Extreme phenotypic heterogeneity in non-expansion spinocerebellar ataxias

Abstract

Although the best-known spinocerebellar ataxias (SCAs) are triplet repeat diseases, many SCAs are not caused by repeat expansions. The rarity of individual non-expansion SCAs, however, has made it difficult to discern genotype-phenotype correlations. We therefore screened individuals who had been found to bear variants in a non-expansion SCA-associated gene through genetic testing, and after we eliminated genetic groups that had fewer than 30 subjects, there were 756 subjects bearing single-nucleotide variants or deletions in one of seven genes: CACNA1A (239 subjects), PRKCG (175), AFG3L2 (101), ITPR1 (91), STUB1 (77), SPTBN2 (39), or KCNC3 (34). We compared age at onset, disease features, and progression by gene and variant. There were no features that reliably distinguished one of these SCAs from another, and several genes-CACNA1A, ITPR1, SPTBN2, and KCNC3-were associated with both adult-onset and infantile-onset forms of disease, which also differed in presentation. Nevertheless, progression was overall very slow, and STUB1-associated disease was the fastest. Several variants in CACNA1A showed particularly wide ranges in age at onset: one variant produced anything from infantile developmental delay to ataxia onset at 64 years of age within the same family. For CACNA1A, ITPR1, and SPTBN2, the type of variant and charge change on the protein greatly affected the phenotype, defying pathogenicity prediction algorithms. Even with next-generation sequencing, accurate diagnosis requires dialogue between the clinician and the geneticist.

Keywords: Spinocerebellar Ataxia, SCA, CACNA1A, PRKCG, AFG3L2, ITPR1, STUB1, SPTBN2, KCNC3, onset.

Figure 1

Age at onset distribution and disease features beyond ataxia in seven non-expansion SCAs (A) Age at onset distribution for each of the seven genetic groups in our cohort, in descending size of group from top to bottom. The lower and upper hinges correspond to the first and third quartiles (the 25^th and 75^th percentiles). (B) The percentage of affected individuals in each group with signs beyond cerebellar ataxia. The majority of disease features affect fewer than one in four members of a given genetic group, indicating considerable heterogeneity.

Figure 2

Infantile, juvenile, and adult-onset CACNA1A phenotypes and their correlations with variant location and amino acid properties (A) Infantile, juvenile, and adult-onset phenotypes differed in their clinical presentations, but no single feature was exclusive to one category. (B) Distributions of ages at onset for each of the variant type observed in CACNA1A. The lower and upper hinges correspond to the first and third quartiles (the 25^th and 75^th percentiles) for all boxplots in the figure. (C) Distributions of ages at onset for each CACNA1A missense variant according to their location in the protein by repeat region. Variants within transmembrane segment S4 were found in all the repeats, but in segment S5 they were located only in repeats IV (n = 7) and III (n = 1) and exclusively associated with very-early-onset disease. (D) Amino acid change properties also influence age at onset. On the left are the initial amino acid properties and at the bottom are the amino acid properties post-mutation. The majority of mutations affected positive residues. (E) Diagram of CACNA1A shows the locations of missense and loss-of-function variants (above and below the gene, respectively) in this cohort.

Figure 3

Amino acid properties and variant characteristics in PRKCG (SCA14) and AFG3L2 (SCA28) (A) Top: distributions of ages at onset for each type of mutation observed in PRKCG. The lower and upper hinges correspond to the first and third quartiles (the 25^th and 75^th percentiles) in all the boxplots in the figure. Frameshifts and indels seem to have a narrower range of onset, but the number of subjects is too small to judge with certainty. Middle: the majority of variants in PRKCG (70%) affected non-polar residues. Bottom: diagram of PRKCG showing the locations of variants in this cohort. (B) Top: AFG3L2 missense variants produce a wide range of ages at onset. Middle: nearly half the AFG3L2 mutations affected non-polar residues. Bottom: diagram of AFG3L2 showing the locations of variants in our cohort.

Figure 4

Missense variants dominate infantile onset in ITPR1 (SCA15/29), but no pattern is discernible with STUB1 (SCA48) (A) Top: infantile- and adult-onset ITPR1-affected individuals were differentiated primarily by the presence of intellectual disability. Middle: missense mutations in ITPR1 were strongly associated with infantile cases. Bottom: diagram of variant locations in ITPR1. (B) Top: age at onset in STUB1-associated disease did not correlate with variant type. Middle: two-thirds of variants affected non-polar residues. Bottom: diagram of variant locations in STUB1.

Figure 5

Correlations between variant type and amino acid changes in SPTBN2 (SCA5) and KCNC3 (SCA13) with early- and later-onset phenotypes (A) Left: the majority of infantile-onset SCA5-affected individuals have intellectual disability, which is strongly associated with missense variants and charge loss in the spectrin repeats. The majority of mutations changed the residue from one non-polar amino acid to another. Right: missense mutations were associated with the earliest age at onset (top) and with charge loss in a spectrin repeat (middle panel). The bottom right shows the location of variants, which favored the calponin homology domain and early spectrin repeats. (B) Intellectual disability is also prominent in SCA13 infantile-onset disease (left), which is strongly associated with mutations affecting amino acids in the region following c.1259G>A (p.Arg420His) (GenBank: NM_004977.3) (right). Mutations clustered in the S4 and S5 domains (right, bottom).