Breast Cancer: Recurrent Genomic Alterations - Revision history

Kgeiersbach at 17:22, 10 December 2025

2025-12-10T17:22:21Z

← Older revision		Revision as of 12:22, 10 December 2025
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	\|sequence variants		\|sequence variants
	\|Diseases: recurrent in phyllodes tumor		\|Diseases: recurrent in phyllodes tumor
	\|26437033; 33844099; 33782741; 35691725		\|[https://pubmed.ncbi.nlm.nih.gov/26437033/ 26437033]; 33844099; 33782741; 35691725
	\|-		\|-
	\|''SF3B1''		\|''SF3B1''

Kgeiersbach at 19:30, 25 August 2025

2025-08-25T19:30:56Z

← Older revision		Revision as of 14:30, 25 August 2025
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	\|amplification, altered expression, sequence variants		\|amplification, altered expression, sequence variants
	\|Disease: metastatic BC; overexpression associated with poor prognosis; Therapy: resistance to CDK4/6 inhibitors. Additionally, CCNE1 amplification or activating mutations may be sensitive to inhibitors of Cdk2, the protein that Cyclin E1 binds and activates. Other potential therapies include combined Cdk and Akt or PI3K inhibitors, and Wee1 inhibitors.		\|Disease: metastatic BC; overexpression associated with poor prognosis; Therapy: resistance to CDK4/6 inhibitors. Additionally, CCNE1 amplification or activating mutations may be sensitive to inhibitors of Cdk2, the protein that Cyclin E1 binds and activates. Other potential therapies include combined Cdk and Akt or PI3K inhibitors, and Wee1 inhibitors.
	\|[https://pubmed.ncbi.nlm.nih.gov/30807234/ 30807234]; [https://pubmed.ncbi.nlm.nih.gov/30665374/ 30665374]; [https://pubmed.ncbi.nlm.nih.gov/32885893/ 32885893]; [https://pubmed.ncbi.nlm.nih.gov/35005994/ 35005994]; [https://pubmed.ncbi.nlm.nih.gov/23185313/ 23185313]		\|[https://pubmed.ncbi.nlm.nih.gov/40243688/ 40243688];[https://pubmed.ncbi.nlm.nih.gov/30807234/ 30807234]; [https://pubmed.ncbi.nlm.nih.gov/30665374/ 30665374]; [https://pubmed.ncbi.nlm.nih.gov/32885893/ 32885893]; [https://pubmed.ncbi.nlm.nih.gov/35005994/ 35005994]; [https://pubmed.ncbi.nlm.nih.gov/23185313/ 23185313]
	\|-		\|-
	\|''CD274''		\|''CD274''

