The Gaussian kernel is one of the most important kernels, applicable to many research fields, including scientific computing and data science. In this paper, we present asymptotic analysis of the Gaussian kernel matrix in high dimension under a statistical model of noisy data. The main result is a nice combination of Karoui's asymptotic analysis with procedures of constrained low rank matrix approximations. More specifically, Karouli clarified an important asymptotic structure of the Gaussian kernel matrix, leading to strong consistency of the eigenvectors, though the eigenvalues are inconsistent. This paper focuses on the above results and presents a consistent estimator with the use of the smallest eigenvalue, whenever the target kernel matrix tends to low rank in the asymptotic regime. Importantly, asymptotic analysis is given under a statistical model representing partial noise. Although a naive estimator is inconsistent, applying an optimization method for low rank approximations with constraints, we overcome the difficulty caused by the inconsistency, resulting in a new estimator with strong consistency in rank deficient cases.