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Background: X-linked myotubular myopathy (XLMTM) is a rare congenital myopathy resulting from dysfunction of the protein myotubularin encoded by the MTM1 gene. XLMTM has a high neonatal and infantile mortality rate due to a severe myopathic phenotype and respiratory failure. However, in a minority of XLMTM cases, patients present with milder phenotypes and achieve ambulation and adulthood. Notable facial dysmorphia is also present., Methods: We investigated the genotype-phenotype correlations in newly diagnosed XLMTM patients in a patients' cohort (previously published data plus three novel variants, n = 414). Based on the facial gestalt difference between XLMTM patients and unaffected controls, we investigated the use of the Face2Gene application., Results: Significant associations between severe phenotype and truncating variants ( p < 0.001), frameshift variants ( p < 0.001), nonsense variants ( p = 0.006), and in/del variants ( p = 0.036) were present. Missense variants were significantly associated with the mild and moderate phenotype ( p < 0.001). The Face2Gene application showed a significant difference between XLMTM patients and unaffected controls ( p = 0.001)., Conclusions: Using genotype-phenotype correlations could predict the disease course in most XLMTM patients, but still with limitations. The Face2Gene application seems to be a practical, non-invasive diagnostic approach in XLMTM using the correct algorithm.