Kgeiersbach at 19:21, 25 August 2025

2025-08-25T19:21:47Z

← Older revision		Revision as of 14:21, 25 August 2025
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	\|3		\|3
	\|Loss of function		\|Loss of function
	\|613484		\|[https://omim.org/entry/613484?search=613484&highlight=613484 613484]
	\|SPEN		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=SPEN SPEN]
	\|SPEN breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=SPEN&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true SPEN breast]
	\|sequence variants, altered expression		\|sequence variants, altered expression
	\|Diseases: altered in 1-2% of invasisive breast carcinoma (CBioPortal); recent evidence suggests SPEN acts as a tumor suppressor in ER-positive breast cancer and overexpressed SPEN sensitizes HR-positive breast cancer cells to the effects of tamoxifen; more mutations detected in patients with ER+/PR- breast cancer or detectable MRD		\|Diseases: altered in 1-2% of invasisive breast carcinoma (CBioPortal); recent evidence suggests SPEN acts as a tumor suppressor in ER-positive breast cancer and overexpressed SPEN sensitizes HR-positive breast cancer cells to the effects of tamoxifen; more mutations detected in patients with ER+/PR- breast cancer or detectable MRD
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	\|2		\|2
	\|Loss of function		\|Loss of function
	\|[https://omim.org/entry/~~613484~~?search=~~613484~~&highlight=~~613484~~ 602216]		\|[https://omim.org/entry/602216?search=602216&highlight=602216 602216]
	\|STK11		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=STK11 STK11]
	\|STK11 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=STK11&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true STK11 breast]
	\|sequence variants		\|sequence variants
	\|Diseases: syndromic risk for hereditary BC and other cancers (Peutz-Jeghers syndrome) (high penetrance, but most mutations detected in tumors are somatic not germline). Lkb1 activates AMPK and negatively regulates the mTOR pathway in response to cellular energy levels. Therapy: may be responsive to mTOR inhibitors.		\|Diseases: syndromic risk for hereditary BC and other cancers (Peutz-Jeghers syndrome) (high penetrance, but most mutations detected in tumors are somatic not germline). Lkb1 activates AMPK and negatively regulates the mTOR pathway in response to cellular energy levels. Therapy: may be responsive to mTOR inhibitors.
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	\|2		\|2
	\|Gain of function		\|Gain of function
	\|137290		\|[https://omim.org/entry/137290?search=137290&highlight=137290 137290]
	\|TACSTD2		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TACSTD2 TACSTD2]
	\|TACSTD2 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=TACSTD2&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TACSTD2 breast]
	\|altered expression		\|altered expression
	\|Diseases: mBC. Trop-2 is protein product of TACSTD2, and is expressed in the majority of breast cancers. Therapy: Trop-2 expression is targeted by antibody-drug conjugate (ADC) sacituzumab govitecan in TNBC and HR+, HER2- mBC previously treated with endocrine therapy, a CDK4/6 inhibitor, and a multiple lines of chemotherapy.		\|Diseases: mBC. Trop-2 is protein product of TACSTD2, and is expressed in the majority of breast cancers. Therapy: Trop-2 expression is targeted by antibody-drug conjugate (ADC) sacituzumab govitecan in TNBC and HR+, HER2- mBC previously treated with endocrine therapy, a CDK4/6 inhibitor, and a multiple lines of chemotherapy.
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	\|2		\|2
	\|Gain of function		\|Gain of function
	\|601621		\|[https://omim.org/entry/601621?search=601621&highlight=601621 601621]
	\|TBX3		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TBX3 TBX3]
	\|TBX3 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=TBX3&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TBX3 breast]
	\|sequence variants, amplification, altered expression		\|sequence variants, amplification, altered expression
	\|Diseases: ER positive BC, Enriched in special subtypes including neuroendocrine tumors, lobular BC; metastatic breast cancer. Therapy: hormone resistance. TBX3 is one of several estrogen receptor transcriptional regulators also including MYC, CTCF, FOXA1.		\|Diseases: ER positive BC, Enriched in special subtypes including neuroendocrine tumors, lobular BC; metastatic breast cancer. Therapy: hormone resistance. TBX3 is one of several estrogen receptor transcriptional regulators also including MYC, CTCF, FOXA1.
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	\|2		\|2
	\|Gain of function		\|Gain of function
	\|187270		\|[https://omim.org/entry/187270?search=187270&highlight=187270 187270]
	\|TERT		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TERT TERT]
	\|TERT breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=TERT&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TERT breast]
	\|amplification, sequence variants		\|amplification, sequence variants
	\|Diseases: phyllodes tumor, more frequent in borderline and malignant tumors (promoter mut); carcinoma (TERT amplification), metaplastic carcinoma (promoter mutation)		\|Diseases: phyllodes tumor, more frequent in borderline and malignant tumors (promoter mut); carcinoma (TERT amplification), metaplastic carcinoma (promoter mutation)
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	\|2		\|2
	\|Gain of function		\|Gain of function
	\|126430		\|[https://omim.org/entry/126430?search=126430&highlight=126430 126430]
	\|TOP2A		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TOP2A TOP2A]
	\|TOP2A breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=TOP2A&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TOP2A breast]
	\|amplification, sequence variants		\|amplification, sequence variants
	\|Therapy: responsiveness to anthracycline inhibitors. Prognosis: increased TOP2A expression is an adverse prognostic indicator.		\|Therapy: responsiveness to anthracycline inhibitors. Prognosis: increased TOP2A expression is an adverse prognostic indicator.
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	\|2		\|2
	\|Loss of function		\|Loss of function
	\|191170		\|[https://omim.org/entry/191170?search=191170&highlight=191170 191170]
	\|TP53		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TP53 TP53]
	\|TP53 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=TP53&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TP53 breast]
	\|sequence variants, other structural rearrangement, altered expression		\|sequence variants, other structural rearrangement, altered expression
	\|Diseases: ~~HER2 positive BC, ER positive BC; metastatic BC~~; syndromic risk for hereditary BC and other cancers (Li-Fraumeni syndrome~~; odds ratio, 3.06; 95% CI, 0.63 to 14.91; in 2022 NEJM study~~). Prognosis: unfavorable. Therapy: mutations in TP53 may increase resistance to ionizing radiation therapy; therapies for TP53mut BC in development.		\|Diseases: All subtypes; enriched in TNBC. Constitutional variants associated with syndromic risk for hereditary BC and other cancers (Li-Fraumeni syndrome). Prognosis: unfavorable. Therapy: mutations in TP53 may increase resistance to ionizing radiation therapy; therapies for TP53mut BC in development.
	\|20301425; 33471991; 28027327; 32636452; 24803582; 14576853; 30504931		\|20301425; 33471991; 28027327; 32636452; 24803582; 14576853; 30504931
	\|-		\|-
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	\|2		\|2
	\|Other/Complex		\|Other/Complex
	\|604386		\|[https://omim.org/entry/604386?search=604386&highlight=604386 604386]
	\|TRPS1		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=TRPS1 TRPS1]
	\|TRPS1 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=TRPS1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true TRPS1 breast]
	\|altered expression		\|altered expression
	\|Diseases: BC all types, diagnostic utility in identifying breast origin (IHC marker), including TNBC where it is useful as GATA3 expression is usually absent. TRPS1 is a GATA gene family member and paralog of GATA3. Overexpression is observed in breast cancer and is of uncertain prognostic significance. Therapy: overexpression is linked to multidrug resistance in BC.		\|Diseases: BC all types, diagnostic utility in identifying breast origin (IHC marker), including TNBC where it is useful as GATA3 expression is usually absent. TRPS1 is a GATA gene family member and paralog of GATA3. Overexpression is observed in breast cancer and is of uncertain prognostic significance. Therapy: overexpression is linked to multidrug resistance in BC.

