Gene Variant Detail

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Gene KIT
Variant V560del
Impact List deletion
Protein Effect gain of function
Gene Variant Descriptions KIT V560del (also reported as V559del) results in the deletion of an amino acid in the juxtamembrane domain (exon 11) of the Kit protein at amino acid 560 (PMID: 12879016). V560del confers a gain of function to Kit, resulting in constitutive, ligand independent phosphorylation of Kit and activation of Akt in cell culture (PMID: 15236194, PMID: 22282465), and transformation of cultured cells (PMID: 19861435).
Associated Drug Resistance

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Transcript NM_000222.2
gDNA chr4:g.54727447_54727449delTTG
cDNA c.1679_1681delTTG
Protein p.V560delV
Source Database RefSeq
Genome Build GRCh38/hg38
Transcript gDNA cDNA Protein Source Database Genome Build
NM_001093772.1 chr4:g.54727458_54727460delAAT c.1678_1680delAAT p.N560delN RefSeq GRCh38/hg38
XM_005265740 chr4:g.54727447_54727449delTTG c.1682_1684delTTG p.V561delV RefSeq GRCh38/hg38
NM_000222.2 chr4:g.54727447_54727449delTTG c.1679_1681delTTG p.V560delV RefSeq GRCh38/hg38
XM_017008179 chr4:g.54727456_54727458delTAA c.1679_1681delTAA p.I560delI RefSeq GRCh38/hg38
XM_017008178.1 chr4:g.54727447_54727449delTTG c.1679_1681delTTG p.V560delV RefSeq GRCh38/hg38
XM_005265742 chr4:g.54727456_54727458delTAA c.1679_1681delTAA p.I560delI RefSeq GRCh38/hg38
XM_005265741.1 chr4:g.54727447_54727449delTTG c.1682_1684delTTG p.V561delV RefSeq GRCh38/hg38
XM_017008179.1 chr4:g.54727456_54727458delTAA c.1679_1681delTAA p.I560delI RefSeq GRCh38/hg38
XM_017008180 chr4:g.54727458_54727460delAAT c.1678_1680delAAT p.N560delN RefSeq GRCh38/hg38
NM_000222 chr4:g.54727447_54727449delTTG c.1679_1681delTTG p.V560delV RefSeq GRCh38/hg38
XM_005265742.3 chr4:g.54727456_54727458delTAA c.1679_1681delTAA p.I560delI RefSeq GRCh38/hg38
NM_001093772 chr4:g.54727458_54727460delAAT c.1678_1680delAAT p.N560delN RefSeq GRCh38/hg38
XM_017008178 chr4:g.54727447_54727449delTTG c.1679_1681delTTG p.V560delV RefSeq GRCh38/hg38
XM_005265740.1 chr4:g.54727447_54727449delTTG c.1682_1684delTTG p.V561delV RefSeq GRCh38/hg38
XM_017008180.1 chr4:g.54727458_54727460delAAT c.1678_1680delAAT p.N560delN RefSeq GRCh38/hg38
XM_005265741 chr4:g.54727447_54727449delTTG c.1682_1684delTTG p.V561delV RefSeq GRCh38/hg38

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Molecular Profile Indication/Tumor Type Response Type Therapy Name Approval Status Evidence Type Efficacy Evidence References
KIT V560del Advanced Solid Tumor sensitive Sunitinib Preclinical Actionable In a preclinical study, Sutent (sunitinib) inhibited growth of transformed cell lines over expressing KIT V560del in culture (PMID: 19861435). 19861435
KIT V560del Advanced Solid Tumor sensitive Imatinib Preclinical Actionable In a preclinical study, Gleevec (imatinib) inhibited growth of transformed cell lines over expressing KIT V560del in culture (PMID: 19861435). 19861435
KIT V560del gastrointestinal stromal tumor sensitive G007-LK + Imatinib Preclinical Actionable In a preclinical study, the combination of G007-LK and Gleevec (imatinib) demonstrated increased anti-tumor activity compared to either agent alone in a mouse model of gastrointestinal stromal tumor expressing Kit V558del (corresponding to human V560del) (PMID: 28611108). 28611108
KIT V560del KIT over exp thymic carcinoma predicted - sensitive Imatinib Case Reports/Case Series Actionable In a clinical case report, a patient with metastatic thymic carcinoma harboring KIT V560del with KIT over expression initially demonstrated stable disease and reduction in metastatic lesions following treatment with Gleevec (imatinib), but progressed after 6 months (PMID: 15201427). 15201427
KIT V560del KIT V654A Advanced Solid Tumor sensitive Nilotinib Preclinical - Cell culture Actionable In a preclinical study, Tasigna (nilotinib) inhibited proliferation of transformed cells expressing a KIT V560del/V654A double mutation in culture (PMID: 17699867). 17699867
