Discovery of a de novo ITPR1 missense mutation in a patient with early-onset cerebellar ataxia: A rare case report of spinocerebellar ataxia 29

Abstract

Background

Spinocerebellar ataxia 29 (SCA29) is a rare genetic disorder characterized by early-onset ataxia, gross motor delay, and infantile hypotonia, and is primarily associated with variants in the ITPR1 gene. Cases of SCA29 in Asia are rarely reported, limiting our understanding of this disease.

Methods

A female Korean infant, demonstrating clinical features of SCA29, underwent evaluation and rehabilitation at our outpatient clinic from the age of 3 months to the current age of 4 years. Trio-based genome sequencing tests were performed on the patient and her biological parents.

Results

The infant initially presented with macrocephaly, hypotonia, and nystagmus, with nonspecific findings on initial neuroimaging. Subsequent follow-up revealed gross motor delay, early onset ataxia, strabismus, and cognitive impairment. Further neuroimaging revealed atrophy of the cerebellum and vermis, and genetic analysis revealed a de novo pathogenic heterozygous c.800C>T, p.Thr267Met missense mutation in the ITPR1 gene (NM_001378452.1).

Conclusion

This is the first reported case of SCA29 in a Korean patient, expanding the genetic and phenotypic spectrum of ITPR1-related ataxias. Our case highlights the importance of recognizing early-onset ataxic symptoms, central hypotonia, and gross motor delays with poor ocular fixation, cognitive deficits, and isolated cerebellar atrophy as crucial clinical indicators of SCA29.

INTRODUCTION

Spinocerebellar ataxias (SCAs) are autosomal dominant neurogenetic disorders with varying heterogeneous clinical presentations, including cerebellar ataxia with diverse extracerebellar manifestations. The predominant SCA type in Korea is SCA2, followed by SCA6 and SCA3 (Kim et al., 2011; Kim & Cho, 2015; Lee et al., 2003). SCA29 (MIM #117360), a rare subtype, remains poorly understood owing to its limited occurrence and unique genetic basis. SCA29 is a rare congenital disorder characterized by gross motor delay, infantile hypotonia, nonprogressive early-onset ataxia, and mild cognitive impairment (Huang et al., 2012; Sasaki et al., 2015; Zambonin et al., 2017). Inositol 1,4,5-trisphosphate receptor, type 1, (ITPR1) gene (MIM #147265) which encodes the 1,4,5-trisphosphate receptor Type 1 (IP3R1) protein, regulates calcium release from the endoplasmic reticulum and is densely expressed in the Purkinje cells of the cerebellum, making it vital for motor coordination. Mutations in ITPR1 result in the loss of IP3R1 channel function and disrupt calcium release, leading to cerebellar degeneration and the characteristic symptoms of SCA29 (Synofzik et al., 2018). Cases of SCA29 in Asia are rarely reported compared to other SCA subtypes (Kim et al., 2011; van Prooije et al., 2021) and such patients with ITPR1 mutations have not been previously reported in Korea.

Here, we present the first case report of a 3-month-old girl diagnosed with SCA29 in Korea and describe the clinical characteristics and identification of a novel de novo ITPR1 missense variant. By comparing our clinical findings with previous reports, we aim to elucidate the genotype–phenotype association of ITPR1-related diseases and add to the expanding phenotype of variations in the ITPR1 gene.

METHODS

Trio-based genome sequencing (GS) tests were performed. Total genomic DNA was derived from samples of blood, and TruSeq DNA PCR-Free (Illumina, San Diego, CA, USA) was used to prepare the genomic libraries which were then sequenced on the NovaSeq6000 system (Illumina). Alignment of the data to the human reference GRCh38 (hg38) sequence was performed using Burrows–Wheeler Aligner software (version 0.7.15-r1140) (Li & Durbin, 2009), and post-processing was performed using Samtools. Variants were classified based on the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines (Richards et al., 2015). Informed consent was obtained from the biological parents of the patient and the study was approved by the ethics committee of Chungnam National University Hospital.

