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Gene KIT
Variant N463S
Impact List missense
Protein Effect unknown
Gene Variant Descriptions KIT N463S lies within Ig-like C2-type domain 5 (exon 9) of the Kit protein (UniProt.org). N463S has been identified in sequencing studies (PMID: 21642685, PMID: 38348622), but has not been biochemically characterized and therefore, its effect on Kit protein function is unknown (PubMed, Nov 2024).
Associated Drug Resistance
Category Variants Paths

KIT mutant KIT exon9 KIT N463S

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Transcript NM_000222.3
gDNA chr4:g.54725898A>G
cDNA c.1388A>G
Protein p.N463S
Source Database RefSeq
Genome Build GRCh38/hg38
Transcript gDNA cDNA Protein Source Database Genome Build
XM_017008180.1 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
XM_017008178 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
XM_017008180 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
NM_001093772.1 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
NM_000222.3 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
NM_000222 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
NM_001093772.2 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
NM_001093772 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
XM_017008178.1 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
NM_001385285.1 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
NM_001385286.1 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38
NM_000222.2 chr4:g.54725898A>G c.1388A>G p.N463S RefSeq GRCh38/hg38

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Molecular Profile Indication/Tumor Type Response Type Therapy Name Approval Status Evidence Type Efficacy Evidence References
KIT exon9 melanoma predicted - sensitive Regorafenib Case Reports/Case Series Actionable In a Phase II trial, second or later-line Stivarga (regorafenib) treatment resulted in a disease control rate of 73.9% (17/23, 2 complete responses, 5 partial responses), an objective response rate of 30.4% (7/23), and median overall survival (mOS) of 21.5 months in patients with melanoma harboring KIT exon 9, 11, 13, or 17 mutations, and improved mOS in patients with non-exon 11 mutations compared to patients with exon 11 mutations (24.9 mo vs 18.3 mo, P=0.042) (PMID: 37741071; NCT02501551). 37741071
KIT exon9 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, 18.3% (26/142) of the patients harbored KIT exon 9 mutations (PMID: 32804590; NCT02571036). 32804590
KIT exon9 gastrointestinal stromal tumor sensitive Ripretinib Guideline Actionable Qinlock (ripretinib) is included in guidelines as fourth-line or subsequent therapy for locally advanced, unresectable, or metastatic gastrointestinal stromal tumor (GIST) patients harboring sensitizing mutations, such as KIT exon 9 mutations (PMID: 34560242; ESMO.org). 34560242 detail...
KIT exon9 gastrointestinal stromal tumor sensitive Regorafenib Guideline Actionable Stivarga (regorafenib) is included in guidelines as third-line or subsequent therapy for locally advanced, unresectable, or metastatic gastrointestinal stromal tumor (GIST) patients harboring sensitizing mutations, such as KIT exon 9 mutations (PMID: 34560242; ESMO.org). 34560242 detail...
KIT exon9 Advanced Solid Tumor sensitive Sunitinib Preclinical Actionable In a preclinical study, transformed cells expressing a KIT exon 9 mutation demonstrated sensitivity to treatment with Sutent (sunitinib) in culture, resulting in reduced cell viability (PMID: 25239608). 25239608
KIT exon9 gastrointestinal stromal tumor no benefit Imatinib + Spartalizumab Phase Ib/II Actionable In a Phase Ib/II trial, the combination of Spartalizumab (PDR001) and Gleevec (imatinib) was tolerable but demonstrated limited efficacy in Phase II, with an objective response rate of 0% (0/29), a disease control rate of 37.9% (11/29), median progression-free survival of 2.3 months, and overall survival of 9.5 months in patients with gastrointestinal stromal tumor harboring KIT exon 9 (n=8), exon 11 (n=17), or other mutations (PMID: 38662455). 38662455
KIT exon9 Advanced Solid Tumor resistant Regorafenib Preclinical Actionable In a preclinical study, Stivarga (regorafineb) had no effect on transformed cells expressing a KIT exon 9 mutation in culture (PMID: 25239608). 25239608
KIT exon9 gastrointestinal stromal tumor sensitive Imatinib Guideline Actionable Gleevec (imatinib) is included in guidelines for gastrointestinal stromal tumor (GIST) patients harboring sensitizing mutations, such as KIT exon 9 mutations, as adjuvant therapy for patients with localized disease and as first-line therapy for patients with locally advanced, unresectable, or metastatic disease (PMID: 34560242; ESMO.org). 34560242 detail...
KIT exon9 gastrointestinal stromal tumor sensitive Imatinib Guideline Actionable Gleevec (imatinib) is included in guidelines for patients with gastrointestinal stromal tumor (GIST) harboring KIT exon 9 mutations (NCCN.org). detail...
KIT exon9 Advanced Solid Tumor sensitive Ponatinib Preclinical Actionable In a preclinical study, transformed cells expressing a KIT exon 9 mutation demonstrated sensitivity to treatment with Iclusig (ponatinib) in culture, resulting in reduced cell viability (PMID: 25239608). 25239608
KIT exon9 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 9 (n=3), exon 11 (n=10), or other (n=3), however, the trial was discontinued due to toxicity concerns (PMID: 30101387). 30101387
KIT exon9 Advanced Solid Tumor resistant Imatinib Preclinical Actionable In a preclinical study, Gleevec (imatinib) had no effect on transformed cells expressing a KIT exon 9 mutation in culture (PMID: 25239608). 25239608
KIT exon9 gastrointestinal stromal tumor no benefit Ponatinib Phase II Actionable In a Phase II trial, Iclusig (ponatinib) treatment did not result in clinical benefit in gastrointestinal stromal tumor patients with KIT exon 9 mutations who had failed prior tyrosine kinase inhibitor treatment (PMID: 35091442; NCT01874665). 35091442
KIT exon9 gastrointestinal stromal tumor sensitive Sunitinib Clinical Study - Cohort Actionable In a retrospective analysis, GIST patients with KIT exon 9 mutations showed improved progression-free survival (PFS), overall survival, and objective response rate (ORR) compared to patients with exon 11 mutations, with a median PFS of 12.3 months vs. 7.0 months, and an ORR of 19% (8/42) vs. 6% (9/143) following treatment with Sutent (sunitinib) (PMID: 26772734). 26772734
KIT exon9 gastrointestinal stromal tumor sensitive Sunitinib Guideline Actionable Sutent (sunitinib) is included in guidelines as second-line or subsequent therapy for locally advanced, unresectable, or metastatic gastrointestinal stromal tumor (GIST) patients harboring sensitizing mutations, such as KIT exon 9 mutations (PMID: 34560242; ESMO.org). detail... 34560242
KIT exon9 gastrointestinal stromal tumor predicted - sensitive IDRX-42 Phase I Actionable In a Phase I trial, IDRX-42 treatment demonstrated safety and resulted in 9 partial responses among 39 evaluable patients with gastrointestinal stromal tumors harboring a KIT exon 11 (n=27), exon 9 (n=13), or exon 8 (n=2) mutation with a clinical benefit rate of 71% overall and 100% as second-line treatment (J Clin Oncol 42, 2024 (suppl 16; abstr 11501); NCT05489237). detail...
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 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 melanoma predicted - sensitive Ripretinib Phase I Actionable In a Phase I trial, Qinlock (ripretinib) treatment demonstrated manageable safety and preliminary efficacy in patients with KIT-mutated melanoma, and led to an objective response rate of 23% (6/26, 1 complete and 5 partial responses), a median progression-free survival of 7.3 months, and a median duration of response of 9.1 months (PMID: 35753087; NCT02571036). 35753087
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 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 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 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 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...