Molecular Profile Indication/Tumor Type Response Type Therapy Name Approval Status Evidence Type Efficacy Evidence References
KIT exon 11 del gastrointestinal stromal tumor no benefit Adavosertib Preclinical - Cell line xenograft Actionable In a preclinical study, Adavosertib (MK-1775) treatment resulted in reduced cell viability of gastrointestinal stromal tumor cells harboring a KIT exon 11 deletion in culture, but did not lead to improved tumor growth inhibition or prolonged survival compared to controls in cell line xenograft models (PMID: 33320833). 33320833
KIT exon 11 del gastrointestinal stromal tumor sensitive Avapritinib Preclinical - Cell line xenograft Actionable In a preclinical study, Ayvakit (avapritinib) inhibited cell growth and induced cell cycle arrest in gastrointestinal stromal tumor cells harboring a KIT exon 11 deletion in culture, and inhibited tumor growth and led to prolonged survival in cell line xenograft models (PMID: 33320833). 33320833
KIT exon 11 del gastrointestinal stromal tumor sensitive Avapritinib Preclinical - Cell culture Actionable In a preclinical study, Ayvakit (avapritinib) inhibited Kit phosphorylation and proliferation of gastrointestinal stromal tumor cells harboring KIT exon 11 deletion in culture (PMID: 31085175). 31085175
KIT exon 11 del gastrointestinal stromal tumor sensitive Ripretinib Preclinical - Cell line xenograft Actionable In a preclinical study, Qinlock (ripretinib) inhibited Kit phosphorylation and proliferation of gastrointestinal stromal tumor cells harboring KIT exon 11 deletion, resulted in tumor regression in cell line xenograft models (PMID: 31085175). 31085175
KIT exon 11 del gastrointestinal stromal tumor sensitive Adavosertib + Avapritinib Preclinical - Cell line xenograft Actionable In a preclinical study, the combination of Adavosertib (MK-1775) and Ayvakit (avapritinib) demonstrated an additive effect on inhibiting cell growth and inducing apoptosis in gastrointestinal stromal tumor cells harboring a KIT exon 11 deletion in culture, and inhibited tumor growth and led to prolonged survival in cell line xenograft models (PMID: 33320833). 33320833
KIT exon 11 del gastrointestinal stromal tumor predicted - sensitive Imatinib Phase III Actionable In a Phase III trial, gastrointestinal stromal tumor patients harboring KIT exon 11 deletions or indels demonstrated improved improved recurrence-free survival (RFS) with 3-year adjuvant Gleevec (imatinib) treatment (5-year RFS, 70%), compared to patients receiving 1-year treatment (5-year RFS, 41.3%) (PMID: 28334365). 28334365
KIT exon 11 del gastrointestinal stromal tumor predicted - sensitive Imatinib Preclinical - Cell culture Actionable In a preclinical study, Gleevec (imatinib) inhibited Kit phosphorylation and proliferation of gastrointestinal stromal tumor cells harboring KIT exon 11 deletion in culture (PMID: 31085175). 31085175
KIT exon 11 del gastrointestinal stromal tumor sensitive Regorafenib Preclinical - Cell culture Actionable In a preclinical study, Stivarga (regorafenib) inhibited Kit phosphorylation and proliferation of gastrointestinal stromal tumor cells harboring KIT exon 11 deletion in culture (PMID: 31085175). 31085175
KIT exon 11 del gastrointestinal stromal tumor sensitive Sunitinib Preclinical - Cell culture Actionable In a preclinical study, Sutent (sunitinib) inhibited Kit phosphorylation and proliferation of gastrointestinal stromal tumor cells harboring KIT exon 11 deletion in culture (PMID: 31085175). 31085175
KIT exon 11 del gastrointestinal stromal tumor sensitive Midostaurin Preclinical - Cell culture Actionable In a preclinical study, Rydapt (midostaurin) inhibited Kit phosphorylation and proliferation of gastrointestinal stromal tumor cells harboring KIT exon 11 deletion in culture (PMID: 31085175). 31085175
KIT act mut Advanced Solid Tumor sensitive PLX9486 Preclinical Actionable In a preclinical study, PLX9486 inhibited KIT mutations, including exon 17 mutations, and demonstrated in vivo and in vitro activity against tumors harboring KIT exon 17 mutations (Cancer Res February 1, 2016 76; IA32). detail...
