Clinical and Functional Characterization of Three Homozygous NTRK1 Variants and A Brief Comparison of the Literature

Abstract Background Loss-of-function variants in the NTRK1 gene, which encodes the NGF receptor TrkA, cause Hereditary Sensory and Autonomic Neuropathy IV (HSAN4/CIPA), a rare autosomal recessive disorder. Clinical heterogeneity among HSAN4/CIPA patients suggests that distinct variant types exert qualitatively different effects on TrkA structure and function. This study investigated the structural, functional, and clinical implications of three NTRK1 variants—p.His569Gln, p.Glu590Gln, and c.1177 + 2T > A—identified in five patients presenting with variable HSAN4/CIPA phenotypes. Methods Computational structural analyses, including rotamer scanning, DynaMUT2 stability predictions, and in silico splicing tools (MaxEntScan, SpliceAI), were employed to characterize each variant. Results The p.His569Gln, located within the kinase domain adjacent to the kinase insert domain (KID), increased TrkA stability (ΔΔG + 0.37 kcal·mol⁻¹), restricted conformational flexibility, and disrupted the αC-in arrangement and activation loop dynamics essential for NGF-induced signaling, consistent with a severe loss-of-function profile. p.Glu590Gln, situated at the ATP-binding hinge region, preserved backbone-mediated ATP contacts while subtly modulating local polarity and hydration through tolerable rotamer rearrangements, supporting a hypomorphic, partial loss-of-function effect concordant with a milder clinical presentation. The c.1177 + 2T > A splice donor variant disrupted the canonical GU dinucleotide at the + 2 position, predicted to near-completely abrogate normal splicing via exon skipping, cryptic donor activation, or intron retention, yielding a functionally null allele. Conclusion These findings indicate that the clinical severity of NTRK1 -associated pain insensitivity disorder is associated with the location of the mutation, its molecular consequences, and functional outcomes; this provides a mechanistic framework for the correlations observed in NTRK1 -associated pain insensitivity and contributes to the development of mutation-specific diagnostic and treatment strategies.