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Original article
Spinocerebellar ataxia type 15: diagnostic assessment, frequency, and phenotypic features
  1. Matthis Synofzik1,2,
  2. Christian Beetz3,
  3. Claudia Bauer4,
  4. Michael Bonin4,
  5. Elena Sanchez-Ferrero3,
  6. Tanja Schmitz-Hübsch5,
  7. Ullrich Wüllner5,
  8. Thomas Nägele6,
  9. Olaf Riess4,
  10. Ludger Schöls1,2,
  11. Peter Bauer4
  1. 1Department of Neurology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
  2. 2German Centre of Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany
  3. 3Institute of Clinical Chemistry, University of Jena, Jena, Germany
  4. 4Department of Medical Genetics, University of Tübingen, Tübingen, Germany
  5. 5Department of Neurology, University of Bonn, Bonn, Germany
  6. 6Department of Neuroradiology, University of Tübingen, Tübingen, Germany
  1. Correspondence to Dr Ludger Schöls, Clinical Neurogenetics, Department of Neurology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Hoppe-Seyler-Str. 3, D 72076 Tübingen, Germany; ludger.schoels{at}


Background To guide time- and cost-efficient analyses of the increasing number of autosomal-dominant spinocerebellar ataxia genes (SCAs), more information about frequency distributions, phenotypic characteristics and optimal diagnostic strategies is warranted.

Objective To assess the prevalence and phenotypic spectrum of SCA15 and to confirm multiplex ligation-dependent probe amplification (MLPA) as a robust and efficient strategy for routine molecular diagnosis.

Methods Fifty-six German SCA families negative for common repeat expansions were screened for ITPR1 deletions by MLPA. Samples with conspicuous MLPA data were additionally assessed by high-density single nucleotide polymorphism (SNP) array to confirm MLPA results and further determine the size of deletions. The phenotype of patients harbouring ITPR1 deletions was characterised by standardised clinical, electrophysiological and imaging assessment.

Results SCA15 accounted for 8.9% (5/56) of SCA families negative for common SCA repeat expansions. All deletions detected by MLPA were confirmed by SNP array. One of the ITPR1 deletions preserved exons 1 and 2 in the 5′ prime UTR of the ITPR1 gene. All patients with SCA15 (n=10) presented with slowly progressive cerebellar ataxia and vermal cerebellar atrophy, while clinical and electrophysiological signs of extracerebellar affection were mild and more variable.

Conclusions SCA15 is the most common non-trinucleotide repeat SCA in Central Europe. Screening for ITPR1 deletions should be considered in patients with slowly progressive SCA, vermal cerebellar atrophy and prominent tremor after excluding common SCA repeat expansions. Promoter and exon 2 of ITPR1 may be preserved from the deletion in some cases of SCA15.

  • Spinocerebellar ataxias
  • genetics
  • prevalence studies
  • cerebellum
  • movement disorders
  • neurology
  • movement disorders (other than Parkinson's)

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Spinocerebellar ataxias (SCAs) are a clinically and genetically heterogeneous group of autosomal-dominant cerebellar ataxias with an overall prevalence of 3/100 000.1 2 Up to now, 28 SCA loci have been identified, and more than 60% of all SCAs are caused by CAG repeat expansions in the SCA1, SCA2, SCA3, SCA6 and SCA7 genes.1 Patients with autosomal-dominant ataxia who are negative for these mutations present a diagnostic challenge as the remaining SCA mutations include very low frequency genes (eg, SCA113 or SCA284) and gene candidates that still warrant further confirmation (eg, SCA205 or SCA306). To guide cost- and time-efficient genetic screening, more information about frequency, phenotypic characteristics and optimal diagnostic strategies in recently identified SCA subtypes is highly warranted.

SCA15 was recently found to be caused by multi-exon deletions and, more rarely and still debated, by missense mutations in the ITPR1 gene (inositol 1, 4, 5-triphosphate receptor, type 1).7–10 The phenotype of SCA15 has been studied in only a relatively few patients as only nine SCA15 families have been identified world wide,10 11 and the frequency of SCA15 in the European population is still unknown. In addition, the most efficient diagnostic method remains to be settled as several different molecular genetic techniques have been used to detect ITPR1 deletions—in particular, deletion-specific PCR,9 different DNA microarrays7 8 or multiplex ligation-dependent probe amplification (MLPA).10 We here determined the frequency and phenotypic spectrum of SCA15 by screening a large cohort of SCA families negative for common SCA repeat expansions for deletions in the ITPR1 gene by a customised MLPA assay.

