrated that GAL1 knockdown significantly reduced migration and invasiveness, highlighting its role in oncogenic processes.

Prognostic evidence:

Prognostic: The abstract indicates that NUSAP1 may serve as a valuable indicator of poor survival in CESC, suggesting a correlation between the variant and disease outcome independent of therapy.

Prognostic evidence:

Prognostic: The study reports that overexpression of SQLE is significantly associated with worse overall survival (OS) and disease-free survival (DFS) in patients with HCC, indicating that this variant correlates with disease outcome independent of therapy. The hazard ratio and statistical significance further support its role as a prognostic biomarker for HCC.

Prognostic, Oncogenic evidence:

Oncogenic: The study indicates that FAM83A is an over-expressed oncogene in non-small cell lung cancer (NSCLC) and plays a role in tumorigenesis, as evidenced by the inhibition of cell proliferation and tumor growth upon silencing FAM83A. This suggests that FAM83A contributes to tumor development and progression in NSCLC.

Prognostic: The abstract mentions that high expression levels of FAM83A in NSCLC are associated with poor prognosis, indicating that this variant correlates with disease outcome independent of therapy.

Diagnostic, Prognostic, Oncogenic evidence:

Prognostic: The study indicates that high miR-31 expression is significantly associated with poorer mortality and shorter median survival time in patients with advanced CRC, suggesting that it serves as a prognostic biomarker.

Diagnostic: The abstract mentions that the study evaluates the potential of miRNAs as prognostic biomarkers for patients with advanced CRC, and specifically highlights the association of miR-31 with the BRAF V600E mutation, indicating its role in classifying disease subtypes.

Oncogenic: The results section discusses the role of miR-31 in regulating BRAF protein expression and its association with the BRAF V600E mutation, suggesting that this variant contributes to tumor progression in CRC.

Diagnostic, Prognostic evidence:

Prognostic: The study indicates that the upregulation of MYBL2 expression is significantly associated with poor overall survival (OS) in patients with clear cell renal cell carcinoma (ccRCC), suggesting that it can independently predict prognosis. This is supported by the use of Cox regression analysis to assess the relationship between MYBL2 expression and patient outcomes.

Diagnostic: The abstract mentions that MYBL2 expression is significantly associated with various clinicopathological factors, which implies its potential use in classifying or defining disease characteristics in ccRCC. The analysis of MYBL2 expression in relation to tumor stage and histological grade further supports its role in disease classification.

Prognostic, Functional evidence:

Prognostic: The study indicates that elevated BCL11A levels are correlated with unfavorable overall survival (OS) in patients with triple-negative breast cancer (TNBC), suggesting that this variant may serve as a prognostic marker for disease outcome.

Functional: The results demonstrate that BCL11A-knockdown significantly inhibited proliferation, migration, and invasion in TNBC cell lines, indicating that the variant alters molecular functions related to tumor growth and metastasis.

Oncogenic, Functional evidence:

Oncogenic: The study demonstrates that SLC6A14 is essential for colon cancer, indicating that its up-regulation contributes to tumor development and progression. The evidence includes the reduction of tumor growth upon silencing SLC6A14 and the protective effect of its deletion in mouse models of colon cancer.

Functional: The research shows that blocking SLC6A14 with alpha-methyltryptophan induces amino acid deprivation, decreases mTOR activity, increases autophagy, promotes apoptosis, and suppresses cell proliferation and invasion. This indicates that the variant alters molecular functions related to cancer cell survival and growth.

Predictive, Oncogenic evidence:

Predictive: The study discusses how low CHD1 levels correlate with shorter clinical responses to enzalutamide, indicating that the F877L variant may influence treatment response, which is a key aspect of predictive evidence.

Oncogenic: The F877L variant is described as a positive control in an in vivo screen, where it is shown to contribute to tumor development in the context of enzalutamide treatment, demonstrating its role in tumor progression.

Predictive, Oncogenic evidence:

Predictive: The study identifies loss of AKT1 p.E17K as a mechanism of acquired resistance to AZD5363, suggesting that this variant may correlate with treatment response, thereby serving as a predictive biomarker for sensitivity to the therapy.

Oncogenic: The mention of loss of AKT1 p.E17K in the context of acquired resistance implies that this somatic variant may contribute to tumor progression or development, indicating its oncogenic potential.

Predictive, Prognostic, Oncogenic evidence:

Predictive: The study indicates that MALAT1 expression is high in sorafenib-resistant HCC cells and that knockdown of MALAT1 increases sorafenib sensitivity, suggesting a correlation between MALAT1 levels and response to sorafenib treatment.

Prognostic: The findings show that upregulated MALAT1 is closely correlated with poor survival outcomes in patients with HCC, indicating its potential role as a prognostic biomarker.

Oncogenic: The study describes MALAT1 as an oncogene that promotes cell proliferation, migration, and epithelial-mesenchymal transition in HCC cells, demonstrating its contribution to tumor development and progression.

Predictive evidence:

Predictive: The study discusses the use of the DNA-PK inhibitor M3814 (peposertib) in combination with ionizing radiation (IR) and DSB-inducing agents, indicating that the variant correlates with enhanced sensitivity to these therapies, which is a key aspect of predictive evidence. The results show that M3814 sensitizes multiple cancer cell lines to IR, supporting its potential as a therapeutic strategy.