KIT act mut skin melanoma sensitive Imatinib Guideline Actionable Gleevec (imatinib) is included in guidelines as second-line therapy for metastatic or unresectable cutaneous melanoma patients with KIT activating mutations (NCCN.org). detail...
KIT act mut gastrointestinal stromal tumor sensitive Pexidartinib Preclinical - Cell line xenograft Actionable In a preclinical study, PLX3397 inhibited growth of gastrointestinal stromal tumor cell lines harboring KIT activating mutations in culture and in cell line xenograft models (PMID: 24583793). 24583793
KIT act mut gastrointestinal stromal tumor not applicable N/A Guideline Diagnostic KIT activating mutations aid the diagnosis of gastrointestinal stromal tumor (NCCN.org). detail...
KIT act mut gastrointestinal stromal tumor sensitive Cabozantinib Preclinical Actionable In a preclinical study, Cometriq (cabozantinib) decreased cell viability in imatinib-sensitive and resistant gastrointestinal stromal tumor (GIST) cell lines harboring KIT activating mutations in culture, and induced tumor regression in KIT-mutant GIST mouse models (PMID: 25836719). 25836719
KIT mutant gastrointestinal stromal tumor predicted - sensitive Avapritinib Phase I Actionable In a Phase I (NAVIGATOR) trial, Ayvakit (avapritinib) treatment resulted in an objective response rate of 13% (7/52, 7 partial responses) and a disease control rate of 63% (33/52) in patients with KIT-mutant gastrointestinal stromal tumor (The CTOS 2018 Annual Meeting, Nov 14-17, Rome Italy, Paper 012 3027631; NCT02508532). detail...
KIT mutant gastrointestinal stromal tumor sensitive Imatinib + Infigratinib Preclinical - Pdx Actionable In a preclinical study, Truseltiq (infigratinib) and Gleevec (imatinib) combination treatment demonstrated enhanced antitumor activity in patient derived xenograft models of gastrointestinal stromal tumor harboring KIT mutations (PMID: 25673643). 25673643
KIT mutant melanoma sensitive Nilotinib Phase II Actionable In a Phase II trial, Tasigna (nilotinib) treatment resulted in complete response in 4% (1/25), durable partial response in 16% (4/25), and stable disease in 56% (14/25) of melanoma patients harboring KIT mutations (PMID: 28843487; NCT01168050). 28843487
KIT mutant melanoma sensitive Nilotinib Phase II Actionable In a Phase II trial, Tasigna (nilotinib) treatment in patients with melanoma harboring KIT mutations resulted in an overall response rate of 26.2% (11/42), which included 11 patients with a partial response, a median duration of response of 7.1 months, and an overall survival of 18 months (PMID: 28327988; NCT01028222). 28327988
KIT mutant gastrointestinal stromal tumor predicted - sensitive Ripretinib Phase I Actionable In a Phase I trial, Qinlock (ripretinib) was well tolerated, resulted in an objective response in 11.3% (16/142, 16 partial responses) and stable disease in 61.3% (87/142) of patients with advanced gastrointestinal stromal tumor harboring KIT (exon 11, n=103; exon 9, n=26; other, n=6) or PDGFRA mutations (n=7), with a median progression-free survival of 5.6 months (PMID: 32804590; NCT02571036). 32804590
KIT mutant gastrointestinal stromal tumor predicted - sensitive Ripretinib Phase I Actionable In a Phase I trial, Qinlock (ripretinib) demonstrated preliminary safety and efficacy in patients with advanced solid tumors, including KIT-mutant gastrointestinal stromal tumor (GIST), with 1 patient harboring KIT exon 11 and 17 mutations demonstrating a partial response, and 7/7 KIT-mutant GIST patients demonstrating a partial metabolic response (EORTC-NCI-AACR 2016, Abs 7LBA). detail...
KIT mutant gastrointestinal stromal tumor not applicable N/A Clinical Study Diagnostic KIT mutations are used in the diagnosis of gastrointestinal stromal tumors (PMID: 25193432, PMID: 26276366, PMID: 25729899). 25193432 26276366 25729899
KIT exon11 gastrointestinal stromal tumor predicted - sensitive Ponatinib Phase II Actionable In a Phase II trial, Iclusig (ponatinib) treatment resulted in partial response in 7% (2/27), stable disease in 59% (16/27), a median progression free survival of 4.3 months and a median overall survival of 15.0 months in gastrointestinal stromal tumor patients harboring KIT exon 11 mutations after prior tyrosine kinase inhibitor treatment failure (J Clin Oncol 33, 2015 (suppl; abstr 10535)). detail...