RESULTS Clinical presentation

A 3-month-old female patient was referred to our rehabilitation outpatient clinic with symptoms of nystagmus, right head-tilt torticollis, and hypotonia. She was delivered at 39 weeks and 6 days of gestation, with a birth weight of 2.78 kg and had no significant perinatal history. At the age of 2 months, the child underwent a brain magnetic resonance imaging (MRI) due to macrocephaly, but no specific abnormal findings were discovered. She was unable to elevate her head at prone positioning and exhibited weak head-righting reactions along with a decreased cervical extension during the Landau reaction. Ophthalmologic examination revealed opsoclonus and nystagmus, but normal optic nerve and disc function. The initial evaluation suggested opsoclonus-myoclonus-ataxia syndrome and the parents elected to have the patient practice trunk tone-building exercises at home.

At the age of 6 months, the patient began displaying ataxic trunk movements. Wandering eye movements were ophthalmologically interpreted as intermittent conjugated ocular bobbing which was indicative of central brain dysfunction. At 11 months, the opsoclonus spontaneously improved but was replaced by strabismus and delayed visual maturation. By 15 months old, she could not control her trunk, so the patient could not attain a sitting posture. Conversely, notable advancement in fine motor development was observed, demonstrated by the acquisition of successful object transfer and purposeful pincer grasping by 14 months. At 15 months, Bayley Scales of Infant and Toddler Development (BSID) assessments showed delayed motor development equivalent to the 1 percentile (gross motor equivalent to 7 months) (Table 1). Consequently, physical therapies were initiated for motor delays. Ataxic movements, coupled with failures in crawling, sitting, and standing, persisted until 24 months of age. At 30 months, follow-up BSID assessment indicated motor function at the 0.5 percentile (gross motor equivalent to 7 months) (Table 1). The Functional Independence Measure for Children (WeeFIM) yielded a cumulative score of 23 points and cognition was evaluated to be at the 1 percentile (equivalent to 17 months), strongly indicating cognitive impairment.

TABLE 1 Evaluation of Bayley Scales of Infant and Toddler Development (BSID) 15 months and 30 months revealing a notable delay in gross motor development.

BSID	Percentile at 15 months (equivalent age)	Percentile at 30 months (equivalent age)
Cognitive	2 (10 months)	1 (17 months)
Language	13 (11 months)	1 (13–14 months)
Motor	1 (gross—7 months/fine—12 months)	0.5 (gross—7 months/fine—21 months)
Social–emotional	37 (n/a)a	2 (n/a)
Adaptive behavior	4 (n/a)	0.2 (n/a)

Abbreviation: BSID, Bayley Scales of Infant and Toddler Development.

^aAge-equivalent predictions are not available for the social–emotional and adaptive behavior categories in BSID evaluations.

The Sequenced Language Scale for Infant tests at 31 months of age revealed both expressive and receptive communication at the 1 percentile, equivalent to 16 and 10 months, respectively. At age 4, the patient continued to struggle with standing and could not walk independently concurrently exhibiting deficits in balance. Gait training employing posterior walkers and a bilateral hinged-type ankle-foot orthosis resulted in a pronounced ataxic gait characterized by a wide-based gait and overshooting of both legs. Although the patient could use Edison chopsticks (utensils designed for individuals with disabilities to facilitate easier use), both hands showed dysmetric movements and mild tremors.

The initial brain MRI conducted at 2 months revealed a nonspecific brain shape and parenchyma. However, a follow-up brain MRI at 30 months revealed distinct isolated cerebellar atrophy, with notable effects on the superior cerebellum and vermis, consistent with previous reports on SCA29 (Ngo et al., 2019; Romaniello et al., 2022; Tada et al., 2016). At 4 years of age, brain MRI confirmed the persistence of cerebellar atrophy especially in the superior cerebellum and vermis (Figure 1).

FIGURE 1. Comparison of brain magnetic resonance imaging (MRI) images showing cerebellar vermis atrophy at 30 months (b) and 4 years (c) that was not observed at 2 months (a).

Genetic analysis

The initial manifestations of infantile hypotonia prompted the genetic investigations including the spinal muscular atrophy (SMN1) gene deletion, Prader–Willi methylation PCR and chromosomal microarray, but the results of all tests were negative.