Material and methods

Patient selection and assessment

A consecutive series of 274 German families with autosomal-dominant transmission of ataxia was recruited from ataxia clinics in Bochum, Bonn and Tübingen (=all SCAs). From this sample, we selected those index patients for SCA15 screening who were negative for repeat expansions causing SCA1, SCA2, SCA3, SCA6, SCA7, SCA8, SCA10, SCA12, SCA17 and DRPLA, and for mutations causing SCA11, SCA14 and SCA27, yielding a cohort of 60 index patients (=unexplained SCAs). Four of these patients were excluded from the study owing to a small quantity and/or insufficient quality of the respective DNA samples. Mean age of onset of spinocerebellar ataxia of the remaining index patients (n=56) was 43.8 ± 17.4 years (range 3–71). Fifty per cent (28/56) of the index patients presented with pure cerebellar ataxia and 50% with non-cerebellar signs like gaze palsy, epilepsy, spasticity, dystonia, Parkinsonism or peripheral neuropathy.

All index patients and, if available, further affected family members were assessed (a) by a clinical examination by a movement disorder specialist (MS, LS) to identify cerebellar and non-cerebellar features; (b) by the Scale for the Assessment and Rating of Ataxia (SARA)12 to determine severity and progression of ataxia; (c) by MRI and (d) by electrophysiological studies (including nerve conduction studies, motor evoked potentials and sensory evoked potentials).

Molecular genetic analyses

As a first step, MLPA was used to screen for ITPR1 deletions. We designed a MLPA assay targeting the gene's promoter as well as exons 2, 8, 18, 41 and 54 and intron 4 with one probe each (ie, seven probes in total). These targets were selected to cover especially 5′ portions of the ITPR1 gene as all deletions reported previously included at least exons 1–10.10 11 Six probes targeting different chromosomes were included for reference. (ITPR1 MLPA probe sequences, reference MLPA probes for other genomic regions and size distribution of MLPA probes in the ITPR1 assay are given in online supplementary table 1.) Pertinent oligonucleotides were obtained from MWG-Biotech (Germany) and reagents were taken from the EK1 kit offered by MRC-Holland (The Netherlands); they were applied according to the manufacturers' instructions. Analysis of MLPA data was carried out in analogy to previously described MLPA analyses.13

In a second step, a high-density single nucleotide polymorphism (SNP) array was used for validation purposes and determination of the size of the deletion in all index cases for which MLPA suggested the presence of a heterozygous deletion. Samples were evaluated by an Affymetrix 6.0 SNP array platform using copy number variation (CNV) and analysed with the Affymetrix CN4 algorithms within GTC version 3. The predicted copy number as well as the start and end of each CNV segment were determined using the Hidden Markov Model incorporated in the software package using the Viterbi algorithm. For the ITPR1-SUMF1 locus approximately 380 markers were looked up for genomic imbalances as indicated by a reduction or amplification of hybridisation signal (CNV) or excess of homozygosity. For the mathematical computation of the CNV sizes a sliding window method is used.

To investigate the potential effect of the 5′ end on expression of the ITPR1 gene in family F34, a quantitative real-time PCR (qPCR) was designed for amplicons in exon 3 (including the start codon) and exon 6 of the ITPR1 gene. Primers are given in supplementary table 1. PCR amplification was performed in triplicate using a LightCycler 480 system (Roche, Mannheim, Germany) with 10 μl PCR volumes in the 384-well block format using a standard qPCR protocol (15 min at 95°C, 45 cycles with 20 s at 95°C, 40 s at 55°C and 20 s at 72°C, followed by a melting curve from 40°C to 85°C) with hotstart Sybr Green chemistry (Roche, Mannheim, Germany). We established comparable amplification efficiencies for ITPR1 amplicons and reference amplicons within the BCMA, SDC4 and B2MG genes using the relQuant analysis tool of the LightCycler software version 1.5. A reduction in qPCR signal by <70% was defined as indicating a deletion.