Kgeiersbach at 19:07, 25 August 2025

2025-08-25T19:07:28Z

← Older revision		Revision as of 14:07, 25 August 2025
Line 1,322:		Line 1,322:
	\|Loss of function		\|Loss of function
	\|[https://omim.org/entry/612778 612778]		\|[https://omim.org/entry/612778 612778]
	\|SETD2		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=SETD2 SETD2]
	\|SETD2 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=SETD2&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true SETD2 breast]
	\|sequence variants		\|sequence variants
	\|Diseases: recurrent in phyllodes tumor		\|Diseases: recurrent in phyllodes tumor
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	\|2		\|2
	\|Gain of function		\|Gain of function
	\|605590		\|[https://omim.org/entry/605590?search=605590&highlight=605590 605590]
	\|SF3B1		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=SF3B1 SF3B1]
	\|SF3B1 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=SF3B1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true SF3B1 breast]
	\|sequence variants		\|sequence variants
	\|Diseases: TNBC, ER positive luminal BC, adenoid cystic carcinoma		\|Diseases: TNBC, ER positive luminal BC, adenoid cystic carcinoma
Line 1,341:		Line 1,341:
	\|3		\|3
	\|Gain of function		\|Gain of function
	\|603375		\|[https://omim.org/entry/603375?search=603375&highlight=603375 603375]
	\|SMARCA5		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=SMARCA5 SMARCA5]
	\|SMARCA5 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=SMARCA5&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true SMARCA5 breast]
	\|sequence variants, other structural rearrangement, altered expression		\|sequence variants, other structural rearrangement, altered expression
	\|Diseases: invasive ductal carcinoma, adenoid cystic carcinoma. SMARCA5 regulates nucleosome repeat length.		\|Diseases: invasive ductal carcinoma, adenoid cystic carcinoma. SMARCA5 regulates nucleosome repeat length.
Line 1,361:		Line 1,361:
	\|2		\|2
	\|Loss of function		\|Loss of function
	\|602216		\|[https://omim.org/entry/613484?search=613484&highlight=613484 602216]
	\|STK11		\|STK11
	\|STK11 breast		\|STK11 breast

Kgeiersbach at 19:00, 25 August 2025

2025-08-25T19:00:24Z

← Older revision		Revision as of 14:00, 25 August 2025
Line 1,321:		Line 1,321:
	\|2		\|2
	\|Loss of function		\|Loss of function
	\|612778		\|[https://omim.org/entry/612778 612778]
	\|SETD2		\|SETD2
	\|SETD2 breast		\|SETD2 breast