Predictive evidence:

Predictive: The abstract indicates that high expression of NKCC1 regulates epithelial-mesenchymal transition (EMT) in gliomas, suggesting a potential therapeutic strategy that could influence treatment response by targeting this pathway.

Predictive, Diagnostic, Prognostic evidence:

Diagnostic: The study identifies associations between LOXL2 expression status and various molecular characterizations of cervical carcinoma, indicating its potential use in classifying or defining the disease.

Prognostic: High LOXL2 expression was associated with poor overall survival (OS) and poor disease-free survival (DFS) in cervical carcinoma, suggesting that it may serve as a prognostic marker for disease outcomes.

Predictive: The study suggests that LOXL2 may serve as a potential therapeutic target for cervical carcinoma, indicating a correlation with treatment response or sensitivity to therapies targeting this pathway.

Predictive, Diagnostic, Oncogenic evidence:

Oncogenic: The study demonstrates that GPX2 acts as an oncogene in lung adenocarcinoma (LUAD) and promotes cisplatin (DDP) resistance, indicating its role in tumor development and progression. This is supported by the finding that GPX2 was significantly upregulated in DDP-resistant cell lines and its expression correlated with adverse disease-free survival in LUAD cases.

Predictive: The evidence suggests that GPX2 is involved in mediating DDP resistance, as knockdown of GPX2 expression decreased the IC50 values of DDP, indicating a correlation with sensitivity to this specific therapy. The study highlights the role of GPX2 in influencing treatment response in the context of lung adenocarcinoma.

Diagnostic: The study reports that elevated GPX2 expression was found in 58.6% of LUAD cases, indicating its potential use as a biomarker for disease classification and association with adverse outcomes. This suggests that GPX2 could be utilized to define or confirm the presence of a specific disease subtype in lung adenocarcinoma.

Predictive, Oncogenic, Functional evidence:

Predictive: The study indicates that "chemical inhibition of CDK5 blocks the metastatic spread of patient-derived melanomas," suggesting that the variant's activity correlates with resistance to metastatic progression, which is relevant for therapeutic strategies.

Oncogenic: The findings demonstrate that CDK5 is essential for the metastatic spread of melanoma, indicating that it contributes to tumor progression, which aligns with the definition of an oncogenic variant.

Functional: The research shows that CDK5 alters the molecular function by "directly phosphorylating an intermediate filament protein, vimentin," which affects the assembly of vimentin filaments, highlighting its role in cellular invasiveness.

Predictive, Oncogenic evidence:

Predictive: The study discusses how the inhibition of Pin1 sensitizes BRCA1-proficient tumors to PARP inhibitors, indicating a correlation with treatment response. The mention of "sensitized breast tumors to olaparib" suggests that the variant's effect is related to the response to a specific therapy.

Oncogenic: The research highlights that loss of Pin1 or introduction of a BRCA1-mutant affects the ability of BRCA1 to localize to repair foci and augments DNA damage, indicating that these variants contribute to tumor development or progression. The context of BRCA1's role in homologous recombination and DNA repair supports the oncogenic classification.

Predictive, Oncogenic evidence:

Predictive: The study discusses how the EGFRL858R variant is associated with resistance to osimertinib and highlights the importance of understanding resistance mutations for determining subsequent treatment approaches, indicating a correlation with therapy response.

Oncogenic: The variant EGFRL858R is described as a driver mutation in the context of lung adenocarcinoma, suggesting its role in tumor development and progression, particularly in the transgenic mouse models used in the study.

Prognostic, Oncogenic evidence:

Prognostic: The abstract indicates that the downregulation of hsa-miR-143 positively correlates with adverse prognosis in renal cell carcinoma (RCC), suggesting that this variant may be associated with disease outcome independent of therapy.

Oncogenic: The study suggests that hsa-miR-143 acts as a potential tumor suppressor, and its involvement in inhibiting cell adhesion, migration, and epithelial-mesenchymal transition (EMT) implies a role in tumor development or progression, which aligns with oncogenic behavior.

Prognostic evidence:

Prognostic: The abstract states that CTGF is an "unfavorable and independent prognostic marker for glioma patients," indicating that the variant correlates with disease outcome, specifically in terms of prognosis for glioma.

Predictive, Diagnostic, Prognostic evidence:

Predictive: The study suggests that OTUD4 may serve as a predictive factor for several human cancers, indicating its potential role in response to treatment or therapy.

Prognostic: The results indicate that OTUD4 could be a useful biomarker for the prognosis of human cancers, correlating with disease outcomes such as survival or progression.

Diagnostic: The mention of OTUD4 as a potential molecular target for diagnosis implies its role in classifying or defining certain cancers, supporting its use as a diagnostic biomarker.

Predictive evidence:

Predictive: The abstract mentions that ponatinib demonstrates activity against T315I mutant clones, indicating that this variant correlates with response to the therapy, specifically the third-generation TKI ponatinib. This suggests that the presence of the T315I variant is predictive of treatment efficacy with ponatinib in patients with CML and Ph+ ALL.

Diagnostic, Prognostic evidence:

Prognostic: The abstract states that hsa-mir-124 expressions were associated with overall survival in BRCA patients, indicating a correlation with disease outcome independent of therapy.

Diagnostic: The abstract mentions that hsa-mir-124 expressions are associated with tumor molecular phenotype and pathologic characteristics in BRCA, suggesting its potential use as a biomarker for classification or diagnosis of the disease.

