[Paper-level Aggregated] PMCID: PMC3366948

Evidence Type(s): Oncogenic, Functional, Predisposing, Diagnostic, Prognostic

Justification: Oncogenic: The text states that JAK2 and JAK3 are known oncogenes in leukemia, and specific mutations such as M511I and A572V have been shown to induce leukemia in mice, indicating their oncogenic potential. Functional: The M511I mutation was shown to transform IL3 dependent 32D cells and induce T-ALL in mice, demonstrating a functional impact on cellular behavior. Predisposing: The presence of mutations in JAK2 and JAK3 in T-ALL patients suggests a predisposition to developing this type of leukemia, as these mutations were identified in patient samples. Diagnostic: The identification of specific mutations in JAK2 and JAK3 in T-ALL patients can serve as diagnostic markers for the disease, as indicated by their presence in patient samples. Prognostic: The somatic status of the H1297Y variant in TET1, confirmed in a remission sample, suggests that it may have implications for prognosis in T-ALL patients.

Gene→Variant (gene-first): MST1R(4486):A35V PMS2(5395):C192Y TYK2(7297):R1027H JAK3(3718):A572 JAK3(3718):A572T JAK3(3718):A572V JAK3(3718):M511I TET1(80312):H1297Y

Genes: MST1R(4486) PMS2(5395) TYK2(7297) JAK3(3718) TET1(80312)

Variants: A35V C192Y R1027H A572 A572T A572V M511I H1297Y

[Paragraph-level] PMCID: PMC3366948 Section: RESULTS PassageIndex: 22

Evidence Type(s): Oncogenic, Functional

Justification: Oncogenic: The passage discusses the presence of TYK2 mutations in T-ALL cell lines and suggests that these mutations may not represent an oncogenic event important for leukemia development in vivo, indicating a potential role in tumor progression. Functional: The analysis of the transforming properties of the TYK2 variants in Ba/F3 cells indicates that the variants do not show major differences in function compared to wild type TYK2, suggesting an assessment of molecular function.

Gene→Variant (gene-first): 4486:A35V 5395:C192Y 7297:R1027H

Genes: 4486 5395 7297

Variants: A35V C192Y R1027H

[Paragraph-level] PMCID: PMC3366948 Section: RESULTS PassageIndex: 18

Evidence Type(s): Oncogenic

Justification: Oncogenic: The variant H1297Y is described as a somatic variant confirmed in a patient case, indicating its contribution to tumor development or progression in the context of T-ALL.

Gene→Variant (gene-first): 80312:H1297Y

Genes: 80312

Variants: H1297Y

[Paragraph-level] PMCID: PMC3366948 Section: RESULTS PassageIndex: 15

Evidence Type(s): Oncogenic, Functional

Justification: Oncogenic: The passage describes that the M511I mutation transformed IL3 dependent 32D cells and induced T-ALL in mice, indicating its role in tumor development. Additionally, the A572V mutation was shown to transform cytokine dependent hematopoietic cells and induce leukemia in mice, further supporting its oncogenic potential. Functional: The passage discusses how specific mutations in JAK3, such as A572T and A572V, alter the function of the protein, as evidenced by their ability to transform cells and induce leukemia, indicating a change in molecular or biochemical function.

Gene→Variant (gene-first): 3718:A572 3718:A572T 3718:A572V 3718:M511I

Genes: 3718

Variants: A572 A572T A572V M511I

[Paragraph-level] PMCID: PMC3366948 Section: RESULTS PassageIndex: 22

Evidence Type(s): Oncogenic, Functional

Justification: Oncogenic: The passage discusses the presence of TYK2 mutations in T-ALL cell lines and suggests that these mutations may not represent an oncogenic event important for leukemia development in vivo, indicating a potential role in tumor progression. Functional: The analysis of the transforming properties of the TYK2 variants in Ba/F3 cells indicates that the variants do not show major differences in function compared to wild type TYK2, suggesting an assessment of molecular function.

Gene→Variant (gene-first): 4486:A35V 5395:C192Y 7297:R1027H

Genes: 4486 5395 7297

Variants: A35V C192Y R1027H

[Paragraph-level] PMCID: PMC3366948 Section: RESULTS PassageIndex: 18

Evidence Type(s): Oncogenic

Justification: Oncogenic: The variant H1297Y is described as a somatic variant confirmed in a patient case, indicating its contribution to tumor development or progression in the context of T-ALL.

Gene→Variant (gene-first): 80312:H1297Y

Genes: 80312

Variants: H1297Y

[Paragraph-level] PMCID: PMC3366948 Section: RESULTS PassageIndex: 15

Evidence Type(s): Oncogenic, Functional

Justification: Oncogenic: The passage describes that the M511I mutation transformed IL3 dependent 32D cells and induced T-ALL in mice, indicating its role in tumor development. Additionally, the A572V mutation was shown to transform cytokine dependent hematopoietic cells and induce leukemia in mice, further supporting its oncogenic potential. Functional: The passage discusses how specific mutations in JAK3, such as A572T and A572V, alter the function of the protein, as evidenced by their ability to transform cells and induce leukemia, indicating a change in molecular or biochemical function.

Gene→Variant (gene-first): 3718:A572 3718:A572T 3718:A572V 3718:M511I

Genes: 3718

Variants: A572 A572T A572V M511I