KIT exon11 gastrointestinal stromal tumor predicted - sensitive PLX9486 Phase I Actionable In a Phase I trial, PLX9486 demonstrated safety and preliminary efficacy, resulted in a progression-free survival of more than 24 weeks and partial response in 8.3% (2/24) of patients with advanced solid tumors, 20 of these patients had gastrointestinal stromal tumor that progressed on Gleevec (imatinib mesylate), and most harbored KIT exon 11 and exon 17 mutations (Journal of Clinical Oncology 36, no. 15_suppl (May 20 2018) 11509-11509; NCT02401815). detail...
KIT exon11 gastrointestinal stromal tumor sensitive Imatinib + MK2206 Preclinical - Cell line xenograft Actionable In a preclinical study, the combination of Gleevec (imatinib) and MK2206 increased growth inhibition and decreased viability of gastrointestinal stromal tumor (GIST) cell lines harboring KIT exon 11 mutations in culture, and improved survival and inhibited tumor growth in a KIT exon 11-mutant GIST cell line xenograft model, with increased efficacy compared to either agent alone (PMID: 27370604). 27370604
KIT exon11 gastrointestinal stromal tumor sensitive Imatinib Guideline Actionable Gleevec (imatinib) is included in guidelines for patients with gastrointestinal stromal tumor (GIST) harboring KIT exon 11 mutations (NCCN.org). detail...
KIT exon11 gastrointestinal stromal tumor sensitive Imatinib Phase III Actionable In a Phase III trial, a long-term analysis of gastrointestinal stromal tumor (GIST) patients treated with Gleevec (imatinib) demonstrated patients harboring KIT exon 11 mutations had a median progression-free survival of 39.4 months, and median overall survival was not reached, with 69.1% of patients with KIT exon 11 mutations alive at 5 years (PMID: 26687836; NCT00367861). 26687836
KIT exon11 gastrointestinal stromal tumor sensitive Imatinib Guideline Actionable Gleevec (imatinib) is included in the guidelines for patients with advanced/metastatic gastrointestinal stromal tumor (GIST) with KIT exon 11 mutations (PMID: 30188977; ESMO.org). 30188977 detail...
KIT exon11 gastrointestinal stromal tumor sensitive Imatinib Phase III Actionable In a Phase III trial, Gleevec (imatinib) treatment resulted in longer overall survival (OS) (66 vs 40 months) in gastrointestinal stromal tumor (GIST) patients harboring KIT exon 11 mutations compared to KIT and PDGFRA wild-type patients, while subtypes of KIT exon 11 mutations (deletion, insertation/duplication, point mutation) did not affect OS outcome (PMID: 28196207; NCT00009906). 28196207
KIT exon11 gastrointestinal stromal tumor decreased response Sunitinib Clinical Study - Cohort Actionable In a retrospective analysis, GIST patients with KIT exon 11 mutations showed decreased benefit compared to patients with exon 9 mutations, with median PFS of 7.0 months with exon 11 mutations vs. 12.3 months with exon 9 mutations, and an ORR of 6% (9/143) vs. 19% (8/42) following treatment with Sutent (sunitinib) (PMID: 26772734). 26772734
KIT exon11 gastrointestinal stromal tumor no benefit Imatinib + Infigratinib Phase I Actionable In a Phase I trial, Truseltiq (infigratinib) and Gleevec (imatinib) combination therapy resulted in stable disease as best response in 58% (7/12) of patients with advanced gastrointestinal stromal tumor harboring KIT mutations in exon 11 (n=10), exon 9 (n=3), or other (n=3), however, the trial was discontinued due to toxicity concerns (PMID: 30101387). 30101387
KIT exon11 melanoma sensitive Nilotinib Phase II Actionable In a Phase II trial, Tasigna (nilotinib) resulted in an overall response rate of 26.2% (11/41), which included a partial response of 38.5% (10/26) and a progression free survival of 5.4 months in melanoma patients harboring KIT exon 11 mutations (PMID: 28327988). 28327988
KIT exon11 melanoma sensitive Nilotinib Phase II Actionable In a Phase II trial, Tasigna (nilotinib) treatment resulted in complete response in 5% (1/19) and partial response in 21% (4/19) of melanoma patients harboring KIT exon 11 or exon 13 mutations (PMID: 28843487; NCT01168050). 28843487