Genetic screening

MLPA suggested partial ITPR1 deletions in 5/56 index patients, but provided no evidence for multiplications (figure 1; for detailed individual quantitative MLPA data, see supplementary table 2). Pedigrees of SCA15 families are provided in supplementary figure 1. In family F34 the deletion did not affect the 5′ end of the ITPR1 gene: MLPA in all three affected family members showed that this ITPR1 deletion preserved the promoter region and exon 2 of ITPR1 (figure 1 and supplementary table 2).

Figure 1

Multiplex ligation-dependent probe amplification (MLPA) readouts for all patients with the spinocerebellar ataxia gene 15 (SCA15) and heterozygous ITPR1 gene deletions. (A) MLPA analysis allowed for the relative gene dosage measurements in seven localisations throughout the ITPR1 gene: hybridisation probes have been placed in the promoter, in exon 2, intron 4, exon 8, exon 18, exon 41 and at the 3 prime end in exon 54. Dark grey bars visualise the minimal length of heterozygous ITPR1 deletions and demonstrate at least four different deletion sizes in our five families. (B) Exemplary MLPA data. Mean and SEM of healthy controls (n=15) and patients with SCA15 (3 (exon 54) to 9 (introns 4 and 8) observations; see also part (A)). Moreover, the relative peak area for patient F34-III-2 is shown in grey bars vertical for the respective fragments. Values around 1.0 indicate the presence of the normal two copies, whereas values around 0.5 suggest a heterozygous deletion. chr, chromosome; ex, exon; in, intron; prom, promoter; for calculation of relative signal value see ‘Material and methods’ section.

In four of five index patients, heterozygous genomic ITPR1 deletions were confirmed by copy number analysis by SNP array. In these patients 176–383 markers were included in the deletion regions. Deletions—as measured by CNV—spanned approximately 183–423 kb (for details see table 1 and figure 2). The size of one deletion (F06-III-8) could not be determined by SNP-array analysis as compromised DNA quality did not allow accurate measurements (technical failure). Deletions in F39, F48 and F49 affected partly both the ITPR1 gene and the SUMF1 gene, without including the 3′ prime of the ITPR1 gene (figure 2). In family F34, CNV array analysis partially differed from the MLPA results by predicting the border of the ITPR1 deletion about 10 kb upstream of that defined by the MLPA markers (figure 2).

Table 1

Single nucleotide polymorphism (SNP) array analysis in patients with the spinocerebellar ataxia gene 15 (SCA15)

Figure 2

Copy number variation analysis for six patients with the spinocerebellar ataxia gene 15 (SCA15) and heterozygous ITPR1 gene deletions. Copy number plots of the relative gene dosage in the SCA15 region for three samples of family F34 (F34-III-2, F34-IV-3, F34-IV-4), F39-III-4, F48-III-7 and F49-III-3 are shown. F06-III-8 gave low-quality results owing to degraded DNA (not shown). A ruler with genomic coordinates and the relative position of the ITPR1 and SUMF1 gene is shown. All individual deletion sizes (as determined by single nucleotide polymorphism array copy number variation) are shown as horizontal bars and labelled with the family code. Moreover, the exact position of all multiplex ligation-dependent probe amplification (MLPA) probes (promoter and exon 2 are very close to each other) and of the qPCR fragments is shown.

Since MLPA data in all affected members of family F34 consistently suggested that the deletion starts between exon 2 and intron 4 we designed a qPCR with primers covering the ATG triplet in exon 3 of ITPR1. In all three affected members of family F34 qPCR indicated the start codon to be deleted (qPCR fragment localisations are shown in figure 2).

The ITPR1 deletions co-segregated with the disease in kindred F34 and F48 (figure 1). In F06 and F49 no further family members were available for genetic testing. In F39, the father of the index patient had died and no DNA was available, but pertinent clinical records confirmed affection by cerebellar ataxia.

