Novel biallelic variants expand the SLC5A6-related phenotypic spectrum

Abstract

The sodium (Na⁺):multivitamin transporter (SMVT), encoded by SLC5A6, belongs to the sodium:solute symporter family and is required for the Na⁺-dependent uptake of biotin (vitamin B7), pantothenic acid (vitamin B5), the vitamin-like substance α-lipoic acid, and iodide. Compound heterozygous SLC5A6 variants have been reported in individuals with variable multisystemic disorder, including failure to thrive, developmental delay, seizures, cerebral palsy, brain atrophy, gastrointestinal problems, immunodeficiency, and/or osteopenia. We expand the phenotypic spectrum associated with biallelic SLC5A6 variants affecting function by reporting five individuals from three families with motor neuropathies. We identified the homozygous variant c.1285 A > G [p.(Ser429Gly)] in three affected siblings and a simplex patient and the maternally inherited c.280 C > T [p.(Arg94*)] variant and the paternally inherited c.485 A > G [p.(Tyr162Cys)] variant in the simplex patient of the third family. Both missense variants were predicted to affect function by in silico tools. 3D homology modeling of the human SMVT revealed 13 transmembrane helices (TMs) and Tyr162 and Ser429 to be located at the cytoplasmic facing region of TM4 and within TM11, respectively. The SLC5A6 missense variants p.(Tyr162Cys) and p.(Ser429Gly) did not affect plasma membrane localization of the ectopically expressed multivitamin transporter suggesting reduced but not abolished function, such as lower catalytic activity. Targeted therapeutic intervention yielded clinical improvement in four of the five patients. Early molecular diagnosis by exome sequencing is essential for timely replacement therapy in affected individuals.

Fig. 1. Secondary structure and 3D model of SMVT and location of amino acid residues substituted in affected individuals.

a Predicted secondary structure of SMVT with 13 membrane spanning α-helices (numbered cylinders in rainbow color). Extra- and intracellular loops connecting the transmembrane α-helices (TMs) are visualized by lines. Dashed lines were used for helices and loops which could not be modeled (b). Amino acid residues affected by variants in patients are shown as gray dots (R in the intracellular cap of TM3: Arg123; Y in TM4: Tyr162; R in TM10: Arg400; S in TM11: Ser429). b 3D model of SMVT and its orientation in the membrane, generated with SWISS-MODEL based on the crystal structure of vSGLT (PDB ID: 3DH4) [15, 16]. The model includes residues 65 to 550 and omits TM1 and the large extracellular loop between TM12 and TM13 (dashed lines in a). The helices are rainbow-colored. The possible substrate localization is visualized by gray spheres. Arg123, Tyr162, Arg400, and Ser429 are colored in gray and represented as stick models. The insets show magnifications to highlight the location of each of the changed residues. The helix 8b is indicated in the inset in the upper left corner. Model modifications and creation of the image were done using UCSF chimera. c Partial amino acid sequence alignment of human SMVT (SLC5A6), vSGLT and human SGLT1 (SLC5A1). Full multiple sequence alignment is shown as Supplementary Fig. 4. TM11 is shown as a cylinder above the alignment. Ser429 and the corresponding residues in vSGLT and SGLT1 are highlighted in gray. Gln428, a residue involved in substrate binding in vSGLT [15, 26], is highlighted in yellow.

Fig. 2. Subcellular localization of ectopically expressed SMVT wildtype and mutants.

HeLa cells were transiently transfected with SLC5A6-EGFP expression constructs as indicated or the pEGFP-N3 empty vector, cultivated for 48 h, fixed, and embedded in mounting solution. Images were acquired with a confocal microscope. Representative images of three independent experiments are shown. Scale bar, 10 µm.