GS analysis revealed a de novo heterozygous missense mutation in the ITPR1 (NM_001378452.1:c.800C>T; p.Thr267Met) gene. This variant was classified as pathogenic using the following ACMG-AMP criteria: PP5, PS2, PP3, PM1, PM2, and PM5 (Richards et al., 2015). While this single nucleotide variant mutation had been previously documented within the ClinVar database, it has not been reported in the gnomAD v2.1, 1000genome&GINSVPON V1.0 public databases of human variation and is the first report in the Korean literature. The ITPR1 c.800C>T mutation was absent in both parents, confirming the de novo nature of the variant.

DISCUSSION

This case report contributes to our understanding of SCA29, a rare genetic disorder with a complex clinical presentation, and offers valuable insights into the clinical features and genetic basis of SCA29. Previous reports have noted substantial clinical heterogeneity among patients with SCA29 (Zambonin et al., 2017). The characteristic presentation of infantile hypotonia, gross motor delay, and early onset ataxia, coupled with ophthalmological abnormalities, raised suspicion of a neurogenetic disorder. This case is among the rare instances wherein a patient initially presenting with macrocephaly and torticollis manifested hypotonia and motor delays as early as 2–3 months of age, with the underlying cause attributed to the development of ocular manifestations indicative of a central disorder. Furthermore, cognitive and language impairments were evident, and neuroimaging revealed isolated atrophy of the superior cerebellum and vermis at 30 months of age that was not observed at 2 months. Genetic analysis revealed a de novo missense mutation in the ITPR1 gene (c.800C>T; p.Thr267Met). The patient exhibited a non-progressive clinical course, with slight but delayed improvements in motor function but remained unable to ambulate independently at 4 years of age. This report provides evidence of an association between pathogenic missense variant in ITPR1 and SCA29, further expanding the phenotypic spectrum associated with variations in this gene.

The current literature on the clinical characteristics of SCA is limited, including for past cases of congenital non-progressive ataxia without a diagnosed mutation in the ITPR1 gene (Steinlin et al., 1998). Previous cases of SCA29 caused by de novo heterozygous mutations in the c.800C>T (p.Thr267Met) locus (Table 2) (Ngo et al., 2019; Sasaki et al., 2015; Synofzik et al., 2018; Zambonin et al., 2017) have shown that the phenotype can be rather diverse. One case report described a patient, who had dysarthria at 6 months, was able to stand with support at 2 years, but remained unable to walk for 6 years in addition to mild intellectual deficits (Sasaki et al., 2015). Brain MRI showed pronounced atrophy in the superior cerebellum and anterior vermis consistent with our findings, as well as progressive atrophy of the pontine tegmentum. Another study reported a case of two siblings presenting with early onset-nonprogressive ataxia (Ngo et al., 2019). The elder sibling first achieved a crutches gait at 7 years and had an IQ of 54 at the school age, whereas the younger sibling attained a crutches gait by 3.5 years and had an IQ of 73 at the school age. Most cases of the c.800C>T (p.Thr267Met) variant have been found to be sporadic; however, an exome sequencing test in this family detected low levels of the variant in the unaffected mother (2/242 reads), suggesting that she was a germline mosaic for the variant (Ngo et al., 2019).

TABLE 2 Summary of clinical and genetic features of patients with ITPR1 variants causing SCA29.

