Detailed Analysis of ITPR1 Missense Variants Guides Diagnostics and Therapeutic Design

Abstract

Background: The ITPR1 gene encodes the inositol 1,4,5-trisphosphate (IP₃ ) receptor type 1 (IP₃ R1), a critical player in cerebellar intracellular calcium signaling. Pathogenic missense variants in ITPR1 cause congenital spinocerebellar ataxia type 29 (SCA29), Gillespie syndrome (GLSP), and severe pontine/cerebellar hypoplasia. The pathophysiological basis of the different phenotypes is poorly understood.

Objectives: We aimed to identify novel SCA29 and GLSP cases to define core phenotypes, describe the spectrum of missense variation across ITPR1, standardize the ITPR1 variant nomenclature, and investigate disease progression in relation to cerebellar atrophy.

Methods: Cases were identified using next-generation sequencing through the Deciphering Developmental Disorders study, the 100,000 Genomes project, and clinical collaborations. ITPR1 alternative splicing in the human cerebellum was investigated by quantitative polymerase chain reaction.

Results: We report the largest, multinational case series of 46 patients with 28 unique ITPR1 missense variants. Variants clustered in functional domains of the protein, especially in the N-terminal IP₃ -binding domain, the carbonic anhydrase 8 (CA8)-binding region, and the C-terminal transmembrane channel domain. Variants outside these domains were of questionable clinical significance. Standardized transcript annotation, based on our ITPR1 transcript expression data, greatly facilitated analysis. Genotype-phenotype associations were highly variable. Importantly, while cerebellar atrophy was common, cerebellar volume loss did not correlate with symptom progression.

Conclusions: This dataset represents the largest cohort of patients with ITPR1 missense variants, expanding the clinical spectrum of SCA29 and GLSP. Standardized transcript annotation is essential for future reporting. Our findings will aid in diagnostic interpretation in the clinic and guide selection of variants for preclinical studies. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Keywords: Gillespie syndrome; IP3R1; ITPR1; cerebellum; next-generation sequencing; spinocerebellar ataxia type 29.

FIG. 1

Pathogenic IP₃R1 missense variants cluster in three functional domains. The ITPR1 gene encodes a protein of 2758 residues with four functional domains (residues 1–223: suppressor [green], residues 226–578: IP₃‐binding [blue], residues 605–2217: regulatory [gray], residues 2227–2758: transmembrane channel [yellow]), and multiple interaction partners. Shown are previously published variants and variants identified as part of the present study, categorized as internal truncating (red square), frameshift (blue circle), missense (yellow circle), and in‐frame codon deletion (red circle), and grouped by diagnosis (SCA29/pontocerebellar hypoplasia [PCH], and GLSP). Homozygous variants are shown in red text, whereas novel variants are highlighted on a white background. Variants associated particularly with PCH are shown in blue text. Variants with published experimental validation are further denoted by a blue star. Each variant is listed with the known number of cases per variant indicating multiple mutational hotspots.

FIG. 2

Different functional clusters of IP₃R1 missense variants guide therapeutic design. (A) Loss‐of‐function (LOF) variants such as p.Thr267Met, p.Arg269Trp, and p.Arg568Gly are likely to require potentiators of IP₃R1 channel function to be targeted therapeutically. (B) Gain‐of‐function (GOF) variants p.Arg36Cys, p.Val1562Met, and p.Ser1502Asp interfere with different suppression mechanisms of the IP₃R1 channel potentially requiring IP₃R1 inhibitors as therapeutics. Polyglutamine‐expansion disorders (ie, SCA2, SCA3, Huntington's disease, and familial Alzheimer's disease) involving a dysregulated IP₃R1 channel may also respond to IP₃R1 inhibition. The figure shows the protein structure for the rat IP₃R1 (Protein Data Bank: 7LHF) and ataxin‐3 (light pink, Protein Data Bank: 3O65).