Alex.Wendorf: Added several links

2025-08-15T20:29:52Z

Added several links

Show changes

Alex.Wendorf: Added some links

2025-08-15T15:12:54Z

Added some links

← Older revision		Revision as of 10:12, 15 August 2025
Line 1,173:		Line 1,173:
	\|[https://omim.org/entry/172420 172420]		\|[https://omim.org/entry/172420 172420]
	\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=PLCG1 PLCG1]		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=PLCG1 PLCG1]
	\|PLCG1 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=PLCG1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true PLCG1 breast]
	\|sequence variants, amplification, altered expression		\|sequence variants, amplification, altered expression
	\|Diseases: sequence alterations recurrent in postradiation angiosarcoma (recurrent p.Arg707Gln mutation). Prognosis: Overexpression predictive of metastases in Luminal A, B breast cancer.		\|Diseases: sequence alterations recurrent in postradiation angiosarcoma (recurrent p.Arg707Gln mutation). Prognosis: Overexpression predictive of metastases in Luminal A, B breast cancer.
	\|24633157; 31362705		\|[https://pubmed.ncbi.nlm.nih.gov/24633157/ 24633157]; [https://pubmed.ncbi.nlm.nih.gov/31362705/ 31362705]
	\|-		\|-
	\|''PRKD1''		\|''PRKD1''

Alex.Wendorf: Added several links

2025-08-14T21:27:33Z

Added several links

Show changes

Alex.Wendorf: Added some links

2025-08-14T14:36:23Z

Added some links

← Older revision		Revision as of 09:36, 14 August 2025
Line 971:		Line 971:
	\|2		\|2
	\|Gain of function		\|Gain of function
	\|190198		\|[https://omim.org/entry/190198 190198]
	\|NOTCH1		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=NOTCH1 NOTCH1]
	\|NOTCH1 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=NOTCH1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true NOTCH1 breast]
	\|sequence variants, amplification		\|sequence variants, amplification
	\|Diseases: enriched in TNBC, solid basaloid subtype of adenoid cystic carcinoma. Therapy: inactivating mutations potentially targetable with LGK974, a porcupine inhibitor currently in clinical trials. NOTCH activation downregulates p63. Reduced Notch1 expression associates with increased paclitaxel sensitivity.		\|Diseases: enriched in TNBC, solid basaloid subtype of adenoid cystic carcinoma. Therapy: inactivating mutations potentially targetable with LGK974, a porcupine inhibitor currently in clinical trials. NOTCH activation downregulates p63. Reduced Notch1 expression associates with increased paclitaxel sensitivity.
	\|40025676; 37660928; 34599282; 31857685; 26121683; 33384996; 24451948; 24277854;22101766;16166334		\|[https://pubmed.ncbi.nlm.nih.gov/40025676/ 40025676]; [https://pubmed.ncbi.nlm.nih.gov/37660928/ 37660928]; [https://pubmed.ncbi.nlm.nih.gov/34599282/ 34599282]; [https://pubmed.ncbi.nlm.nih.gov/31857685/ 31857685]; [https://pubmed.ncbi.nlm.nih.gov/26121683/ 26121683]; [https://pubmed.ncbi.nlm.nih.gov/33384996/ 33384996]; [https://pubmed.ncbi.nlm.nih.gov/24451948/ 24451948]; [https://pubmed.ncbi.nlm.nih.gov/24277854/ 24277854]; [https://pubmed.ncbi.nlm.nih.gov/22101766/ 22101766]; [https://pubmed.ncbi.nlm.nih.gov/16166334/ 16166334]
	\|-		\|-
	\|''NOTCH2''		\|''NOTCH2''
	\|2		\|2
	\|Gain of function		\|Gain of function
	\|600275		\|[https://omim.org/entry/600275 600275]
	\|NOTCH2		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=NOTCH2 NOTCH2]
	\|NOTCH2 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=NOTCH2&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true NOTCH2 breast]
	\|sequence variants, amplification		\|sequence variants, amplification
	\|Diseases: enriched in TNBC, solid basaloid subtype of adenoid cystic carcinoma. NOTCH activation downregulates p63.		\|Diseases: enriched in TNBC, solid basaloid subtype of adenoid cystic carcinoma. NOTCH activation downregulates p63.
	\|31857685		\|[https://pubmed.ncbi.nlm.nih.gov/31857685/ 31857685]
	\|-		\|-
	\|''NOTCH3''		\|''NOTCH3''
	\|2		\|2
	\|Gain of function		\|Gain of function
	\|600276		\|[https://omim.org/entry/600276 600276]
	\|NOTCH3		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=NOTCH3 NOTCH3]
	\|NOTCH3 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=NOTCH3&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true NOTCH3 breast]
	\|sequence variants, amplification		\|sequence variants, amplification
	\|Diseases: enriched in TNBC, solid basaloid subtype of adenoid cystic carcinoma. NOTCH activation downregulates p63.		\|Diseases: enriched in TNBC, solid basaloid subtype of adenoid cystic carcinoma. NOTCH activation downregulates p63.
	\|31857685; 33384996;29795369;28108512;30180881		\|[https://pubmed.ncbi.nlm.nih.gov/31857685/ 31857685]; [https://pubmed.ncbi.nlm.nih.gov/33384996/ 33384996]; [https://pubmed.ncbi.nlm.nih.gov/29795369/ 29795369]; [https://pubmed.ncbi.nlm.nih.gov/28108512/ 28108512]; [https://pubmed.ncbi.nlm.nih.gov/30180881/ 30180881]
	\|-		\|-
	\|''NOTCH4''		\|''NOTCH4''
	\|2		\|2
	\|Gain of function		\|Gain of function
	\|164951		\|[https://omim.org/entry/164951 164951]
	\|NOTCH4		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=NOTCH4 NOTCH4]
	\|NOTCH4 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=NOTCH4&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true NOTCH4 breast]
	\|sequence variants, amplification		\|sequence variants, amplification
	\|Diseases: Diseases: enriched in TNBC, solid basaloid subtype of adenoid cystic carcinoma.		\|Diseases: Diseases: enriched in TNBC, solid basaloid subtype of adenoid cystic carcinoma.
	\|31857685; 33384996; 32104513; 34284787;20068161		\|[https://pubmed.ncbi.nlm.nih.gov/31857685/ 31857685]; [https://pubmed.ncbi.nlm.nih.gov/33384996/ 33384996]; [https://pubmed.ncbi.nlm.nih.gov/32104513/ 32104513]; [https://pubmed.ncbi.nlm.nih.gov/34284787/ 34284787]; [https://pubmed.ncbi.nlm.nih.gov/20068161/ 20068161]
	\|-		\|-
	\|''NPM1''		\|''NPM1''