Predictive, Oncogenic evidence:

Predictive: The abstract mentions that lifirafenib is an inhibitor with antitumor activity in patients with B-RAFV600-mutated solid tumors, indicating a correlation between the B-RAFV600E variant and response to this specific therapy.

Oncogenic: The results section discusses the role of B-RAF mutations in tumorigenesis, specifically noting that B-RAF mutations occur in a significant percentage of various cancers, which supports the notion that the B-RAFV600E variant contributes to tumor development or progression.

Predictive evidence:

Predictive: The study indicates that low mRNA expression of glycerol-3-phosphate dehydrogenase 1 (GPD1) may predict a poor response to metformin treatment, suggesting a correlation between GPD1 expression levels and therapeutic response to metformin in cancer cell lines. This aligns with the predictive evidence type as it discusses the relationship between a variant and treatment response.

Predictive evidence:

Predictive: The abstract discusses that the HER2 L755S mutation in a patient with metastatic breast cancer led to a partial response to the HER2/EGFR tyrosine kinase inhibitor neratinib, indicating that this variant correlates with sensitivity to a specific therapy. The mention of treatment response and improvement in the patient's condition supports the classification as predictive evidence.

Prognostic, Oncogenic evidence:

Prognostic: The study indicates that high expression levels of WDR12 are dramatically related to shorter overall survival and reduced disease-free survival in glioblastoma, suggesting that it correlates with disease outcome independent of therapy.

Oncogenic: The report suggests that WDR12 drives malignant behavior in glioblastoma, indicating its contribution to tumor development or progression, particularly through the findings from cell biology experiments that demonstrate its role in promoting apoptosis and inhibiting proliferation.

Diagnostic, Prognostic evidence:

Prognostic: The survival analysis revealed that the higher expressions of WNT5A and WNT16 were associated with poor overall survival (OS) in patients with glioma, indicating a correlation between these variants and disease outcome.

Diagnostic: The conclusion states that WNT5A can serve as a candidate to diagnose glioma, suggesting its role in defining or classifying the disease.

Oncogenic evidence:

Oncogenic: The study demonstrates that TFB2M significantly promotes HCC cell proliferation, migration, and invasion, indicating its role in tumor development and progression. Additionally, the findings suggest that TFB2M contributes to xenograft tumorigenesis and lung metastasis, further supporting its oncogenic function in hepatocellular carcinoma.

Prognostic evidence:

Prognostic: The abstract indicates that high WTAP expression is associated with poor prognosis, suggesting that this variant correlates with disease outcome independent of therapy.

Prognostic evidence:

Prognostic: The abstract states that CARD9 is an "independent prognostic factor in NSCLC patients," indicating that the variant correlates with disease outcome independent of therapy. This suggests that the presence of CARD9 has implications for the prognosis of patients with non-small cell lung cancer (NSCLC).

Prognostic, Functional evidence:

Prognostic: The study indicates that high expression of PIK3CD-AS2 is associated with shorter patient survival and poor disease-free survival in p53 wild-type patients, suggesting a correlation with disease outcome independent of therapy.

Functional: The research demonstrates that PIK3CD-AS2 alters the stability of YBX1 by impeding its ubiquitination and degradation, indicating a change in molecular function that affects p53 signaling.

Prognostic, Functional evidence:

Prognostic: The study indicates that patients with higher MAGI-2 expression had longer biochemical recurrence-free survival, suggesting that MAGI-2 serves as a predictor of tumor recurrence in Han Chinese patients with prostate cancer.

Functional: The presence of tryptophan-tryptophan (WW) domains in MAGI-2 is mentioned, which are involved in various protein interactions, indicating that these domains alter the molecular function of MAGI-2 in supporting cell junctions and maintaining cell integrity.

Predictive, Oncogenic evidence:

Predictive: The study discusses the therapeutic potential of combined AXL and HDAC inhibition in H3K27M DIPG cells, indicating that this treatment can reverse the therapy-resistant phenotype and has a synergistic antitumor effect, which correlates with sensitivity to the therapy.

Oncogenic: The abstract mentions that mutations in genes encoding histone 3 (H3K27M) drive the development of DIPG, suggesting that this somatic variant contributes to tumor progression in this specific type of brain cancer.

Predictive evidence:

Predictive: The study discusses the potential of EB1 expression as a response-predictive biomarker of BAL101553 in GBM, indicating that the variant's expression level correlates with treatment response. This suggests that the variant may influence the effectiveness of the therapy being tested.

Predictive, Diagnostic evidence:

Predictive: The study discusses how low levels of POLA1, POLE, and POLE2 protein expression in NSCLC and colorectal cancer cells correlate with sensitivity to CHK1 inhibitors, indicating that these variants may serve as biomarkers for predicting response to therapy.

Diagnostic: The identification of POLA1, POLE, and POLE2 as potential biomarkers for CHK1 inhibitor sensitivity suggests that these variants can be used to classify or define a specific phenotype in cancer patients, particularly in relation to their response to treatment.

Oncogenic, Functional evidence:

Oncogenic: The study demonstrates that IL-33 significantly increases glioma cell invasion and migration, indicating its role in tumor progression. This suggests that IL-33 contributes to the development or progression of glioma, aligning with the definition of an oncogenic variant.

Functional: The findings show that IL-33 alters molecular functions by upregulating matrix metalloproteinases (MMP2 and MMP9) and increasing the phosphorylation of NF-kappaB, which are indicative of changes in biochemical activity related to glioma cell behavior. This supports the classification of IL-33 as having functional evidence.

