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| Gene | KIT |
| Variant | Y553D |
| Impact List | missense |
| Protein Effect | unknown |
| Gene Variant Descriptions | KIT Y553D lies within the juxtamembrane domain (exon 11) of the Kit protein (PMID: 16226710). Y553D has been identified in sequencing studies (PMID: 37125020, PMID: 30923944, PMID: 37403699), 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 exon11 KIT Y553D |
| Transcript | NM_000222.2 |
| gDNA | chr4:g.54727425T>G |
| cDNA | c.1657T>G |
| Protein | p.Y553D |
| Source Database | RefSeq |
| Genome Build | GRCh38/hg38 |
| Transcript | gDNA | cDNA | Protein | Source Database | Genome Build |
|---|---|---|---|---|---|
| XM_017008178.1 | chr4:g.54727425T>G | c.1657T>G | p.Y553D | RefSeq | GRCh38/hg38 |
| NM_000222.2 | chr4:g.54727425T>G | c.1657T>G | p.Y553D | RefSeq | GRCh38/hg38 |
| Molecular Profile | Indication/Tumor Type | Response Type | Therapy Name | Approval Status | Evidence Type | Efficacy Evidence | References |
|---|---|---|---|---|---|---|---|
| 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 | sensitive | Ripretinib | Phase II | Actionable | In a Phase II trial, second-line Qinlock (ripretinib) treatment demonstrated a favorable safety profile and resulted in similar median progression-free survival (mPFS) compared to Sutent (sunitinib) (10.3 vs 8.3 mo, HR=0.99, p=0.92) in patients with gastrointestinal stromal tumors previously treated with Gleevec (imatinib), longer mPFS (not reached vs 4.9 months, HR=0.46, p=0.03) was observed in patients harboring KIT exon 11 mutations (PMID: 37980854). | 37980854 |
| KIT exon11 | 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 11 mutations (PMID: 34560242; ESMO.org). | 34560242 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 + 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 | 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 tumor 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 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 | 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 |
| KIT exon11 | 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 11 mutations (PMID: 34560242; ESMO.org). | 34560242 detail... |
| 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 | predicted - sensitive | Ponatinib | Phase II | Actionable | In a Phase II trial, Iclusig (ponatinib) treatment in gastrointestinal stromal tumor patients with KIT exon 11 mutations who failed prior therapy versus those without KIT exon 11 mutations led to a 16-week clinical benefit rate of 36% (10/28; 1 partial response (PR), 9 stable disease (SD)) vs 20% (3/15; 3 SD), an objective response rate of 7% (2/28; 2 PR) vs 0% (0/15), and median progression-free survival of 4.0 vs 2.0 mo and overall survival of 14.7 vs 14.3 mo, respectively (PMID: 35091442; NCT01874665). | 35091442 |
| KIT exon11 | 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 11 (n=17), exon 9 (n=8), or other mutations (PMID: 38662455). | 38662455 |
| 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 | Guideline | Actionable | Gleevec (imatinib) is included in guidelines for gastrointestinal stromal tumor (GIST) patients harboring sensitizing mutations, such as KIT exon 11 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 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 | 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 | melanoma | sensitive | Regorafenib | Phase II | 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 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 | 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 | Sunitinib | Clinical Study - Cohort | Actionable | In a retrospective analysis, Sutent (sunitinib) treatment demonstrated efficacy in gastrointestinal stromal tumor (GIST) patients harboring KIT mutations previously treated with Gleevec (imatinib), and resulted in an objective response rate (ORR) of 6% (9/143) and median progression-free survival (mPFS) of 7.0 months in patients with KIT exon 11 mutations, and ORR of 19% (8/42) and mPFS of 12.3 months in patients with KIT exon 9 mutations (PMID: 26772734; NCT01459757). | 26772734 |
| KIT exon11 | 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 11 mutations (PMID: 34560242; ESMO.org). | 34560242 detail... |
| 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 + 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 | 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 | not predictive | Pembrolizumab | Clinical Study | Actionable | In a retrospective analysis, real-world treatment with either Keytruda (pembrolizumab) or Toripalimab (JS001) resulted in a median disease-free survival of 33 months in melanoma patients harboring KIT mutations in either exon 11 (64.8%), exon 13 (17.6%), or exon 17 (17.6%) compared to 32 months in patients with wild-type BRAF, NRAS, and KIT (p=0.200) (PMID: 37403699). | 37403699 |
| KIT exon11 | melanoma | not predictive | Toripalimab-tpzi | Clinical Study | Actionable | In a retrospective analysis, real-world treatment with either Keytruda (pembrolizumab) or Loqtorz (toripalimab-tpzi) resulted in a median disease-free survival of 33 months in melanoma patients harboring KIT mutations in either exon 11 (64.8%), exon 13 (17.6%), or exon 17 (17.6%) compared to 32 months in patients with wild-type BRAF, NRAS, and KIT (p=0.200) (PMID: 37403699). | 37403699 |
| 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 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... |
| 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 | 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 | 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 |