Patient	Variant	Inheritance	Age at onset	Neurologic	Motor function	Ocular	MRI findings	Intellectual disability
Sasaki et al. (2015): patient 1	c.800C>T (p.Thr267Met)	De novo missense	6 months	Ataxia, postural tremor, slurred speech, general hypotonia	Sitting (1 year 6 months), Standing (2 years), Unable to walk at 6 years	Gaze evoked nystagmus	Superior cerebellum, vermis, pontine tegmentum atrophy (slowly progressive)	Mildly delayed, three-word sentences
Ngo et al. (2019): patient 1	c.800C>T (p.Thr267Met)	Missense, Mother germline mosaic	<1 year	Limb and gait ataxia, dysarthria, mild tremor	Crutches ambulation (7 years)	Strabismus, nystagmus, hyper/hypometric saccades	Cerebellar atrophy	First word at 5.5 years
Synofzik et al. (2018): patient 3	c.800C>T (p.Thr267Met)	De novo missense	<2 years	Infantile ataxia	N/A	N/A	N/A	N/A
Huang et al. (2012): patient C	c.1804A>G (p.Asn602Asp)	Missense, Autosomal dominant	8 months	Complex partial seizures Hypotonia, Truncal titubation, appendicular dysmetria	Sitting (6 months)	Gaze evoked nystagmus	Vermis atrophy (progressive)	10 words, 10 signs at 8 months
Das et al. (2017): patient A	c.805C>T (p.Arg269Trp)	Missense, Autosomal dominant	<1 year	Myoclonic jerks, myokymia, hypotonia, wide-based gait	Crawling (3 years), wheelchair bound	N/A	Superior vermis, superior cerebellar atrophy	Mild intellectual disability
Van Dijk et al. (2017)	c.7649T>A (p.Ile2550Asn)	De novo missense	6 months	Truncal titubation, limb ataxia	Poor head control (6 months), Sitting (4 years)	Alternating strabismus	Pontine, cerebellar hypoplasia (no progression)	Speak single words (6 years)
Dudding et al. (2004): patient III-6	c.4657G>A (p.Val1553Met)	Missense, Autosomal dominant inheritance	<6 months	Wide-based ataxic gait, intention tremor, dysarthria, poor balance	Walk unsupported (18 months)	Normal	Cerebellar vermis atrophy	Mild intellectual disability, learning problems
Casey et al. (2017): patient III-1	c.106C>T (p.Arg36Cys)	De novo missense, Autosomal dominant	1 year	High stepping, wide-based gait, dysarthria, dysmorphic epicanthic folds, hypoplastic teeth	Sitting (12 months), Crawling (15 months), Walking (24 months), midline truncal ataxia (4.8 years), fine motor delay	Normal	No cerebellar atrophy	Speech, language delay
Parolin Schnekenberg et al. (2015): patient 2	c.1759A>G (p. Asn602Asp)	De novo missense	6 months	Abnormal head nodding, Hypotonia, ataxia, microcephaly	Delayed head control (6 months), Standing but unable to walk (3 years)	Rotatory nystagmus	Normal brain MRI	Use 15 words at 3 years
Klar et al. (2017): patient V:1	c.5360T>C (p.Leu1787Pro)	Missense, Autosomal recessive	At birth	Hyperreflexia, ataxia, clonus, quadrupedal gait, dysarthria, dysmetria	Unable to walk (23 years), ataxia present as soon as sitting	Normal	Cerebellar atrophy, mostly vermis, sparing of brainstem	Mild intellectual disability
Wang et al. (2018): patient III:3	c.1207-2A>T	Splicing mutation, Autosomal dominant	<1 year	Truncal, limb ataxia, dysarthria, hyporeflexia, action, postural tremor	Wide-based gait (6 years)	Horizontal gaze evoked nystagmus	Vermis atrophy without cerebellum atrophy	Mild cognitive deficit, speaking at 4 years, primary school dropout d/t learning difficulties
Parolin Schnekenberg et al. (2015): patient 3	c.4459_4460delinsGA (p.Ser1487Asp)	Deletion–insertion, Missense change	<1 year	Ataxia, action tremor, postural instability	Sitting (12 months), Crawl (14 months), Few step walking (2.4 years), Unassisted gait (4 years)	Normal	Normal brain MRI	Moderate intellectual disability, speak in simple sentences
Sasaki et al. (2015): patient 3	c.1781C>T (p.Thr594Ile)	De novo missense	At birth	General hypotonia, ataxia, postural tremor (head, arms, trunk)	Head control (3 months), Sitting (2.6 years), unstable walking (12 years)	Oculomotor apraxia, Vertical nystagmus	Diffuse cortical cerebellar atrophy, pontine tegmentum atrophy (progressive)	Moderate delayed intellectual disability, two-word sentences
This study	c.800C>T (p.Thr267Met)	De novo missense	3 months	Macrocephaly, torticollis, hypotonia, truncal and limb ataxia, dysmetria, mild tremors	Rolling (15 months), Sitting (30 months), Standing (Posterior walker gait (4 years)	Opsoclonus, nystagmus, strabismus, delayed visual maturation	Superior cerebellum, vermis atrophy	Severe cognitive impairment, expressive/receptive language deficits

Abbreviation: N/A, information not available.

