KIT V560_Y578del
Gene Variant Detail

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Gene KIT
Variant V560_Y578del
Impact List deletion
Protein Effect gain of function - predicted
Gene Variant Descriptions KIT V560_Y578del results in the deletion of 18 amino acids in the juxtamembrane domain (exon 11) of the Kit protein from amino acids 560 to 578 (PMID: 16226710). V560_Y578del has not been characterized, however similar Kit exon 11 deletions are activating (PMID: 9438854, PMID: 15365079), and therefore, is predicted to lead to a gain of Kit protein function.
Associated Drug Resistance
Category Variants Paths

KIT mutant KIT act mut KIT exon 11 del KIT V560_Y578del

KIT mutant KIT exon11 KIT exon 11 del KIT V560_Y578del

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Transcript NM_000222.3
gDNA chr4:g.54727447_54727503del57
cDNA c.1679_1735del57
Protein p.V560_Y578del19
Source Database RefSeq
Genome Build GRCh38/hg38
Transcript gDNA cDNA Protein Source Database Genome Build
NM_000222 chr4:g.54727447_54727503del57 c.1679_1735del57 p.V560_Y578del19 RefSeq GRCh38/hg38
XM_017008179 chr4:g.54727455_54727511del57 c.1678_1734del57 p.I560_K578del19 RefSeq GRCh38/hg38
NM_001385286.1 chr4:g.54727458_54727514del57 c.1678_1734del57 p.N560_W578del19 RefSeq GRCh38/hg38
NM_001093772.2 chr4:g.54727458_54727514del57 c.1678_1734del57 p.N560_W578del19 RefSeq GRCh38/hg38
XM_005265741.1 chr4:g.54727443_54727499del57 c.1678_1734del57 p.V560_P578del19 RefSeq GRCh38/hg38
NM_000222.3 chr4:g.54727447_54727503del57 c.1679_1735del57 p.V560_Y578del19 RefSeq GRCh38/hg38
XM_005265740 chr4:g.54727443_54727499del57 c.1678_1734del57 p.V560_P578del19 RefSeq GRCh38/hg38
NM_001093772.1 chr4:g.54727458_54727514del57 c.1678_1734del57 p.N560_W578del19 RefSeq GRCh38/hg38
NM_000222.2 chr4:g.54727447_54727503del57 c.1679_1735del57 p.V560_Y578del19 RefSeq GRCh38/hg38
XM_005265742.3 chr4:g.54727455_54727511del57 c.1678_1734del57 p.I560_K578del19 RefSeq GRCh38/hg38
NM_001385288.1 chr4:g.54727455_54727511del57 c.1678_1734del57 p.I560_K578del19 RefSeq GRCh38/hg38
XM_017008180 chr4:g.54727458_54727514del57 c.1678_1734del57 p.N560_W578del19 RefSeq GRCh38/hg38
NM_001385290.1 chr4:g.54727443_54727499del57 c.1678_1734del57 p.V560_P578del19 RefSeq GRCh38/hg38
NM_001385292.1 chr4:g.54727455_54727511del57 c.1678_1734del57 p.I560_K578del19 RefSeq GRCh38/hg38
NM_001385285.1 chr4:g.54727447_54727503del57 c.1679_1735del57 p.V560_Y578del19 RefSeq GRCh38/hg38
XM_017008180.1 chr4:g.54727458_54727514del57 c.1678_1734del57 p.N560_W578del19 RefSeq GRCh38/hg38
NM_001093772 chr4:g.54727458_54727514del57 c.1678_1734del57 p.N560_W578del19 RefSeq GRCh38/hg38
XM_005265741 chr4:g.54727443_54727499del57 c.1678_1734del57 p.V560_P578del19 RefSeq GRCh38/hg38
XM_017008178 chr4:g.54727447_54727503del57 c.1679_1735del57 p.V560_Y578del19 RefSeq GRCh38/hg38
XM_017008179.1 chr4:g.54727455_54727511del57 c.1678_1734del57 p.I560_K578del19 RefSeq GRCh38/hg38
NM_001385284.1 chr4:g.54727443_54727499del57 c.1678_1734del57 p.V560_P578del19 RefSeq GRCh38/hg38
XM_005265742 chr4:g.54727455_54727511del57 c.1678_1734del57 p.I560_K578del19 RefSeq GRCh38/hg38
XM_005265740.1 chr4:g.54727443_54727499del57 c.1678_1734del57 p.V560_P578del19 RefSeq GRCh38/hg38
XM_017008178.1 chr4:g.54727447_54727503del57 c.1679_1735del57 p.V560_Y578del19 RefSeq GRCh38/hg38

