Detailed Analysis of ITPR1 Missense Variants Guides Diagnostics and Therapeutic Design

• Published in: Movement disorders Vol. 39; no. 1; pp. 141 - 151
• Main Authors: Tolonen, Jussi Pekka, Parolin Schnekenberg, Ricardo, McGowan, Simon, Sims, David, McEntagart, Meriel, Elmslie, Frances, Shears, Debbie, Stewart, Helen, Tofaris, George K., Dabir, Tabib, Morrison, Patrick J., Johnson, Diana, Hadjivassiliou, Marios, Ellard, Sian, Shaw‐Smith, Charles, Znaczko, Anna, Dixit, Abhijit, Suri, Mohnish, Sarkar, Ajoy, Harrison, Rachel E., Jones, Gabriela, Houlden, Henry, Ceravolo, Giorgia, Jarvis, Joanna, Williams, Jonathan, Shanks, Morag E., Clouston, Penny, Rankin, Julia, Blumkin, Lubov, Lerman‐Sagie, Tally, Ponger, Penina, Raskin, Salmo, Granath, Katariina, Uusimaa, Johanna, Conti, Hector, McCann, Emma, Joss, Shelagh, Blakes, Alexander J.M., Metcalfe, Kay, Kingston, Helen, Bertoli, Marta, Kneen, Rachel, Lynch, Sally Ann, Martínez Albaladejo, Inmaculada, Moore, Austen Peter, Jones, Wendy D., Becker, Esther B.E., Németh, Andrea H.
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01-01-2024; Wiley Subscription Services, Inc
• Subjects: Alternative splicing; Aniridia; Atrophy; Calcium (intracellular); Calcium signalling; Carbonic Anhydrases - genetics; Carbonic Anhydrases - metabolism; Cerebellar Ataxia - genetics; Cerebellum; Developmental disabilities; Genomes; Genotypes; Gillespie syndrome; Humans; Hypoplasia; Inositol 1,4,5-Trisphosphate Receptors - chemistry; Inositol 1,4,5-Trisphosphate Receptors - genetics; Inositol 1,4,5-Trisphosphate Receptors - metabolism; Inositol trisphosphate; Intellectual Disability; Intracellular Signaling Peptides and Proteins - genetics; Intracellular signalling; IP3R1; ITPR1; Movement disorders; Movement Disorders - complications; Mutation, Missense - genetics; next‐generation sequencing; Phenotypes; spinocerebellar ataxia type 29; Spinocerebellar Degenerations; ITPR1; IP3R1; spinocerebellar ataxia type 29; next-generation sequencing; cerebellum; Gillespie syndrome
• ISSN: 0885-3185; 1531-8257
• DOI: 10.1002/mds.29651

Background
The ITPR1 gene encodes the inositol 1,4,5‐trisphosphate (IP3) receptor type 1 (IP3R1), 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.