Reports of SCA29 associated with alternative ITPR1 variants have been documented (Table 2), facilitating phenotypic comparisons. Although most are missense mutations, the phenotypic variability is diverse (Table 2). One study reported a case of a missense mutation (c.7649T>A; p.I2550N) in the transmembrane domain of the ITPR1 gene, where brain MRI revealed profound hypoplasia of not only the cerebellum but also the pons (van Dijk et al., 2017). Another study reported two patients with an identical missense mutation (c.805C>T; (p.R269W)) but different phenotypes, with one showing mild ataxia, mild cognitive deficits, and vermis atrophy, while the other showed severe ataxia and cognitive disability, but no cerebellar atrophy (Synofzik et al., 2018). In another study, unrelated individuals carrying identical mutations were found to exhibit diverse manifestations of cerebellar dysfunction (Zambonin et al., 2017). One study concluded that the characteristic pattern of superior cerebellar hemispheres and vermis atrophy was present in approximately 83% of patients with mutated ITPR1, suggesting that these MRI findings (with a normal supratentorial brain and cortex) with the clinical features of pediatric ataxia are strong indicators of ITPR1-related disorders and necessitate genetic testing (Romaniello et al., 2022).

ITPR1 encodes IP3R1, a ligand-gated Ca²⁺ channel located within the endoplasmic reticulum. This receptor is prominently expressed within cerebellar Purkinje cells and plays a pivotal role in regulating the intracellular calcium concentration in the endoplasmic reticulum. The IP3R1 protein comprises three main structural domains: an inositol trisphosphate (IP3)-binding domain at the N-terminus, a transmembrane domain at the C-terminus, and a coupling-regulatory region in between. IP3 binding modulates ion channels, facilitating the efflux of calcium ions from the endoplasmic reticulum into the cytoplasm, thereby inducing complex calcium signaling (Foskett, 2010). Previous cases of missense mutations associated with SCA29 have been localized within the coupling-regulatory domain and the binding domain of carbonic anhydrase-related protein VIII (CA8) and inositol trisphosphate receptor-binding protein (IRBIT), which are competitive inhibitors of IP3 (Tada et al., 2016). Normally, IRBIT causes reduced calcium release and mRNA synthesis regulation upon receptor binding (Barresi et al., 2017). However, mutations in the IRBIT-binding domain are hypothesized to decrease the binding of IRBIT to IP3R1 while enhancing the affinity of IP3 to IP3R1, thus inducing dysregulation and exaggeration of calcium channel function (Huang et al., 2012). Mutations in the IRBIT domain have been reported as a cause of nonprogressive congenital ataxia (Barresi et al., 2017). Likewise, threonine at position 267 is located in the IRBIT-binding domain, with the p.Thr267Met variant identified in this study recognized as one constituent of a rare cluster of missense mutations in the ITPR1 gene, indicating its potential as a mutational hotspot (Geisheker et al., 2017; Ngo et al., 2019). Furthermore, other mutations identified in the IP3-binding domain (c.805C>G (p.R269G), c.835A>G (p.K279E), c.830G>T (p.S277I)) and transmembrane domain (c.7516G>A (p.G2506R), c.7649T>C (p.I2550T)) have been reported in patients with SCA29 (Sasaki et al., 2015; Zambonin et al., 2017). One study reported markedly reduced fractional calcium release in vitro in HEK293 cells expressing a de novo ITPR1 variant (c.800C>T (p.T267M), c.805C>T (p.R269W), and c.1702A>G (p.R568G)) upon induction by IP3. This indicated that de novo ITPR1 variants produced a strong loss-of-function effect on IP3-induced calcium release, thus exerting a dominant-negative effect on IP3R1 protein function (Synofzik et al., 2018). Such mechanisms that disrupt intracellular calcium homeostasis and signaling are suggested to cause the dysfunction of Purkinje cells and the degeneration of selective neurons ultimately. However, detailed structural and expression studies are needed to elucidate the precise pathogenesis of this disease.