Prognostic evidence:

Prognostic: The study indicates that elevated IL-33 mRNA levels are associated with inferior survival in glioblastoma patients, suggesting that IL-33 may correlate with disease outcome independent of therapy. This aligns with the definition of prognostic evidence, as it discusses survival outcomes related to the variant.

Diagnostic, Prognostic evidence:

Diagnostic: The study indicates that IL-33 has diagnostic value in gliomas, as it is associated with the clinicopathological features of the disease and can be used as a biomarker for detection.

Prognostic: The results show that high IL-33 expression correlates with shorter progression-free survival and overall survival in glioma patients, indicating its role as an independent factor of poor prognosis.

Predictive, Oncogenic evidence:

Oncogenic: The study discusses the role of beta-catenin signaling in gastric cancer, indicating that dysregulation of this pathway contributes to tumor development and progression, particularly through its interaction with CCL28 and Treg cells.

Predictive: The findings suggest that inhibition of beta-catenin/TCF activity leads to reduced CCL28 expression and Treg cell infiltration, which correlates with tumor progression, indicating that targeting this pathway may influence treatment response in gastric cancer.

Predictive, Diagnostic evidence:

Predictive: The study discusses the correlation between BRD levels, particularly BRD4, and sensitivity to BET degraders like ZBC260, indicating that these levels can predict the response to therapy. The mention of "correlated positively with high sensitivity to BET degraders" supports the classification as predictive evidence regarding treatment response.

Diagnostic: The study identifies molecular markers, specifically BRD levels, that determine cell sensitivity to BET degraders, suggesting that these markers can be used to classify or define a subtype of lung cancer that may respond to specific therapies. This aligns with the diagnostic evidence type as it relates to the identification of disease characteristics.

Predictive, Oncogenic evidence:

Predictive: The abstract discusses how comprehensive genomic profiling can identify genomic alterations that direct treatment targeted therapy, indicating a correlation between the BRAF V600E variant and response to specific therapies. Additionally, the results mention that treatment with dabrafenib in BRAF V600E mutated melanoma can significantly improve overall survival, highlighting the predictive nature of this variant in treatment response.

Oncogenic: The mention of BRAF V600E in the context of metastatic melanoma suggests that this somatic variant contributes to tumor development or progression, as it is associated with a specific cancer type and treatment response. The reference to trials for BRAF V600E further supports its role in oncogenesis.

Diagnostic, Prognostic evidence:

Diagnostic: The study indicates that the expression profile of miRNAs can differentiate between astrocytoma tumors and normal brain tissues, suggesting their potential use as diagnostic markers in defining the signature of astrocytomas.

Prognostic: The results show that low expression of specific miRNAs (hsa-miR-181b and hsa-miR-106a) and high expression of another (hsa-miR-21) are significantly associated with poor patient survival, indicating that these miRNAs can serve as prognostic markers independent of other clinicopathological factors.

Predictive, Oncogenic, Functional evidence:

Oncogenic: The abstract states that Acvr1G328V cooperates with other mutations to induce diffuse gliomas in mice, indicating that this variant contributes to tumor development. This aligns with the definition of an oncogenic variant, as it demonstrates a role in the progression of cancer.

Functional: The abstract mentions that Acvr1G328V upregulates transcription factors to block oligodendroglial cell differentiation, suggesting that this variant alters molecular function. This indicates a change in biochemical activity related to cell differentiation processes.

Predictive: The abstract notes that E6201, a covalent MEK1/2 inhibitor, can inhibit ACVR1 and reduce the growth of ACVR1 mutant glioma xenografts, implying that the presence of the G328V variant may correlate with response to this specific therapy. This suggests a predictive relationship between the variant and treatment response.

Predictive, Diagnostic evidence:

Predictive: The study evaluates the response of mismatch repair-deficient (dMMR) rectal cancer to neoadjuvant chemotherapy, indicating that the variant correlates with resistance to this specific therapy, as evidenced by the progression of disease in 29% of patients receiving chemotherapy.

Diagnostic: The identification of dMMR rectal tumors through IHC and microsatellite instability analysis suggests that the variant is used to classify and confirm the presence of a specific subtype of rectal cancer, particularly in relation to Lynch syndrome.

Predictive, Diagnostic evidence:

Predictive: The study discusses how ATM loss in prostate cancer models does not significantly increase sensitivity to PARP inhibitors but does sensitize tumors to ATR inhibitors, indicating a correlation between the variant and response to specific therapies. This suggests that patients with ATM alterations may benefit more from ATR inhibitor therapy than from PARP inhibitors.

Diagnostic: The abstract mentions that ATM alterations are present in approximately 5% of advanced prostate tumors, indicating its association with a specific subtype of cancer, which supports its use as a biomarker for identifying patients with these alterations.

Diagnostic, Prognostic evidence:

Diagnostic: The abstract states that "SPATS2 expression could be a novel diagnostic biomarker in liver cancer," indicating that the variant is used to classify or define a disease.

Prognostic: The abstract also mentions that SPATS2 expression could serve as a prognostic biomarker, suggesting a correlation with disease outcome independent of therapy.

Prognostic evidence:

Prognostic: The abstract indicates that TUBA1C may serve as a potential prognostic marker for PDAC therapy, suggesting a correlation with disease outcome independent of therapy.