Phenotype and disease progression

Detailed clinical, electrophysiological and imaging characterisation was available for 10 patients and is summarised in tables 2 and 3. Exemplary videos are available as online supplementary material. In these 10 patients, SCA15 presented clinically with a mid-life onset of 44.6 years (range 30–67 years) and a rather uniform phenotype of slowly progressive cerebellar ataxia (∼1.2 SARA points/year, range 0.7–1.7; table 2). A walker or wheelchair was needed around 15–17 years after disease onset. In 9/10 individuals the initial symptom was gait disturbance. Interestingly, three subjects (F34-IV-3, F34-IV-4, F48-III-1) considered themselves to be asymptomatic despite unequivocal signs of cerebellar ataxia and cerebellar atrophy on MRI (figure 3C–F). Two of them had been clinically diagnosed for more than 5 years. This fact again highlights the subtle and slow progression of the disease.

Table 2

Clinical findings in patients with the spinocerebellar ataxia gene 15 (SCA15)

Table 3

MRI and electrophysiology data

Figure 3

Brain imaging of patients with the spinocerebellar ataxia gene 15 (SCA15). MRI and CT brain scans of 7 SCA15 patients demonstrating a highly uniform picture of prominent cerebellar atrophy affecting mainly the vermis (in particular the superior and mid-vermis), with only minor cerebellar hemispheric involvement and complete sparing of the brainstem and cerebral structures. MRI brain scans of patients F39 III-4 (G–J) and F48 III-7 (M–P) were assessed twice within 5 years and 4 years, respectively, indicating minor progression of vermal cerebellar atrophy. Left columns: sagittal view; right columns transverse view; (A, E) T2-weighted images; (B, F, H, J, L, N, P, R) T2 FLAIR; (G, I, K, M, O, Q) T1 flash sequences; (C, D) CT scans. Patient IV-3 of family F34 could not be placed in an MRI head coil owing to comorbid severe ankylosing spondylitis.

As a characteristic feature, action and postural tremor of the hands and partly of the head were found in 7/10 patients. It aggravated the intention tremor which was consistently seen in all subjects. Subjects perceived tremor as one of the most compromising impairments for activities of daily living. In 3/7 subjects action and postural tremor evolved rather late in the disease course (14–17 years after ataxia onset; table 2). Other extracerebellar features included clinical or electrophysiological signs of pyramidal tract affection (4/10 patients), electrophysiological evidence of dorsal column pathology (4/10 patients) and upward gaze palsy (1/10 patients) (tables 2 and 3). Two patients showed psychiatric symptoms already before the onset of ataxia (paranoid-hallucinatory psychosis in F34-IV-3; adjustment disorder in F39-III-4); one elderly patient revealed mild cognitive impairment (F49-III-3) presumably due to vascular encephalopathy. None of the patients showed facial myokymias or buccolingual dyskinesias, which have recently been reported in some patients with SCA15.11 In line with previous findings,14 MRI demonstrated a rather uniform pattern of cerebellar atrophy affecting mainly the vermis (in particular superior and mid-vermal regions), with only minor hemispheric involvement and sparing of brainstem and cerebral structures (figure 3). Atrophy seemed to progress only slowly within 4 and 5 years of follow-up (figure 3 G–J,M–P). However, no data for quantitative volumetric analysis were available.


In our series SCA15 is relatively common, accounting for 8.9% (5/56) of unexplained SCAs and 1.8% (5/274) of all SCAs. This finding exceeds a recent, also MLPA-based, estimate of 2.7% ITPR1 deletions in Australian SCA cases negative for repeat expansions.10 It clearly exceeds the reported prevalence of other “new” SCA subtypes like SCA14,15 SCA11,3 SCA2716 or SCA28.4 Thus, SCA15 seems to be the fifth most common SCA subtype after SCA1, 2, 3 and 6 and is even more common than SCA7, 8 and 17 in the German population.