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Molecular Profile Indication/Tumor Type Response Type Therapy Name Approval Status Evidence Type Efficacy Evidence References
KIT V560_Y578del gastrointestinal stromal tumor sensitive Ponatinib Preclinical - Patient cell culture Actionable In a preclinical study, a patient-derived gastrointestinal stromal tumor (GIST) cell line harboring KIT V560_Y578del demonstrated sensitivity to Iclusig (ponatinib) in culture (PMID: 25239608). 25239608
KIT V560_Y578del gastrointestinal stromal tumor sensitive Imatinib Preclinical Actionable In a preclinical study, a patient derived GIST cell line harboring KIT V560_Y578del demonstrated sensitivity to Gleevec (imatinib) in culture (PMID: 25239608). 25239608
KIT V560_Y578del gastrointestinal stromal tumor sensitive Imatinib Preclinical - Cell culture Actionable In a preclinical study, Gleevec (imatinib) inhibited cell growth and KIT signaling in a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture, but was less potent compared to AZD3229 (PMID: 32350132). 32350132
KIT V560_Y578del gastrointestinal stromal tumor sensitive Imatinib + Infigratinib Preclinical - Cell culture Actionable In a preclinical study, Truseltiq (infigratinib) and Gleevec (imatinib) combination treatment demonstrated enhanced antiproliferative activity in gastrointestinal stromal tumor cells harboring KIT V560_Y578del in culture (PMID: 25673643). 25673643
KIT V560_Y578del gastrointestinal stromal tumor sensitive Olverembatinib Preclinical - Cell line xenograft Actionable In a preclinical study, Olverembatinib (HQP1351) treatment inhibited Kit activity and proliferation of a gastrointestinal stromal tumor (GIST) cell line harboring KIT V560_Y578del in culture, and inhibited tumor growth in a cell line xenograft model (PMID: 31673329). 31673329
KIT V560_Y578del gastrointestinal stromal tumor sensitive Axitinib Preclinical - Cell line xenograft Actionable In a preclinical study, Inlyta (axitinib) inhibited KIT phosphorylation and downstream signaling, reduced proliferation and induced cell-cycle arrest in a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture, and inhibited tumor growth in xenograft models (PMID: 31205508). 31205508
KIT V560_Y578del gastrointestinal stromal tumor sensitive Sunitinib Preclinical - Cell culture Actionable In a preclinical study, Sutent (sunitinib) inhibited proliferation of a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture (PMID: 31205508). 31205508
KIT V560_Y578del gastrointestinal stromal tumor sensitive AZD3229 Preclinical - Cell culture Actionable In a preclinical study, AZD3229 inhibited cell growth and KIT signaling in a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture (PMID: 32350132). 32350132
KIT V560_Y578del gastrointestinal stromal tumor sensitive Avapritinib Preclinical - Cell culture Actionable In a preclinical study, Ayvakit (avapritinib) inhibited cell growth and KIT signaling in a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture, but was less potent compared to AZD3229 (PMID: 32350132). 32350132
KIT V560_Y578del gastrointestinal stromal tumor resistant Ripretinib Preclinical - Cell culture Actionable In a preclinical study, Qinlock (ripretinib) inhibited cell growth and KIT signaling in a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture, but was less potent compared to AZD3229 (PMID: 32350132). 32350132
KIT V560_Y578del gastrointestinal stromal tumor sensitive Regorafenib Preclinical - Cell culture Actionable In a preclinical study, Stivarga (regorafenib) inhibited growth of a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture, but was less potent compared to AZD3229 (PMID: 32350132). 32350132
KIT V560_Y578del gastrointestinal stromal tumor sensitive Copanlisib Preclinical - Cell line xenograft Actionable In a preclinical study, Aliqopa (copanlisib) inhibited cell growth and PI3K signaling in a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture, and inhibited tumor growth in cell line xenograft models (PMID: 32371592). 32371592
KIT V560_Y578del gastrointestinal stromal tumor sensitive Copanlisib + Imatinib Preclinical - Cell line xenograft Actionable In a preclinical study, the combination of Aliqopa (copanlisib) and Gleevec (imatinib) demonstrated enhanced cell growth inhibition and increased apoptosis of gastrointestinal stromal tumor cells harboring KIT V560_Y578del in culture and in cell line xenograft models (PMID: 32371592). 32371592
KIT V560_Y578del gastrointestinal stromal tumor sensitive Nintedanib Preclinical - Cell line xenograft Actionable In a preclinical study, Ofev (nintedanib) decreased Kit phosphorylation and downstream signaling, induced cell-cycle arrest and apoptosis, and inhibited proliferation of a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture, and suppressed tumor growth in cell line xenograft models (PMID: 35194937). 35194937
KIT V560_Y578del gastrointestinal stromal tumor sensitive IDRX-42 Preclinical - Cell line xenograft Actionable In a preclinical study, IDRX-42 inhibited viability of a gastrointestinal stromal tumor cell line harboring KIT V560_Y578del in culture, and induced tumor regression in a cell line xenograft model (PMID: 40018846). 40018846