Detailed Analysis of ITPR1 Missense Variants Guides Diagnostics and Therapeutic Design

Genomics England Research Consortium

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish
Pages (from-to)141-151
Number of pages11
JournalMovement Disorders
Volume39
Issue number1
DOIs
StatePublished - Jan 2024

Funding

FundersFunder number
Adelaide Health Foundation Ireland
Autistica UK
Cambridge South RECGEN/284/12
Health Innovation Challenge FundHICF‐1009‐003
John Fell Oxford University Press Research Fund
National Health Service
Nuffield Department of Clinical Neurosciences
Research Council of Finland356676
UKRI‐BBSRC
UKRI‐MRC
Wellcome Sanger InstituteWT098051
Wellcome Trust223521/Z/21/Z
Heart of England NHS Foundation Trust
Medical Research CouncilMR/V007068/1
National Institute for Health and Care ResearchWT223718/Z/21/Z
Department of Health and Social Care
Cancer Research UK
Action Medical ResearchGN2063
Alzheimer's Society
Ataxia UK
Henry Smith Charity
Alzheimer’s Research UK
John Fell Fund, University of Oxford
Lastentautien Tutkimussäätiö331436
Sigrid Juséliuksen Säätiö
Orionin Tutkimussäätiö
Horizon 2020101023312
Stiftelsen Alma och K. A. Snellman Säätiö
NIHR Oxford Biomedical Research Centre

    Keywords

    • Gillespie syndrome
    • IPR1
    • ITPR1
    • cerebellum
    • next-generation sequencing
    • spinocerebellar ataxia type 29

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