Pathogenic heterozygous TRPM7 variants and hypomagnesemia with developmental delay

Abstract

Background: Heterozygous variants in Transient receptor potential melastatin type 7 (TRPM7), encoding an essential and ubiquitously expressed cation channel, may cause hypomagnesemia, but current evidence is insufficient to draw definite conclusions and it is unclear whether any other phenotypes can occur.

Methods: Individuals with unexplained hypomagnesemia underwent whole-exome sequencing which identified TRPM7 variants. Pathogenicity of the identified variants was assessed by combining phenotypic, functional and in silico analyses.

Results: We report three new heterozygous missense variants in TRPM7 (p.Met1000Thr, p.Gly1046Arg, p.Leu1081Arg) in individuals with hypomagnesemia. Strikingly, autism spectrum disorder and developmental delay, mainly affecting speech and motor skills, was observed in all three individuals, while two out of three also presented with seizures. The three variants are predicted to be severely damaging by in silico prediction tools and structural modeling. Furthermore, these variants result in a clear loss-of-function of TRPM7-mediated magnesium uptake in vitro, while not affecting TRPM7 expression or insertion into the plasma membrane.

Conclusions: This study provides additional evidence for the association between heterozygous TRPM7 variants and hypomagnesemia and adds developmental delay to the phenotypic spectrum of TRPM7-related disorders. Considering that the TRPM7 gene is relatively tolerant to loss-of-function variants, future research should aim to unravel by what mechanisms specific heterozygous TRPM7 variants can cause disease.

Keywords: TRPM7; autism spectrum disorder; developmental delay; genetics; hypomagnesemia.

Graphical Abstract

Figure 1:

Effects of TRPM7-p.Met1000Thr, p.Gly1046Arg and p.Leu1081Arg on Mg²⁺ uptake and cell membrane expression. (A) ²⁵Mg²⁺ uptake after 15 min in cells transfected with mock, WT or variant TRPM7. (B) Quantification of cell surface biotinylation assay for HEK293 cells transfected with WT or variant TRPM7. (C) Representative western blot of cell surface biotinylation assay. (D) ²⁵Mg²⁺ uptake after 15 min in cells co-transfected with WT TRPM7 with either mock or variant. Data points represent three independent experiments. Data are presented as mean ± standard error of the mean. *P < .05; **P < .01.

Figure 2:

Visualization of TRPM7-p.Met1000Thr, p.Gly1046Arg and p.Leu1081Arg in the TRPM7 protein structure. (A) Alignment of the TRPM7 amino acid sequence of different species for the affected residues and surrounding region. Dr, Danio rerio; Gg, Gallus gallus; Hs, Homo sapiens; Mm, Mus musculus; Rn, Rattus norvegicus. (B) Position of the variants in the complete apo state TRPM7 tetramer structure. One subunit (gray) is shown as ribbon diagram, while the other three are shown as Cryo-EM density maps. (C) Zoom-in of the Gly1046 vicinity, showing the Gly1046Arg substitution blocking the pore and the Leu1081Arg substitution affecting the S6 helix just below the pore-forming region. (D) Zoom-in of the Met1000 vicinity, showing the position of this residue in the bend between the S4-S5 linker and the S5 helix. WT residues are shown in gray, variant residues in red. Unaffected subunits of the tetramer are shown in light green, dark green and blue.