KIT exon11 gastrointestinal stromal tumor sensitive Ripretinib Phase I Actionable In a Phase I trial, Qinlock (ripretinib) was well tolerated, resulted in an objective response in 11.3% (16/142, 16 partial responses) and stable disease in 61.3% (87/142) of patients with advanced gastrointestinal stromal tumor harboring KIT (n=135) or PDGFRA mutations (n=7), with a median progression-free survival of 5.6 months, 72.5% (103/142) of the patients harbored KIT exon 11 mutations (PMID: 32804590; NCT02571036). 32804590
KIT exon11 gastrointestinal stromal tumor sensitive Ripretinib Preclinical - Cell line xenograft Actionable In a preclinical study, Qinlock (ripretinib) inhibited Kit phosphorylation and proliferation of gastrointestinal stromal tumor cells harboring a KIT exon 11 deletion mutation in culture, and resulted in tumor regression in cell line xenograft models (PMID: 31085175). 31085175
KIT exon11 gastrointestinal stromal tumor predicted - sensitive Dasatinib Phase II Actionable In a Phase II clinical trial, Sprycel (dasatinib) demonstrated preliminary activity in patients with Gleevec (imatinib)-resistant gastrointestinal stromal tumor (GIST), including patients harboring KIT exon 11 mutations, with a partial response rate of 32% (15/47), median progression-free survival of 2.0 months, and overall survival of 19 months (J Clin Oncol 29: 2011 (suppl; abstr 10006)). detail...
KIT exon11 gastrointestinal stromal tumor predicted - sensitive Pexidartinib + PLX9486 Phase I Actionable In a Phase I trial, PLX9486 and Pexidartinib (PLX3397) combination therapy demonstrated safety and preliminary efficacy, resulted in a partial response rate of 8.3% (1/12) and progression-free survival not yet reached in patients with advanced solid tumors, 11 of these patients had gastrointestinal stromal tumor that progressed on Gleevec (imatinib mesylate), and most harbored KIT exon 11 and exon 17 mutations (Journal of Clinical Oncology 36, no. 15_suppl (May 20 2018) 11509-11509; NCT02401815). detail...
KIT exon11 gastrointestinal stromal tumor sensitive Imatinib + PKF118-310 Preclinical - Cell culture Actionable In a preclinical study, treatment with the combination of PKF118-310 and Gleevec (imatinib) resulted in decreased viability of gastrointestinal stromal tumor (GIST) cell lines harboring KIT exon 11 mutations compared to Gleevec (imatinib) alone, in culture (PMID: 28611108). 28611108
KIT exon11 melanoma predicted - sensitive Imatinib Case Reports/Case Series Actionable In a clinical case study, Gleevec (imatinib) treatment resulted in a partial response in a patient with metastastic anal melanoma harboring a 21 base-pair duplication in KIT exon 11, and reduced pulmonary metastasis by 60% (PMID: 20372153). 20372153
KIT exon11 gastrointestinal stromal tumor sensitive Nilotinib Phase III Actionable In a Phase III trial, a 24 month progression free survival was observed in 69.6% of advanced GIST patients harboring KIT exon 11 mutations when treated with Tasigna (nilotinib) (J Clin Oncol May 2013 vol. 31 no. 15_suppl 10501). detail...
KIT exon11 gastrointestinal stromal tumor sensitive Imatinib + XAV939 Preclinical - Cell culture Actionable In a preclinical study, treatment with the combination of XAV939 and Gleevec (imatinib) resulted in decreased viability of gastrointestinal stromal tumor (GIST) cell lines harboring KIT exon 11 mutations compared to Gleevec (imatinib) alone, in culture (PMID: 28611108). 28611108
KIT exon11 gastrointestinal stromal tumor sensitive Regorafenib Phase II Actionable In a Phase II clinical trial, treatment with Stivarga (regorafenib) resulted in a clinical benefit rate of 76% (25/33), a median progression-free survival (PFS) of 13.2 months, and a median overall survival of 25 months in patients with gastrointestinal stromal tumors, with patients with KIT exon 11 mutations demonstrating the longest PFS of 13.4 months (PMID: 27371698). 27371698
Molecular Profile Protein Effect Treatment Approaches
KIT V560del gain of function KIT Inhibitor
KIT V560del KIT over exp
KIT V560del KIT V654A