Our customised MLPA assay allowed for the consistent measurement of seven target regions distributed over the ITPR1 gene, demonstrating that each family in our series had a unique deletion. Moreover, it revealed that SCA15 can also be caused by heterozygous deletions that spare the first two non-coding exons, while previous studies always demonstrated inclusion of ITPR1-exon 1 in SCA15 deletions.8 10 Whereas MLPA (and qPCR) are locus-specific tools for measuring gene dosage, SNP array copy number analysis has to rely on serial data points in order to size variations. This might explain why the deletion genotyped in all three SCA15 patients of family F34 resulted in consistent results for MLPA (and qPCR), but not for CNV arrays: although the telomeric border was identical for all patients, it did not combine with our MLPA data, and the centromeric border varied for almost 15 000 bases. Moreover, for the mathematical computation of deletion sizes in the CNV array a sliding window method was used, which often leads to overestimation of the deletion size (in our case the questionable region is covered by only nine SNPs). Correspondingly, since MLPA data consistently demonstrated the promoter region and exon 2 of ITPR1 to be preserved in all affected members, we believe that the genomic deletion regions indicated by the CNV array method are too large. To examine the effect of the unusual preservation of the 5′ end we designed a qPCR system, which demonstrated inclusion of the ITPR1 start codon in exon 3 by the deletion. Thus, no proper protein translation can take place and this deletion resembles all other deletions by entailing IPTR1 haploinsufficiency.

Variability of deletion size as found in our and other studies would argue for high-resolution deletion detection systems that completely interrogate all ITPR1 exons. This fact also indicates that our screening by MLPA might even underestimate the true SCA15 prevalence, as this approach may miss small deletions of exons not covered by the MLPA probe sets used in this study. Moreover, this approach cannot reliably detect point mutations in the ITPR1 gene. So far, a single amino acid change of unknown significance has been reported in one patient (c.8581C→T, p.P1059L8). The frequency of ITPR1 point mutations and small deletions in SCA families, however, seems to be very low, as they have not been found in 38 SCA families that were negative for large ITPR1 deletions and common SCA mutations.17 Although our study recommends MLPA as a cost- and time-efficient screening tool for SCA15, for individual tests rather than testing of a cohort, a DNA microarray approach might still be more efficient.

In a comprehensive phenotypic characterisation of our series of patients with SCA15 we confirmed findings of earlier reports with smaller patient numbers11 14 18 and identified several characteristic features that might be helpful for considering ITPR1 deletion screening in patients with unexplained SCAs. Disease progression in our SCA15 cohort was relatively slow (1.2 SARA points/year) compared with SCA2 (1.4 SARA points/year), SCA3 (1.6 SARA points/year) or SCA1 (∼2.2 SARA points/year), yet somewhat faster than in SCA6 (non-linear progression: first year: 0.35 SARA points/year, second year: 1.44 SARA points/year).19 This finding, however, needs to be confirmed in prospective studies with iterative SARA evaluations as retrospective estimation of disease onset in such a slowly progressive disease is difficult. Disabling action and postural tremor, found in 70% of our patients, seems to be characteristic of (albeit not specific to) SCA15.18 It may present as the initial symptom (see patient F48-III-7 and the study by Gardner et al14), or develop more than a decade after onset of ataxia. Intriguingly, all patients (100%) demonstrated cerebellar atrophy, affecting mainly the superior and mid-vermal regions, with only minor hemispheric involvement and sparing of the brainstem and cerebral structures. This atrophy pattern may occur even before subjectively noticed ataxia (patients IV-3 and IV-4 of family F34).

Contrary to earlier perspectives, which considered SCA15 to be a pure cerebellar ataxia,20 extracerebellar features such as pyramidal tract affection, dorsal column pathology or gaze paresis might be associated with SCA15 as well (as they are in many other SCAs1), yet present in a more variable fashion.

In conclusion, we show that SCA15 presents the most common non-trinucleotide repeat SCA in Central Europe. MLPA seems to be a robust and cost-effective screening tool for ITPR1 deletions. Screening for ITPR1 deletions should be particularly performed in patients with unexplained SCA presenting with slowly progressive ataxia, prominent tremor and pronounced vermal atrophy of the cerebellum.


We are grateful to the family members for their participation.


Supplementary materials


  • MS and ChB contributed equally to this study.

  • Funding Supported by the European Union (EUROSCA consortium; LSHM-CT-2004-503304) and the Stiftung für Pathobiochemie und Molekulare Diagnostik (to ChB). MS was supported by a grant from the Volkswagen Stiftung (Az. II/85158).

  • Competing interests None.

  • Ethics approval This study was conducted with the approval of the ethics committee at the University of Tübingen, Germany.

  • Provenance and peer review Not commissioned; externally peer reviewed.