Predisposing, Functional evidence:

Predisposing: The study discusses "germline CHEK2 missense alleles detected in familial breast cancer patients," indicating that these variants are inherited and confer a predisposition to cancer.

Functional: The development of a yeast-based assay to assess "in vivo CHEK2-mediated response to DNA damage" demonstrates that the study evaluates how these variants alter the molecular function of the CHEK2 protein in response to DNA damage.

Predisposing, Functional evidence:

Predisposing: The study discusses germline mutations in CHEK2 as a multiple cancer-predisposing gene that increases breast cancer risk, indicating that these variants confer inherited risk for developing the disease.

Functional: The research developed a complementation assay to quantify CHK2-specific phosphorylation of endogenous protein KAP1, demonstrating that certain variants alter molecular function, specifically in relation to their deleterious effects on protein activity.

Predictive evidence:

Predictive: The study discusses how increased iNOS/NO signaling in tumor cells, influenced by CAFs after radiotherapy, affects the effectiveness of radiotherapy in treating PDAC tumors. This indicates a correlation between the variant's activity and the response to therapy, suggesting that targeting iNOS/NO signaling may improve treatment outcomes.

Predictive, Diagnostic evidence:

Predictive: The study discusses how patients with acquired MET alterations may derive clinical benefit from therapies that target both ALK and MET, indicating a correlation between the presence of these alterations and response to treatment. This suggests that MET amplification is associated with resistance to ALK inhibitors and that targeting MET can improve treatment outcomes.

Diagnostic: The abstract mentions that MET amplification was detected in 15% of tumor biopsies from patients relapsing on next-generation ALK inhibitors, which indicates that MET alterations can be used to classify or confirm a specific subtype of resistance in ALK-positive lung cancer. This association highlights the role of MET amplification as a biomarker for identifying patients who may experience ALK-independent resistance.

Prognostic evidence:

Prognostic: The study indicates that alterations to the p53 tumor suppressor gene are associated with more aggressive disease in breast cancer, evidenced by shortened survival of patients with mutations. Specifically, mutations within exon 4 and those causing denaturation of the protein structure were linked to poor prognosis, highlighting their impact on overall patient survival.

Prognostic, Functional evidence:

Prognostic: The abstract states that mutations at the Arg248 position are significantly associated with shorter patient survival, indicating a correlation between this variant and disease outcome.

Functional: The abstract mentions that ectopic expression of the p53 mutant R282W significantly upregulated CYP3A4 mRNA and protein levels, demonstrating that this variant alters molecular function related to drug metabolism.

Predictive, Prognostic evidence:

Prognostic: The study reports that TP53 mutations are associated with shorter survival and a shorter time to relapse, indicating that these mutations correlate with disease outcomes independent of therapy. This is supported by the statistical significance (P<0.001) mentioned in the results.

Predictive: The abstract discusses how the presence of RAS pathway mutations and JAK2 mutations correlates with shorter survival and higher risks of relapse and death without relapse, suggesting that these mutations may predict clinical outcomes after allogeneic hematopoietic stem-cell transplantation. The specific mention of these associations with transplantation outcomes supports this classification.

Diagnostic, Prognostic evidence:

Diagnostic: The study assesses the frequency of TP53 alterations in acute myeloid leukemia with complex karyotype (CK-AML) and correlates these alterations with other genetic changes, indicating that TP53 mutations are used to classify and define the disease.

Prognostic: The results indicate that patients with TP53 alterations had significantly lower complete remission rates and inferior overall survival, demonstrating that these alterations correlate with disease outcome independent of therapy.

Prognostic evidence:

Prognostic: The study discusses the SNP rs2305089 in relation to local recurrence and overall survival in spinal column chordoma, indicating that this variant correlates with disease outcomes independent of therapy.

Prognostic evidence:

Prognostic: The study discusses the SNP rs2305089 in relation to local recurrence and overall survival in spinal column chordoma, indicating that this variant correlates with disease outcomes independent of therapy.

Predictive, Prognostic evidence:

Prognostic: The study reports that TP53 mutation is strongly associated with a poor prognosis for overall survival in patients with glioblastoma, indicating that the presence of this variant correlates with disease outcome independent of therapy.

Predictive: The findings suggest that mutant TP53 decreases the chemosensitivity of glioblastoma to temozolomide, indicating a correlation between the variant and resistance to this specific therapy.

Prognostic, Oncogenic evidence:

Oncogenic: The study indicates that mutations in the ARID2 gene are commonly found in hepatocellular carcinoma (HCC) and that ARID2 plays a significant role in cancer development, particularly in relation to metastasis. The evidence of ARID2 knockout promoting pulmonary metastasis in HCC mouse models supports the notion that ARID2 mutations contribute to tumor progression.

Prognostic: The abstract mentions a positive association between ARID2 expression and survival of HCC patients, indicating that lower levels of ARID2 correlate with poorer outcomes. This suggests that ARID2 may serve as a prognostic marker for HCC, as its expression levels are linked to disease progression and patient survival.

Prognostic evidence:

Prognostic: The abstract states that YAP1 is an important prognostic biomarker for pancreatic cancer, indicating a correlation with disease outcome independent of therapy. This suggests that the presence of the variant may be associated with survival or progression in patients with pancreatic cancer.