Notably, heterozygous deletions in the ITPR1 gene have been recognized to induce SCA15, characterized by slowly progressive ataxia emerging in adulthood. Most reported SCA15 cases present with a partial or complete deletion of ITPR1 (Tada et al., 2016) which cause reduced expression of the gene indicating that haploinsufficiency of ITPR1 and suppressed calcium signaling is the main mechanism of the disease (Müller, 2021). Conversely, ITPR1 mutations associated with SCA29 are in-frame and are anticipated to alter IP3R1 channel function by a dominant-negative effect, disrupting IP3R1 function or CA8- or IRBIT-mediated regulation of the IP3R1 channel hence reducing calcium release (Ando et al., 2018). This allelic correlation highlights the intrinsic significance of the ITPR1 pathway in sustaining cerebellar functionality. Most pathogenic variants reported in the literature are located within the IRBIT-binding domain, including many mutations linked to SCA29. Conversely, variations responsible for Gillespie syndrome, which is characterized by ataxia, intellectual disability, and bilateral aniridia, tend to occur predominantly at the C-terminus of the protein, particularly within the transmembrane domain (McEntagart et al., 2016; Synofzik et al., 2018). Given the overlapping clinical features of SCA29, SCA15, and Gillespie syndrome, conducting genetic testing for ITPR1 and gaining insights into the pathomechanism associated with the variant's location are essential to ensure an accurate differential diagnosis, enhance the understanding of disease pathophysiology, and determine patient prognosis.

Previous studies have reported delayed improvements in various domains such as motor function, speech, and coordination in individuals with SCA29 (Steinlin et al., 1998; Zambonin et al., 2017). Independent ambulation has been documented in individuals with SCA29 within the age range of 18 months to 12 years (Huang et al., 2012; Sasaki et al., 2015; Steinlin et al., 1998). Similarly, our patient exhibited mild improvements in motor developmental milestones at 4 years of age. Whether these improvements stem from early intervention or are a part of the natural progression of the condition remains unclear. Nonetheless, it is advisable to commence early physical, occupational, and speech-language therapies contingent upon an early diagnosis.

CONCLUSION

Here, we report the identification of a novel ITPR1 missense mutation in a Korean patient with SCA29 and expand the wide spectrum of ITPR1-related ataxias and their known genetic variants. Early onset ataxia, central hypotonia, delay in gross motor milestones, and isolated cerebellar atrophy with poor ocular fixation and cognitive impairment are crucial clinical indicators of this disease. Such features are valuable cues for conducting genetic analysis of the ITPR1 gene, facilitating early diagnosis, and developing therapeutic plans. Early physiotherapeutic interventions are essential to maximize potential improvements in ambulation and gross motor function in non-progressive congenital disorders such as SCA29. Further research on the pathogenic and molecular mechanisms of this disorder is necessary to develop targeted therapeutic approaches and improve patient outcomes.

AUTHOR CONTRIBUTIONS

Jae In Lee: Conceptualization, writing of the original draft, review, editing, and investigation. Ja Young Choi: Conceptualization, writing—review, editing. Shin-Seung Yang: Conceptualization, supervision, resources, writing—editing, review.

ACKNOWLEDGMENTS

This study was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF-2020M3E5D7085175) funded by the Ministry of Health and Welfare, Ministry of Science and ICT, Ministry of Trade Industry and Energy, Korea Disease Control and Prevention Agency (The National Project of Bio Big Data).

CONFLICT OF INTEREST STATEMENT

The authors declare no conflicts of interest.

DATA AVAILABILITY STATEMENT

The data supporting the findings of this study are available from the corresponding author upon reasonable request.

ETHICS STATEMENT

The study was approved by the ethics committee of Chungnam National University Hospital.

PATIENT CONSENT STATEMENT

The patient and family (legal guardians) provided their consent to participate.