Alex.Wendorf: Added a link

2025-08-13T20:16:48Z

Added a link

← Older revision		Revision as of 15:16, 13 August 2025
Line 823:		Line 823:
	\|[https://omim.org/entry/601335 601335]		\|[https://omim.org/entry/601335 601335]
	\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=MAP2K4 MAP2K4]		\|[https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=MAP2K4 MAP2K4]
	\|MAP2K4 breast		\|[https://www.cbioportal.org/results/oncoprint?cancer_study_list=acbc_mskcc_2015%2Cbreast_cptac_gdc%2Cbrca_hta9_htan_2022%2Cbrca_metabric%2Cbreast_msk_2025%2Cbreast_msk_2018%2Cbrca_pareja_msk_2020%2Cbrca_mskcc_2019%2Cbreast_alpelisib_2020%2Cbrca_smc_2018%2Cbrca_bccrc_xenograft_2014%2Cbfn_duke_nus_2015%2Cbrca_bccrc%2Cbrca_broad%2Cbrca_sanger%2Cbrca_tcga_pub2015%2Cbrca_tcga%2Cbrca_tcga_pub%2Cbrca_tcga_pan_can_atlas_2018%2Cbrca_tcga_gdc%2Cbrca_jup_msk_2020%2Cbrca_mapk_hp_msk_2021%2Cmbc_msk_2021%2Cbrca_aurora_2023%2Cbrca_dfci_2020%2Cbrca_igr_2015%2Cbreast_ink4_msk_2021%2Cilc_msk_2023%2Cbrca_cptac_2020%2Cbrca_mbcproject_wagle_2017%2Cbrca_mbcproject_2022%2Cbrca_fuscc_2020&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=MAP2K4&geneset_list=%20&tab_index=tab_visualize&Action=Submit&exclude_germline_mutations=true MAP2K4 breast]
	\|sequence variants, other structural rearrangement		\|sequence variants, other structural rearrangement
	\|Preclinical study suggests sensitivity to MEK and ERK inhibitors		\|Preclinical study suggests sensitivity to MEK and ERK inhibitors