Predictive, Diagnostic, Prognostic evidence:

Predictive: The study indicates that high APOBEC3B expression is associated with improved progression-free survival and sensitivity to cisplatin and carboplatin, suggesting that it may serve as a predictive biomarker for therapeutic response to platinum-based chemotherapy.

Prognostic: The results show that high APOBEC3B expression correlates with improved progression-free survival and moderately with overall survival, indicating its potential role as a prognostic factor independent of therapy.

Diagnostic: The study identifies APOBEC3B as a candidate biomarker for detection and intervention in clear cell ovarian carcinoma, suggesting its use in classifying or confirming the disease.

Predictive, Prognostic evidence:

Prognostic: The abstract states that "IL-6 was significantly associated with poor prognosis in patients with esophageal cancer," indicating that the variant correlates with disease outcome independent of therapy.

Predictive: The mention of "treatment resistance" in the context of targeting IL-6 suggests that this variant may correlate with resistance to specific therapies, indicating its predictive value for treatment response.

Predictive, Prognostic evidence:

Predictive: The study found that preoperative plasma levels of IL-6 and IL-6sR were independent predictors of lymphovascular invasion, metastases to lymph nodes, disease recurrence, and disease-specific survival, indicating their potential role in predicting treatment outcomes.

Prognostic: The results indicated that high levels of IL-6 and IL-6sR predicted disease-specific survival, demonstrating their correlation with disease outcomes independent of therapy.

Prognostic evidence:

Prognostic: The study identifies high levels of serum IL-6 as an independent adverse prognostic variable for overall survival in patients with hormone-refractory metastatic breast cancer, indicating a correlation between IL-6 levels and poor survival outcomes.

Prognostic, Oncogenic evidence:

Prognostic: The study indicates that low BAP1 mRNA levels are associated with overall survival (OS) in cutaneous melanoma (CM) patients, with specific hazard ratios provided (HR = 0.73), suggesting a correlation between the variant and disease outcome independent of therapy.

Oncogenic: The presence of BAP1 point mutations, including E30K and P30, is discussed in the context of their unknown significance in tumors, indicating that these somatic variants may contribute to tumor development or progression, although they were not associated with overall survival in CM.

Predictive, Prognostic evidence:

Prognostic: The abstract states that "all three genes were associated with a poor prognosis in human patients," indicating that the variants correlate with disease outcome independent of therapy. This suggests that the presence of these proteins is linked to survival rates in patients with pancreatic ductal adenocarcinoma (PDAC).

Predictive: The abstract mentions that "precise interventions targeting cancer cell-derived matrisome proteins, such as AGRN, SERPINB5, and CSTB, may represent preferred potential therapeutic targets," which implies that these variants could influence treatment response or resistance, thus providing predictive evidence regarding their role in therapy.

nan evidence:

Missing abstract

Prognostic evidence:

Prognostic: The study reports that glioma patients with higher expression of KIF3C had longer survival time, indicating a correlation between KIF3C expression and disease outcome independent of therapy. This is further supported by subgroup analysis showing that higher KIF3C expression predicted longer survival time in the low-grade glioma group.

Predictive, Oncogenic evidence:

Predictive: The study discusses how ATRX mutations lead to increased sensitivity to the WEE1 inhibitor AZD1775, indicating a correlation between the ATRX variant and response to this specific therapy. This suggests that targeting WEE1 could be a therapeutic strategy for ATRX-deficient cancers, highlighting the predictive nature of the variant in relation to treatment response.

Oncogenic: The abstract mentions that ATRX is frequently mutated in tumors, including gliomas and liver cancers, and that these mutations contribute to tumor growth and survival, which aligns with the definition of oncogenic variants that drive tumor development or progression. The identification of ATRX mutations as a target for therapeutic intervention further supports its role in oncogenesis.

Predictive, Prognostic, Oncogenic evidence:

Prognostic: The abstract states that "Low levels of ARID1A were associated with a poor prognosis," indicating that the variant correlates with disease outcome independent of therapy.

Oncogenic: The abstract mentions that "Depletion of ARID1A activated an oncogenic transcriptome that drove SCC progression," suggesting that the variant contributes to tumor development or progression.

Predictive: The abstract discusses the potential of parthenolide as a treatment for patients with low ARID1A expression, indicating that the variant's status may correlate with response to this specific therapy.

Predictive, Oncogenic evidence:

Predictive: The study discusses the use of KRASG12C inhibitors and their effects on signaling and viability, indicating a correlation with treatment response and resistance mechanisms. The mention of "adaptive feedback" and "enhance efficacy" suggests that the variant's presence influences the effectiveness of specific therapies targeting KRASG12C.

Oncogenic: The abstract describes KRAS as the most commonly mutated oncogene and discusses the KRASG12C mutation in the context of tumor development and progression, indicating that this somatic variant contributes to cancer biology. The focus on the KRASG12C mutation and its role in signaling pathways further supports its classification as oncogenic.

Oncogenic, Functional evidence:

Oncogenic: The study describes a partial duplication of the switch 2 domain of K-Ras in a patient with juvenile myelomonocytic leukaemia, indicating that this somatic variant contributes to tumor development or progression, as it is associated with a myeloproliferative neoplasm characterized by driver Ras pathway mutations.

Functional: The variant is shown to result in a protein with altered electrophoretic mobility, suggesting that the duplication affects the molecular function of K-Ras, specifically its conformation and possibly its interaction with other proteins, as indicated by the immunoblot analysis.

