Widening the infantile hypotonia with psychomotor retardation and characteristic Facies-1 Syndrome's clinical and molecular spectrum through NALCN in-silico structural analysis

Abstract

Introduction: Infantile hypotonia with psychomotor retardation and characteristic facies-1 (IHPRF1, MIM#615419) is a rare, birth onset, autosomal recessive disorder caused by homozygous or compound heterozygous truncating variants in NALCN gene (MIM#611549) resulting in a loss-of-function effect.

Methods: We enrolled a new IHPRF1 patients' cohort in the framework of an international multicentric collaboration study. Using specialized in silico pathogenicity predictors and ad hoc structural analyses, we assessed the mechanistic consequences of the deleterious variants retrieved on NALCN structure and function.

Results: To date 38 different NALCN variants have been retrieved from 33 different families, 26 from unrelated and 22 from related patients. We report on five new IHPRF1 patients from four different families, harboring four newly identified and one previously retrieved variant that exhibited a markedly significant functional impact, thereby compromising the functionality of the protein complex.

Discussion: By widening the functional spectrum of biallelic variants affecting the NALCN gene, this article broadens the IHPRF1 syndrome's genotype-phenotype correlation and gives new insight into its pathogenic mechanism, diagnosis, and clinical management.

Keywords: CLIFAHDD; IHPRF1; NALCN; channelosome complex; genotype-phenotype correlation; rhythmic behaviors; structural biology.

FIGURE 1

Heatmap of main clinical features frequencies of present cohort compared to literature. On the right, the colored scale depicts patients’ features frequency; from absence and/or very low frequency: light green to very high frequency: deep green. On the left, features retrieved in the whole cohort reported per HPO codes.

FIGURE 2

Pictures of two patients from the present cohort. From (A–D), pictures of patient 1 (from 9 months of age to 2 years and 7 months). (A, B) pictures depict severe emaciation of the patient and hypotonia whereas before neurosurgery. Pictures (C, D) show patient 1’s clinical improvement and weight gain after surgery. (E, F) (respectively taken at 18 months and 2 years and 7 months of age) depict the patient 1’s dysmorphic features: triangular face, high forehead, large ears, and mild convergent strabismus. (G, H) show patient 4 facial gestalt: triangular face, broad forehead, bitemporal narrowing and the presence of NG tube for enteral feeding.

FIGURE 3

IHPRF1-associated LoF known variants along the NALCN protein. (top) known NALCN variants colored by protein effect (five splicing variants not included). The protein is made up of four homologous domains: DI (blue, 36–331), DII (green, 384–604), DIII (yellow, 887–1163), DIV (orange, 1209–1457), each with six transmembrane segments. Red arrows indicate variants retrieved in the present study.

FIGURE 4

Brain MRI pre and post-surgery in patient 1 of present cohort. (A) Brain MRI pre surgery. (B) Brain MRI post-surgery. Red arrow shows the cystic lesion.

FIGURE 5

3D structure of the NALCN protein. (A) Functional domains: ion transport domain and the selectivity filter highlighted in cyan and yellow, respectively. Focus on the breakage of a disulphide bond. (B) Each box shows the impact of a different variant on the protein structure. In particular, the portions of the native protein that are lost due to the frameshift, nonsense, and splicing (the two putative consequences) variants are shown.