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Background  Tumor genotype plays a crucial role in clinical management of GIST. Whether genetic polymorphism of  KIT  may influence GIST patient outcome is unclear.    Methods  We investigated the biological and clinical significance of the presence of  KIT  exon 10 variant (c.1621 A &gt; C),  KIT   L541  , in a transfected cell line (3 T3 L541) and in two retrospectively collected series of 109 GIST patients in total. The control group consisted of 60 healthy donors collected at the French department of blood transfusion.    Results  In the 3 T3 L541 cell line, KIT L541  protein exhibited a spontaneous phosphorylation status comparable to that of wild-type KIT but displayed a phosphorylation pattern of AKT and ERK1/2 that was found similar to that of the classical mutated forms of the KIT receptor. Of 109 patients enrolled in this retrospective translational research study, 24 (22 %) harboured  KIT   L541  , similarly to the control group of healthy donors ( n  = 10 of 60, 17 %). A higher prevalence of the variant  KIT   L541   was observed in patients with metastatic status at diagnosis ( KIT   L541   correlated nine of 22 versus 15 of 87,  p  = 0.02). In addition, patients with  KIT   L541   and localized GIST had a higher rate of relapse at 5 years and lower relapse free survival at 5 years in univariate, as well as in multivariate analysis. Response rate and duration of response to imatinib was similar in  KIT   L541   and  KIT   M541   patients.    Conclusion   KIT   L541   genotype is associated with a higher risk of metastasis at diagnosis and a higher risk of relapse in GIST patients.    Electronic supplementary material  The online version of this article (doi:10.1186/s12885-015-1817-5) contains supplementary material, which is available to authorized users.

KIT exon 10 variant (c.1621 A > C) single nucleotide polymorphism as predictor of GIST patient outcome