Predictive, Prognostic, Oncogenic evidence:

Prognostic: The study indicates that KRAS mutation is significantly associated with worse overall survival (OS) and disease-free survival (DFS) in early stage resected NSCLC, suggesting that the presence of this mutation correlates with poorer disease outcomes.

Predictive: The findings also show that KRAS mutation is associated with inferior outcomes of epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) treatment and chemotherapy, indicating that this variant may predict resistance to these therapies.

Oncogenic: The paper discusses KRAS as the most frequently mutated oncogene in NSCLC, which implies that mutations in this gene contribute to tumor development and progression, supporting its classification as an oncogenic variant.

Oncogenic, Functional evidence:

Oncogenic: The study investigates the effect of the C118S mutation on tumorigenesis, demonstrating that KrasC118S alleles impede urethane-induced lung tumorigenesis, indicating that this somatic variant contributes to tumor development.

Functional: The abstract discusses how the thiol residue of cysteine 118 (C118) is crucial for the activation of Ras proteins through redox-dependent reactions, suggesting that the C118S mutation alters the molecular function of Ras, impacting its activation and subsequent signaling pathways.

Predictive, Oncogenic evidence:

Predictive: The study discusses how the BRAF V600E mutation correlates with treatment response, specifically noting that combination therapy with BRAF and multitargeting TK inhibitors may be more effective than single-agent therapies, indicating a predictive relationship between the variant and therapy response.

Oncogenic: The BRAF V600E mutation is implicated in tumor development and progression, as evidenced by the significant inhibition of proliferation, colony formation, invasion, and migration in BRAF V600E thyroid cancer cell lines, demonstrating its role as a somatic variant contributing to cancer behavior.

Predictive, Diagnostic evidence:

Predictive: The study demonstrates that the addition of panitumumab to chemotherapy significantly improves progression-free survival (PFS) in patients with wild-type (WT) KRAS tumors, indicating that KRAS status is predictive of treatment response to panitumumab. The results show a clear correlation between the presence of WT KRAS and improved outcomes with the therapy, highlighting the variant's role in determining sensitivity to treatment.

Diagnostic: The study uses KRAS status to classify patients into wild-type and mutant categories, which is essential for determining eligibility for panitumumab treatment. This classification is indicative of the variant's role in defining a specific disease subtype (mCRC with WT KRAS), thus supporting its use as a diagnostic marker.

Predictive, Prognostic evidence:

Prognostic: The abstract states that the KRAS mutation had an adverse impact on the prognosis for stage IV CRC patients, indicating that the presence of this mutation correlates with disease outcome independent of therapy.

Predictive: The results section discusses the mutation status of the KRAS gene as a predictive marker for the response to anti-EGFR antibody therapies in patients with metastatic colorectal cancer, suggesting that specific mutations, including G13D, are associated with sensitivity or resistance to treatment.

Functional evidence:

Functional: The study provides evidence that specific mutations in the rasH gene alter molecular function, particularly in terms of GTPase activity and guanine nucleotide exchange rates. For instance, the mutation Val-146 resulted in a significant increase in nucleotide exchange, which is directly linked to its transforming potential, demonstrating a clear alteration in biochemical function.

Oncogenic, Functional evidence:

Oncogenic: The study discusses the role of activated Kras2 mutations in the development of lung tumors, indicating that these mutations contribute to tumor progression, particularly in the context of loss of the wildtype Kras2 allele. The evidence of activating Kras2 mutations in all chemically induced lung tumors supports the classification of this variant as oncogenic.

Functional: The abstract mentions that wildtype Kras2 inhibits colony formation and tumor development in transformed cells, suggesting that it alters molecular function related to tumor suppression. This indicates that the variant has a functional role in regulating cellular processes associated with tumorigenesis.

nan evidence:

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Predictive, Diagnostic, Oncogenic evidence:

Diagnostic: The study examines the association of KIT and PDGFRA mutations with clinicopathological factors in gastrointestinal stromal tumors (GIST), indicating that these mutations can be used to classify or define the disease and its subtypes.

Predictive: The conclusion states that the determination of KIT and PDGFRA mutations should be additional parameters for better prediction of GISTs clinical behavior, suggesting a correlation with treatment response or disease progression.

Oncogenic: The presence of specific mutations in the KIT gene, particularly the deletion/insertion mutations affecting codons 557/558, is associated with potentially malignant clinical behavior, indicating that these somatic variants contribute to tumor development or progression.

Predictive evidence:

Predictive: The study assesses the dose dependency of response and progression-free survival with imatinib for metastatic GIST, indicating that the variant correlates with treatment response and sensitivity to the therapy. The findings show a significant difference in progression-free survival between the two dosing regimens, which supports the predictive nature of the variant in relation to therapy outcomes.

Predictive, Oncogenic evidence:

Predictive: The study identifies high levels of Trop2 as predictive of recurrence in localized prostate cancer and suggests that these levels could indicate sensitivity to Trop2-targeting therapies and PARP1 inhibition, highlighting the variant's role in treatment response.

Oncogenic: The findings indicate that Trop2 drives prostate cancer growth and induces a neuroendocrine phenotype, demonstrating its contribution to tumor development and progression, which is characteristic of oncogenic behavior.

Predictive, Diagnostic evidence:

Predictive: The study discusses the activity of afatinib in patients with tumors harboring uncommon EGFR mutations, including T790M, and evaluates key endpoints such as overall response rate and time to treatment failure, indicating a correlation with treatment response.

Diagnostic: The variant T790M is categorized among uncommon EGFR mutations, suggesting its role in defining the subtype of NSCLC and its association with specific treatment responses.

Predictive evidence:

Predictive: The study discusses that patients with BRAF V600 mutation-positive pLGG may benefit from treatment with dabrafenib, indicating a correlation between the BRAF V600 mutation and response to this specific therapy. The mention of objective response rates (ORRs) further supports the predictive nature of the variant in relation to treatment outcomes.

Diagnostic, Prognostic evidence:

Prognostic: The study indicates that ATRX alterations are associated with a significantly improved overall survival (OS) rate in glioma patients, suggesting that these mutations correlate with disease outcome independent of therapy.

Diagnostic: The authors mention that ATRX mutations have clinical implications for the molecular diagnosis of gliomas, indicating that these mutations can provide diagnostic information for classifying or confirming the disease.

Diagnostic, Prognostic evidence:

Prognostic: The study indicates that patients who are PAX3/FOXO1 positive have a significantly poorer outcome compared to other groups, suggesting that this variant correlates with disease outcome independent of therapy. The mention of "significantly poorer outcome" directly supports its classification as prognostic evidence.

Diagnostic: The abstract discusses the incorporation of the PAX3/FOXO1 fusion gene status into a risk-stratification scheme, which implies that this variant is used to classify or define a subtype of rhabdomyosarcoma. The use of the term "fusion gene status" indicates its role in diagnosis and classification of the disease.

Predictive evidence:

Predictive: The study identifies EGFR amplification as a potential biomarker to predict sensitivity to PARP inhibition, indicating that this variant correlates with the response to talazoparib treatment in glioblastoma patients. The results demonstrate that EGFR-amplified glioma sphere-forming cells showed remarkable sensitivity to talazoparib, supporting the predictive nature of this variant in therapy selection.

Predisposing evidence:

Predisposing: The study discusses familial cases of rhabdoid tumors linked to heterozygous SMARCB1 germline mutations, indicating that these mutations confer inherited risk for developing the disease. Additionally, the identification of a germline mutation in SMARCA4 in two sisters with rhabdoid tumors further supports the notion of inherited predisposition to this cancer type.

Diagnostic, Prognostic, Oncogenic evidence:

Diagnostic: The study discusses BCOR-CCNB3 sarcoma (BCS) as a recently defined genetic entity among undifferentiated round cell sarcomas, indicating that it is classified based on its genetic alterations, such as BCOR internal tandem duplication (ITD) and BCOR-MAML3. This classification suggests that the presence of these variants is used to define and confirm the disease subtype.

Prognostic: The follow-up data indicates a 5-year overall survival rate of 72% for patients with BCS, which is reported independently of any specific therapy context. This suggests that the variant correlates with disease outcome, making it prognostic in nature.

Oncogenic: The abstract mentions that BCS shows consistent BCOR overexpression and that the morphologic features and immunoprofile overlap with other tumors exhibiting BCOR oncogenic upregulation. This indicates that the BCOR genetic alterations contribute to tumor development or progression, classifying it as oncogenic.

Diagnostic, Oncogenic evidence:

Diagnostic: The study identifies a new fusion between BCOR and CCNB3 as a powerful diagnostic marker for a specific subgroup of sarcoma, indicating its role in classifying and defining this disease subtype.

Oncogenic: The presence of the BCOR-CCNB3 fusion is described as contributing to tumor development, as it activates S phase in NIH3T3 cells, demonstrating its role in oncogenesis.

Diagnostic, Oncogenic evidence:

Diagnostic: The study discusses the BCOR-CCNB3 fusion gene as a marker for genetic subclassification of undifferentiated unclassified sarcomas, indicating its potential use in reproducible diagnosis. The identification of this fusion in multiple cases supports its role in defining a specific subtype of sarcoma.

Oncogenic: The presence of the BCOR-CCNB3 fusion gene in undifferentiated spindle cell sarcomas suggests that it contributes to tumor development, as indicated by its identification in multiple tumor samples and the context of its association with a specific cancer type.

Oncogenic evidence:

Oncogenic: The study discusses the EWS-WT1 chimaeric protein resulting from the t(11;22)(p13;q12) translocation, indicating that this fusion contributes to tumor development by inducing the expression of PDGFA, which is associated with the reactive fibrosis characteristic of desmoplastic small round-cell tumor (DSRT). This suggests that the EWS-WT1 fusion plays a role in the oncogenic process of this specific malignancy.

Oncogenic evidence:

Oncogenic: The study discusses the EWS-WT1 chimeric protein resulting from the t(11;22)(p13;q12) translocation, indicating that this somatic variant contributes to the malignant phenotype of desmoplastic small round cell tumor (DSRCT) and is involved in tumor development and progression. The mention of the dysregulated expression of EWS-WT1 targets further supports its role in oncogenesis.

Diagnostic, Oncogenic evidence:

Diagnostic: The abstract states that "immunohistochemical testing for the SMARCB1/INI1 antibody has been considered useful in confirming the histologic diagnosis of malignant rhabdoid tumors," indicating that the variant is used to define or confirm a specific disease subtype.

Oncogenic: The abstract describes SMARCB1/INI1 as a "potent and bona fide tumor suppressor" and discusses its interactions with pathways related to tumor proliferation and progression, suggesting that alterations in this gene contribute to tumor development or progression.